Contacts of the helix formed by residues 1524 - 1536 (chain B) in PDB entry 2YIN
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 ILE1524 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1516B TYR* 4.3 7.6 - - + -
1522B LEU 4.0 8.1 - - - +
1523B PRO* 1.3 72.4 - - + +
1525B ASN* 1.3 83.5 + - - +
1526B PRO 3.2 2.7 - - - -
1527B LEU* 2.6 23.2 + - + +
1528B SER* 3.0 22.3 + - - +
1587B HIS* 4.9 7.2 - - + +
1590B ARG* 3.3 45.8 - - + +
1591B VAL* 4.8 11.0 - - + -
1592B SER* 4.9 12.8 - - - +
1595B LEU* 5.3 4.3 - - + -
74D GLN* 5.0 9.9 - - - +
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Residues in contact with ASN1525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1523B PRO* 3.5 2.4 - - + +
1524B ILE* 1.3 88.3 - - - +
1526B PRO* 1.3 71.2 - - + +
1527B LEU 3.0 0.2 + - - -
1528B SER* 3.3 7.1 + - - -
1529B MET* 3.0 25.9 + - - +
1595B LEU* 4.3 8.8 - - - +
3D ALA* 5.2 10.2 + - + +
4D ILE 6.1 0.2 - - - -
5D LYS* 3.8 41.7 + - + +
56D TRP* 4.3 2.6 - - - +
74D GLN* 4.0 28.5 + - - +
76D ASP* 4.7 3.6 + - - -
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Residues in contact with PRO1526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1512B MET* 3.6 19.3 - - + +
1516B TYR* 3.7 11.2 - - - +
1523B PRO* 3.6 19.5 - - + +
1524B ILE 3.5 2.9 - - - -
1525B ASN* 1.3 92.3 - - + +
1527B LEU* 1.3 57.8 + - - +
1529B MET* 4.1 10.3 - - + +
1530B LEU* 3.6 14.7 + - - +
3D ALA* 4.3 12.6 - - + -
52D ASN* 3.4 31.0 - - - +
54D GLY* 6.5 0.7 - - - -
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Residues in contact with LEU1527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1512B MET* 3.6 31.4 - - + -
1513B ILE* 5.4 3.4 - - + +
1516B TYR* 3.7 28.0 + - + -
1524B ILE* 2.6 21.9 + - + +
1526B PRO* 1.3 72.3 - - - +
1528B SER* 1.3 68.3 + - - +
1529B MET 3.2 0.9 - - - -
1530B LEU* 3.1 2.7 + - + -
1531B LEU* 3.0 51.1 + - + +
1583B GLY* 4.4 12.3 - - - +
1586B ILE* 4.1 25.8 - - + -
1587B HIS* 4.2 16.8 - - - +
1590B ARG* 5.9 1.1 - - + -
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Residues in contact with SER1528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1524B ILE* 3.0 20.5 + - - +
1525B ASN* 3.6 10.8 + - - -
1527B LEU* 1.3 75.3 - - - +
1529B MET* 1.3 65.1 + - - +
1531B LEU* 3.7 0.7 - - - +
1532B ASN* 2.9 27.3 + - - +
1587B HIS* 2.7 36.2 + - - -
1595B LEU* 5.1 6.1 - - - +
1598B PHE* 4.0 14.0 - - - -
1602B MET* 4.4 2.8 - - - +
5D LYS* 5.8 0.4 - - - -
56D TRP* 4.0 13.0 - - - -
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Residues in contact with MET1529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1525B ASN 3.0 15.2 + - - +
1526B PRO* 4.1 8.7 - - + +
1528B SER* 1.3 80.4 - - - +
1530B LEU* 1.3 68.5 + - + +
1533B GLY 3.2 7.1 + - - -
39D ASN* 2.6 61.3 + - + +
40D TYR 3.5 20.4 - - - +
41D SER* 4.1 12.8 - - - -
54D GLY* 3.5 30.3 - - - -
55D LEU 3.5 8.5 - - - +
56D TRP* 3.3 33.1 - - + +
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Residues in contact with LEU1530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1508B LYS* 4.4 31.2 - - + +
