Contacts of the helix formed by residues 1620 - 1630 (chain A) in PDB entry 2FR1
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU1620 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1613A VAL* 4.8 1.9 - - + +
1614A PRO* 3.8 17.3 - - + +
1617A SER* 2.5 34.0 + - - -
1618A VAL 4.1 0.9 + - - -
1619A ALA* 1.3 78.3 + - - +
1621A LEU* 1.3 62.8 + - - +
1623A ARG* 3.1 16.7 + - - +
1624A HIS* 3.1 30.0 + - - +
1640A LEU* 3.6 26.6 - - + +
1641A ARG* 3.6 30.5 - - - +
1642A ALA* 3.7 21.1 + - - +
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Residues in contact with LEU1621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1486A THR* 3.5 37.0 - - + +
1489A ALA* 5.4 1.1 - - + -
1490A ALA* 4.5 13.5 - - + +
1529A LEU* 5.2 0.2 - - + -
1531A LEU* 4.7 4.5 - - + -
1571A VAL* 4.1 27.6 - - + -
1611A VAL* 4.6 4.3 - - + -
1613A VAL* 3.8 27.0 - - + +
1618A VAL* 3.1 13.4 + - + +
1620A GLU* 1.3 75.2 + - - +
1622A ALA* 1.3 58.9 + - - +
1623A ARG 2.8 5.7 + - - -
1625A LEU* 2.8 57.6 + - + +
1640A LEU* 4.0 11.2 - - + -
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Residues in contact with ALA1622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1489A ALA* 3.2 31.2 + - + +
1492A GLU* 4.5 11.0 - - + +
1493A ALA* 3.7 22.6 - - + +
1618A VAL* 3.0 15.9 + - + +
1619A ALA* 3.8 3.8 - - - +
1621A LEU* 1.3 75.0 - - - +
1623A ARG* 1.3 58.2 + - - +
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Residues in contact with ARG1623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1619A ALA* 3.0 32.1 + - - +
1620A GLU* 3.4 28.9 + - - +
1621A LEU 2.8 0.6 + - - -
1622A ALA* 1.3 80.6 - - - +
1624A HIS* 1.3 85.6 + - + +
1625A LEU 3.8 0.2 - - - -
1626A ALA* 5.5 0.9 - - - -
1641A ARG 4.6 1.4 + - - -
1642A ALA* 3.9 24.0 + - - +
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Residues in contact with HIS1624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1620A GLU* 3.1 26.8 + - + +
1623A ARG* 1.3 110.2 - - + +
1625A LEU* 1.3 68.7 + - - +
1626A ALA 3.2 2.9 - - - -
1627A ALA* 3.1 14.7 + - + +
1628A VAL* 2.9 27.1 + - + +
1640A LEU* 4.1 19.0 - - + +
1641A ARG 5.1 7.4 - - - -
1644A GLY* 5.2 6.4 - - - -
1645A VAL* 3.5 28.6 + - + +
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Residues in contact with LEU1625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1490A ALA* 3.8 37.2 - - + +
1493A ALA* 4.0 8.5 - - + -
1494A LEU* 4.0 15.5 - - + -
1529A LEU* 3.8 36.6 - - + -
1569A TRP* 6.0 0.2 - - + -
1571A VAL* 5.4 0.9 - - + -
1611A VAL* 5.9 3.8 - - + -
1620A GLU 4.5 0.2 + - - -
1621A LEU* 2.8 39.4 + - + +
1622A ALA 4.8 0.2 - - - -
1623A ARG 3.8 0.4 - - - -
1624A HIS* 1.3 76.5 - - - +
1626A ALA* 1.3 63.6 + - - +
1628A VAL* 3.1 12.9 + - + +
1629A VAL* 3.0 34.4 + - + +
1640A LEU* 4.8 1.2 - - - +
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Residues in contact with ALA1626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1467A PRO* 4.4 8.5 - - + -
1470A LEU* 4.5 3.0 - - - +
1493A ALA* 3.9 14.7 + - + +
1494A LEU* 5.1 1.3 - - - -
1497A ALA* 3.9 27.6 - - + -
1623A ARG 5.5 1.1 - - - +
1624A HIS 3.2 0.8 - - - -
1625A LEU* 1.3 81.4 - - - +
1627A ALA* 1.3 63.5 + - - +
1629A VAL* 3.2 17.3 - - - +
1630A SER* 2.8 18.9 + - - -
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Residues in contact with ALA1627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1464A ALA* 3.2 32.0 - - + +
1466A GLU 5.6 0.2 - - - +
1467A PRO* 3.8 30.4 - - + +
1623A ARG 5.9 0.2 - - - +
1624A HIS* 3.1 16.3 + - + +
1626A ALA* 1.3 78.6 - - - +
1628A VAL* 1.3 61.8 + - - +
1630A SER 3.5 0.5 - - - +
1631A GLY* 3.1 19.9 + - - -
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Residues in contact with VAL1628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1464A ALA* 4.5 7.6 - - + -
1569A TRP* 3.6 39.1 - - + -
1611A VAL* 3.8 18.6 - - + -
1624A HIS* 2.9 30.9 + - + +
1625A LEU* 3.1 13.4 + - + +
1627A ALA* 1.3 78.3 - - - +
1629A VAL* 1.3 64.4 + - + +
1630A SER 3.4 0.7 + - - -
1631A GLY* 3.7 6.6 + - - +
1635A GLU 5.1 1.6 - - - +
1638A LEU* 4.1 24.2 - - + -
1640A LEU* 4.6 12.8 - - + -
1645A VAL* 5.5 2.0 - - + -
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Residues in contact with VAL1629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1470A LEU* 3.8 24.7 - - + +
1474A TRP* 3.5 38.0 - - + -
1494A LEU* 4.4 4.5 - - + -
1529A LEU* 5.3 0.9 - - + -
1569A TRP* 3.9 35.7 + - + +
1625A LEU* 3.0 30.8 + - + +
1626A ALA* 3.2 19.3 - - - +
1628A VAL* 1.3 76.1 - - + +
1630A SER* 1.3 57.5 + - - +
1631A GLY 3.6 1.2 + - - -
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Residues in contact with SER1630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1466A GLU 3.1 16.8 - - - +
1467A PRO* 2.6 32.6 + - - +
1468A ALA* 5.3 0.7 - - - +
1469A ARG 4.1 2.0 - - - -
1470A LEU* 3.5 24.0 - - - +
1626A ALA 2.8 20.1 + - - -
1627A ALA 3.5 2.7 - - - -
1629A VAL* 1.3 79.4 - - - +
1631A GLY* 1.3 58.5 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il