In terms of relations with the Vatican, it would be tough to imagine a better run for the Palestinians than the one they’ve enjoyed over the past week.

On Wednesday, the Vatican announced its first bilateral treaty with the “State of Palestine.” During a meeting Saturday, Pope Francis affectionately referred to Palestinian President Mahmoud Abbas, with whom he enjoys a close relationship, as an “angel of peace.”

(The Vatican issued a clarification saying the remark came in the context of presenting Abbas with a bronze medal depicting an angel, suggesting it wasn’t simply a gratuitous tribute, but that did little to lessen Israeli umbrage.)

On Sunday, the pontiff canonized two 19th-century nuns as the first-ever Palestinian saints. Taken together, many Israelis saw the gestures as the Vatican tipping its hand.

In truth, this is hardly the first time Israel has detected a pro-Palestinian slant in Rome.

St. John Paul II, for instance, was widely perceived as a friend of Judaism and of Israel. Yet it irritated Israelis no end that John Paul II also met PLO leader Yasser Arafat 12 times over the course of his papacy, treating him as a serious statesman rather than the gun-toting thug most Israelis perceived him to be.

After the first such meeting in 1982, reaction from then-Israeli Prime Minister Menachem Begin was pointed.

“What else can one say,” Begin said, “except to express disgust?”

Likewise, Pope Benedict XVI stirred Israeli resentment during a May 2009 trip to the Holy Land, when he criticized Israel’s security barrier separating the West Bank from Jerusalem.

During a visit to the Aida camp, home to some 3,000 Palestinian refugees that was opened after the 1948 Arab/Israeli war, Benedict affirmed his audience’s “legitimate aspirations for permanent homes [and] for an independent Palestinian State.”

The Vatican’s subsequent adoption of the term “State of Palestine,” after a November 2012 UN vote to admit Palestine as a non-member observer state, came under Benedict XVI.

To the extent there really is a pro-Palestinian tilt in some Vatican quarters, three factors help explain it.

1. Europeans favor the Palestinians.
The Vatican is a European institution and its diplomatic corps is predominantly European, mostly Italian. European biases tend to form the “default setting” of Vatican diplomacy, the instinctive line the Vatican falls back on in the absence of anything pulling it in a different direction.

Just as a pro-Israeli impulse is in the water of American politics, sympathy for the Palestinians tends to be the European norm.

2. The Vatican supports small states – and the UN.
The Vatican sees itself as the world’s smallest state and thus feels a natural affinity for other small states, especially when the perception is that a major world power – in this case, the United States through its support of Israel – has that small state at a disadvantage.

Bundled with that is strong support for the United Nations, and for multilateral approaches to virtually every foreign policy question.

It often strikes people as odd that the Vatican is so robustly pro-UN, given the battles it has waged with some UN agencies over population control. For better or worse, however, support for the global body is a bedrock principle of Vatican diplomacy.

3. Holy Land Christians are Palestinians.
The overwhelming majority of the Christians in the Holy Land are Palestinian Arabs, including the bishops and other clergy the Vatican relies upon to get its bearings in terms of what’s happening on the ground.

Over the years, the Catholic bishops of the Middle East have typically been strongly pro-Palestinian. Most have not gone as far as Greek Melkite Archbishop Hilarion Capucci, who was arrested in 1974 and later convicted by an Israeli court for smuggling guns to the PLO in the trunk of his Mercedes sedan, but many sympathized with Capucci’s aims.

In part, Palestinian Christians are conscious of their status as a minority within an overwhelmingly Muslim society, and thus sometimes feel the need to prove their Arab loyalties by being especially vocal in their criticism of Israel and their support for the Palestinian cause.

The Vatican is aware of that dynamic, and generally comes off as more cautious and balanced than the local bishops. Nevertheless, those voices can’t help but have a strong impact on the way Rome thinks.

These conditions are permanent, but there’s another factor: Francis is the first pope from the developing world, and as such, he probably brings a special degree of instinctive sympathy for what he sees as oppressed and struggling peoples.

This perceived pro-Palestinian impulse stirs deep resentment on the Israeli side, and not merely because of its broader geopolitical ramifications or the Catholic Church’s checkered history with anti-Semitism.

Israelis also insist that as the region’s lone real democracy, they do a far better job protecting religious freedom, including the rights of Christians, then anyone else in the neighborhood. At a time when Pope Francis has made anti-Christian persecution a signature cause, they argue, the Vatican should be pointing to Israel as a model rather than undercutting its standing.

(That claim is vigorously contested by many Palestinian Christians, who, among other things, say that Israeli security policies split Christian families and make access to holy sites difficult if not impossible.)

No doubt, the Vatican will find ways in the days to come to signal that its gestures to the Palestinians are not intended to come at the expense of its relationship with Israel. Francis is committed to Catholic/Jewish relations, among other things relying on his close friend, Argentine Rabbi Abraham Skorka, as an informal channel of communication with the wider Jewish world and with Israel.

In the end, however, Israelis and their supporters probably will continue to suspect the Vatican of a basic pro-Palestinian prejudice. That perception pre-dates Francis, but after this week it seems fair to say it’s unlikely to change on his watch.