Contacts of the helix formed by residues 1524 - 1536 (chain A) in PDB entry 3B13
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1516A TYR* 4.0 13.0 - - + -
1522A LEU 4.7 4.3 - - - +
1523A PRO* 1.3 72.3 - - - +
1525A ASN* 1.3 72.0 + - - +
1526A PRO 3.2 1.6 - - - -
1527A LEU* 3.0 22.2 + - + +
1528A SER* 3.0 27.1 + - - +
1587A HIS* 4.5 7.0 - - + +
1590A ARG* 3.3 45.5 - - + +
1591A VAL* 4.3 19.7 - - + +
1592A SER* 4.4 6.7 - - - +
1595A LEU* 4.0 22.7 - - + -
74B GLN* 5.2 4.3 - - - +
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Residues in contact with ASN1525 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1523A PRO* 3.3 4.5 - - + +
1524A ILE* 1.3 80.6 - - - +
1526A PRO* 1.3 67.1 - - + +
1528A SER* 3.2 7.0 + - - -
1529A MET* 2.9 30.6 + - - +
1595A LEU* 3.9 23.7 - - - +
3B ALA* 5.7 4.8 - - + +
4B ILE 6.2 0.7 - - - -
5B LYS* 3.8 41.0 + - + +
56B TRP* 3.8 4.7 - - + +
74B GLN* 4.0 21.4 + - - +
76B ASP* 5.3 2.0 + - - -
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Residues in contact with PRO1526 (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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1512A MET* 4.1 12.5 - - + +
1515A GLN* 6.1 1.3 - - - +
1516A TYR* 3.6 11.9 - - + +
1523A PRO* 3.4 21.1 - - + +
1525A ASN* 1.3 96.7 - - + +
1527A LEU* 1.3 56.2 + - - +
1529A MET* 3.5 12.3 + - + +
1530A LEU* 3.0 30.0 + - - +
3B ALA* 4.5 12.8 - - + -
52B ASN* 4.0 21.1 - - - +
54B GLY* 6.5 0.4 - - - -
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Residues in contact with LEU1527 (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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1512A MET* 3.2 36.5 - - + +
1513A ILE* 5.4 2.7 - - + +
1516A TYR* 3.8 25.3 + - + -
1524A ILE* 3.0 15.3 + - + +
1526A PRO* 1.3 75.1 - - - +
1528A SER* 1.3 67.6 + - - +
1530A LEU 3.2 0.2 + - - -
1531A LEU* 2.9 51.2 + - + +
1583A GLY* 3.9 11.7 - - - +
1586A ILE* 4.0 13.7 - - + -
1587A HIS* 3.9 37.7 - - + +
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Residues in contact with SER1528 (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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1524A ILE* 3.0 24.5 + - - +
1525A ASN* 3.5 9.5 + - - -
1527A LEU* 1.3 77.6 - - - +
1529A MET* 1.3 65.5 + - - +
1532A ASN* 2.9 27.2 + - - +
1587A HIS* 2.9 27.1 + - - -
1595A LEU* 4.7 2.6 - - - +
1598A PHE* 3.5 23.4 - - - -
1602A MET* 4.7 1.8 - - - -
56B TRP* 3.5 15.0 - - - -
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Residues in contact with MET1529 (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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1525A ASN 2.9 13.4 + - - +
1526A PRO* 3.6 11.0 - - + +
1528A SER* 1.3 76.4 - - - +
1530A LEU* 1.3 72.0 + - + +
1532A ASN* 4.2 0.4 - - - +
1533A GLY 3.0 8.3 + - - -
39B ASN* 2.5 40.7 + - + +
40B TYR 3.3 26.2 - - - +
41B SER* 4.0 13.2 - - - +
52B ASN* 6.1 0.2 - - - +
54B GLY* 3.4 12.3 - - - -
55B LEU 3.3 31.9 - - - +
56B TRP* 3.1 36.7 - - + +
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Residues in contact with LEU1530 (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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1508A LYS* 3.5 44.0 - - + +
1509A ILE* 4.1 15.7 - - + -
1512A MET* 3.6 40.2 - - + -
1526A PRO 3.0 17.5 + - - +
1527A LEU 4.0 1.3 - - - +
1529A MET* 1.3 82.0 - - + +