1509B ILE* 4.0 36.3 - - + +
1512B MET* 4.1 25.8 - - + -
1526B PRO 3.6 15.8 + - - +
1527B LEU 3.1 4.2 + - - +
1529B MET* 1.3 87.3 - - + +
1531B LEU* 1.3 77.6 + - + +
1533B GLY* 3.6 1.0 + - - -
1534B ILE* 3.3 31.7 + - + +
39D ASN* 5.2 2.0 - - - +
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Residues in contact with LEU1531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1509B ILE* 4.4 15.5 - - + -
1513B ILE* 5.9 0.2 - - + -
1527B LEU* 3.0 41.8 + - + +
1528B SER 3.8 2.0 - - - +
1530B LEU* 1.3 80.4 - - + +
1532B ASN* 1.3 53.0 + - - +
1534B ILE* 3.0 5.0 + - - +
1535B VAL* 2.7 40.3 + - + +
1580B LEU* 4.2 23.8 - - + +
1583B GLY* 3.6 38.6 - - - +
1584B ILE* 4.4 6.1 - - + +
1587B HIS* 4.0 17.3 - - + +
1602B MET* 4.0 13.7 - - - -
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Residues in contact with ASN1532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1528B SER 2.9 17.7 + - - +
1529B MET 4.2 1.6 - - - +
1531B LEU* 1.3 77.6 - - - +
1533B GLY* 1.3 57.4 + - - +
1534B ILE 3.0 0.2 + - - -
1535B VAL* 4.3 0.9 - - - +
1536B ASP* 2.7 52.0 + - - +
1598B PHE* 3.8 33.3 - - + -
1602B MET* 3.7 24.8 - - + +
39D ASN* 4.7 3.7 - - - +
56D TRP* 4.2 12.4 - - + -
71D SER* 5.4 1.8 + - - -
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Residues in contact with GLY1533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1529B MET 3.2 11.8 + - - -
1530B LEU 4.0 0.9 - - - -
1532B ASN* 1.3 77.7 - - - +
1534B ILE* 1.3 61.1 + - - +
1536B ASP 4.5 2.5 - - - -
1537B PRO* 3.6 13.4 - - - +
37D PHE* 3.7 3.8 - - - +
38D ASP* 3.2 36.1 + - - -
39D ASN* 3.5 19.8 - - - +
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Residues in contact with ILE1534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1505B ALA* 4.3 16.8 - - + +
1508B LYS* 6.5 0.4 - - - -
1509B ILE* 3.8 27.4 - - + -
1530B LEU* 3.3 27.4 + - + +
1531B LEU 3.0 7.6 + - - +
1533B GLY* 1.3 78.2 - - - +
1535B VAL* 1.3 67.1 + - - +
1536B ASP 3.5 0.2 - - - -
1537B PRO* 3.8 9.9 - - - +
1543B PHE* 5.8 3.3 - - - -
1576B GLN* 3.6 25.1 - - - +
1580B LEU* 3.9 21.1 - - + +
1609B LEU* 4.9 4.9 - - - +
37D PHE* 3.8 35.1 - - + -
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Residues in contact with VAL1535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1531B LEU* 2.7 20.9 + - + +
1532B ASN* 4.0 2.0 - - - +
1534B ILE* 1.3 81.3 - - - +
1536B ASP* 1.3 61.7 + - + +
1537B PRO* 3.5 6.2 - - - +
1580B LEU* 3.7 31.4 - - + -
1584B ILE* 4.2 19.3 - - + -
1602B MET* 3.5 33.2 - - + +
1605B CYS* 3.7 20.9 - - + +
1606B PHE* 4.0 10.1 - - + +
1609B LEU* 3.8 19.1 - - + +
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Residues in contact with ASP1536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1532B ASN* 2.7 39.3 + - - +
1533B GLY* 4.5 1.6 - - - -
1535B VAL* 1.3 77.2 - - + +
1537B PRO* 1.3 59.1 - - - +
1538B ALA* 3.0 17.1 + - - +
1605B CYS* 4.2 24.0 - - - -
38D ASP* 3.9 3.6 - - - +
64D TYR* 4.4 23.4 + - - -
67D LEU* 5.1 7.8 - - - +
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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