Contacts of the helix formed by residues 1524 - 1536 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1516C TYR* 4.0 5.4 - - + -
1522C LEU 3.7 1.5 + - - +
1523C PRO* 1.3 71.7 - - - +
1525C ASN* 1.3 73.5 + - - +
1526C PRO* 3.1 3.4 - - - -
1527C LEU* 2.7 31.2 + - + +
1528C SER* 2.8 36.0 + - - +
1587C HIS* 4.4 8.7 - - + +
1590C ARG* 3.5 43.1 - - + +
1591C VAL* 4.6 18.6 - - + +
1592C SER* 5.0 7.6 - - - +
1595C LEU* 3.9 22.4 - - + -
74D GLN* 5.6 1.6 - - - +
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Residues in contact with ASN1525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1523C PRO* 3.4 5.0 - - + +
1524C ILE* 1.3 82.1 - - - +
1526C PRO* 1.3 66.3 - - + +
1528C SER* 3.3 3.1 + - - -
1529C MET* 2.9 31.4 + - - +
1595C LEU* 3.9 23.9 - - - +
3D ALA* 6.1 6.0 - - + +
5D LYS* 4.0 30.2 + - + +
56D TRP* 3.7 7.0 - - + +
74D GLN* 4.5 23.9 + - - +
76D ASP* 5.4 1.6 + - - -
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Residues in contact with PRO1526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1512C MET* 3.9 17.4 - - + +
1516C TYR* 3.7 9.6 - - - +
1523C PRO* 3.6 15.7 - - + +
1524C ILE 3.3 4.0 - - - -
1525C ASN* 1.3 96.6 - - + +
1527C LEU* 1.3 57.2 + - - +
1529C MET* 3.8 10.2 - - + +
1530C LEU* 3.0 31.2 + - - +
3D ALA* 5.9 6.3 - - + -
52D ASN* 4.1 20.0 - - - +
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Residues in contact with LEU1527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1512C MET* 4.1 25.5 - - + -
1513C ILE* 5.7 1.8 - - + +
1516C TYR* 3.7 30.4 + - + -
1524C ILE* 2.7 20.6 + - + +
1526C PRO* 1.3 72.9 - - - +
1528C SER* 1.3 65.7 + - - +
1531C LEU* 2.9 62.0 + - + +
1583C GLY* 4.1 6.7 - - - +
1586C ILE* 3.8 30.3 - - + -
1587C HIS* 4.0 23.3 - - + +
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Residues in contact with SER1528 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1524C ILE* 2.8 31.9 + - - +
1525C ASN* 3.5 11.2 - - - -
1527C LEU* 1.3 71.9 - - - +
1529C MET* 1.3 58.3 + - - +
1532C ASN* 2.9 36.2 + - - +
1587C HIS* 2.7 32.0 + - - -
1595C LEU* 4.3 2.0 - - - +
1598C PHE* 3.7 8.3 - - - -
1602C MET* 3.4 2.0 - - - +
56D TRP* 3.6 19.1 - - - -
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Residues in contact with MET1529 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1525C ASN 2.9 18.2 + - - +
1526C PRO* 3.8 9.4 - - + +
1528C SER* 1.3 78.0 - - - +
1530C LEU* 1.3 71.8 + - + +
1533C GLY* 3.0 8.5 + - - -
39D ASN* 2.8 42.2 + - + +
40D TYR 3.4 39.0 - - - +
41D SER* 4.2 12.3 - - - -
54D GLY* 3.7 11.4 - - - -
55D LEU 3.5 19.5 - - - +
56D TRP* 3.4 30.5 - - + +
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Residues in contact with LEU1530 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1508C LYS* 4.2 25.6 - - + +
1509C ILE* 4.0 29.4 - - + +
1512C MET* 3.7 33.4 - - + -
1526C PRO 3.0 19.3 + - - +
1527C LEU* 4.0 2.2 - - + +
1529C MET* 1.3 85.6 - - + +
1531C LEU* 1.3 69.5 + - + +