1531A LEU* 1.3 72.0 + - + +
1533A GLY* 3.2 3.9 + - - -
1534A ILE* 3.0 35.8 + - + +
38B ASP 5.0 1.7 - - - +
39B ASN* 4.9 0.9 - - - +
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Residues in contact with LEU1531 (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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1509A ILE* 4.2 17.9 - - + -
1527A LEU* 2.9 44.7 + - + +
1530A LEU* 1.3 75.4 - - + +
1532A ASN* 1.3 64.6 + - - +
1534A ILE* 2.8 14.5 + - - +
1535A VAL* 2.9 19.7 + - + +
1580A LEU* 3.8 36.1 - - + +
1583A GLY* 3.5 31.9 - - - +
1584A ILE* 3.8 11.4 - - + +
1587A HIS* 4.1 8.1 - - + -
1602A MET* 3.7 13.5 - - - -
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Residues in contact with ASN1532 (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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1528A SER 2.9 16.9 + - - +
1529A MET* 4.2 2.0 - - - +
1531A LEU* 1.3 78.6 - - - +
1533A GLY* 1.3 60.0 + - - +
1535A VAL* 4.3 1.3 - - - +
1536A ASP* 2.8 50.2 + - - +
1598A PHE* 3.2 35.2 - - + -
1601A ARG* 6.1 0.7 - - - +
1602A MET* 3.5 24.5 - - + +
1605A CYS* 6.0 0.3 - - - -
39B ASN* 5.1 2.6 - - - +
56B TRP* 4.6 7.7 - - - -
71B SER* 4.6 4.8 + - - -
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Residues in contact with GLY1533 (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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1529A MET 3.0 11.1 + - - -
1530A LEU 3.5 2.9 - - - -
1531A LEU 3.1 0.2 + - - -
1532A ASN* 1.3 77.3 - - - +
1534A ILE* 1.3 59.0 + - - +
1536A ASP 4.7 0.7 - - - -
1537A PRO* 3.6 14.4 - - - +
37B PHE* 3.8 0.5 - - - +
38B ASP* 3.0 40.1 + - - -
39B ASN* 3.4 21.4 - - - +
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Residues in contact with ILE1534 (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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1505A ALA* 4.4 13.0 - - + +
1508A LYS* 5.7 0.4 - - + -
1509A ILE* 3.5 32.1 - - + -
1530A LEU* 3.0 28.8 + - + +
1531A LEU* 2.8 8.3 + - - +
1533A GLY* 1.3 78.4 - - - +
1535A VAL* 1.3 62.7 + - - +
1536A ASP 3.4 0.7 - - - -
1537A PRO* 3.4 9.7 - - - +
1543A PHE* 5.8 2.5 - - + -
1576A GLN* 3.8 20.4 - - - +
1580A LEU* 3.8 26.9 - - + +
1609A LEU* 5.1 3.8 - - - +
37B PHE* 3.6 34.7 - - + -
38B ASP 5.8 0.2 - - - +
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Residues in contact with VAL1535 (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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1531A LEU* 2.9 25.3 + - - +
1532A ASN* 4.1 5.2 - - - +
1534A ILE* 1.3 73.4 - - - +
1536A ASP* 1.3 60.0 + - + +
1537A PRO* 3.4 5.9 - - - +
1580A LEU* 3.6 30.3 - - + -
1584A ILE* 4.2 16.6 - - + -
1602A MET* 4.0 10.8 - - + +
1605A CYS* 3.8 14.4 - - + +
1606A PHE* 3.6 38.8 - - + +
1609A LEU* 4.6 15.8 - - + +
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Residues in contact with ASP1536 (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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1532A ASN* 2.8 33.7 + - - +
1533A GLY* 4.2 1.9 - - - +
1535A VAL* 1.3 79.2 - - + +
1537A PRO* 1.3 57.4 - - - +
1538A ALA* 2.8 28.1 + - - +
1601A ARG* 3.6 22.7 + - - +
1605A CYS* 3.6 22.5 - - + -
38B ASP* 4.1 3.6 - - - +
64B TYR* 4.8 11.0 + - - -
67B LEU* 5.6 0.2 - - - +
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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