1533C GLY* 3.3 2.3 + - - -
1534C ILE* 3.0 39.7 + - + +
38D ASP 5.3 1.9 - - - +
39D ASN* 6.0 0.2 - - - -
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Residues in contact with LEU1531 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1509C ILE* 4.4 17.9 - - + -
1527C LEU* 2.9 50.9 + - + +
1530C LEU* 1.3 79.5 - - + +
1532C ASN* 1.3 67.5 + - - +
1534C ILE* 3.0 3.7 + - - +
1535C VAL* 2.9 31.5 + - + +
1580C LEU* 4.1 25.8 - - + +
1583C GLY* 3.6 34.5 - - - +
1584C ILE* 3.9 6.3 - - + +
1587C HIS* 4.3 9.4 - - + -
1602C MET* 3.9 12.3 - - - -
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Residues in contact with ASN1532 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1528C SER 2.9 13.8 + - - +
1529C MET 4.4 0.4 - - - +
1531C LEU* 1.3 77.4 - - - +
1533C GLY* 1.3 57.0 + - - +
1535C VAL* 4.5 1.1 - - - +
1536C ASP* 2.9 52.4 + - - +
1598C PHE* 3.5 26.0 - - + -
1601C ARG* 5.8 2.1 - - - +
1602C MET* 3.2 39.8 - - + +
1605C CYS* 5.9 0.3 - - - -
39D ASN* 5.3 2.4 - - - +
56D TRP* 4.6 9.4 - - + -
71D SER* 4.7 4.8 + - - -
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Residues in contact with GLY1533 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1529C MET 3.0 13.6 + - - -
1530C LEU 3.6 1.6 - - - -
1532C ASN* 1.3 78.5 - - - +
1534C ILE* 1.3 60.2 + - - +
1536C ASP 4.8 0.2 - - - -
1537C PRO* 3.4 16.8 - - - +
37D PHE* 4.1 0.2 - - - +
38D ASP* 3.4 35.4 + - - -
39D ASN* 3.5 21.0 - - - +
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Residues in contact with ILE1534 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1505C ALA* 4.2 15.0 - - + +
1508C LYS* 6.0 0.2 - - + -
1509C ILE* 3.7 27.6 - - + -
1530C LEU* 3.0 32.6 + - + +
1531C LEU 3.0 4.4 + - - +
1533C GLY* 1.3 77.6 - - - +
1535C VAL* 1.3 62.8 + - - +
1537C PRO* 3.5 8.4 - - - +
1543C PHE* 6.1 0.3 - - - -
1576C GLN* 3.5 28.9 - - - +
1580C LEU* 3.7 21.0 - - + +
1609C LEU* 5.2 2.4 - - - +
37D PHE* 3.8 36.4 - - + -
38D ASP 5.8 0.4 - - - +
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Residues in contact with VAL1535 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1531C LEU* 2.9 23.0 + - + +
1532C ASN* 4.2 4.0 - - - +
1534C ILE* 1.3 77.3 - - - +
1536C ASP* 1.3 59.4 + - + +
1537C PRO* 3.3 6.9 - - - +
1580C LEU* 3.6 35.4 - - + -
1584C ILE* 4.4 14.1 - - + -
1602C MET* 4.0 10.5 - - + +
1605C CYS* 3.9 15.2 - - + +
1606C PHE* 3.7 33.4 - - + +
1609C LEU* 4.5 15.7 - - + +
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Residues in contact with ASP1536 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1532C ASN* 2.9 37.5 + - - +
1533C GLY* 4.2 0.9 - - - +
1535C VAL* 1.3 78.7 - - + +
1537C PRO* 1.3 58.6 - - - +
1538C ALA* 2.9 14.8 + - - +
1601C ARG* 3.7 21.7 + - - +
1605C CYS* 3.8 22.7 - - + -
38D ASP* 3.8 3.8 - - - +
64D TYR* 3.5 26.2 + - - -
67D LEU* 5.9 0.5 - - - +
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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