Contacts of the helix formed by residues 1495 - 1499 (chain A) in PDB entry 3GD7
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 ARG1495 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1430A LEU 4.6 1.2 + - - -
1431A TYR* 2.8 64.2 + - - +
1434A PRO* 4.7 0.6 - - - +
1440A ALA* 3.3 19.8 + - - +
1443A ILE* 2.8 29.7 + - - +
1444A GLY* 4.4 2.8 - - - -
1446A PRO 5.7 0.2 + - - -
1448A MET* 3.5 39.9 - - + +
1449A ASN* 4.2 0.4 - - - -
1494A ILE* 1.3 77.9 - - - +
1496A PRO* 1.3 65.5 - - + +
1497A GLU* 3.3 30.7 - - - +
1498A HIS* 2.8 38.0 + - + +
1499A LEU* 3.3 8.3 + - - +
1560A ARG 5.0 0.6 + - - -
1562A HIS* 4.6 6.0 + - + -
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Residues in contact with PRO1496 (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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1446A PRO* 4.0 11.2 - - + +
1447A LYS 3.7 22.2 - - - +
1448A MET* 4.2 0.9 - - - -
1449A ASN* 3.5 10.3 - - - +
1494A ILE 4.0 0.7 - - - +
1495A ARG* 1.3 83.5 - - + +
1497A GLU* 1.3 74.6 + - - +
1498A HIS 3.2 0.7 + - - -
1499A LEU* 3.4 17.2 + - + +
1537A VAL* 3.3 40.2 - - + +
1538A TYR 4.1 0.7 - - - -
1539A ARG* 3.4 40.9 + - + +
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Residues in contact with GLU1497 (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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1431A TYR* 2.6 30.7 + - - -
1444A GLY* 5.1 5.7 - - - -
1446A PRO 3.9 10.2 - - - +
1495A ARG* 3.3 16.6 + - - +
1496A PRO* 1.3 97.9 - - - +
1498A HIS* 1.3 70.0 + - + +
1499A LEU 3.5 4.4 - - - +
1539A ARG* 3.7 43.1 + - - +
1560A ARG* 5.5 0.3 + - - -
1521C ASN* 3.7 20.9 - - + +
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Residues in contact with HIS1498 (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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1431A TYR* 3.2 40.0 + + - -
1432A HIS* 4.9 4.2 - - - -
1494A ILE* 4.0 15.3 - - + -
1495A ARG* 2.8 27.1 + - + +
1497A GLU* 1.3 85.7 - - + +
1499A LEU* 1.3 65.0 + - - +
1500A LEU* 3.5 5.5 + - - +
1557A PRO* 3.1 21.6 - - - +
1560A ARG* 3.3 61.7 + - + +
1562A HIS* 5.4 6.7 - + - -
1573A ARG* 5.5 1.6 - - - -
1577A GLU* 4.8 3.8 - - - -
1520C GLY 5.4 1.0 + - - -
1521C ASN* 5.4 3.1 - - + -
1542C ASP* 5.1 3.0 + - - -
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Residues in contact with LEU1499 (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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1449A ASN* 3.9 9.2 - - - +
1494A ILE* 3.5 28.9 - - + -
1495A ARG 3.3 8.9 + - - +
1496A PRO* 3.4 6.0 + - + +
1497A GLU 4.2 4.5 - - - +
1498A HIS* 1.3 79.3 - - - +
1500A LEU* 1.3 63.8 + - - +
1501A PRO* 4.5 1.2 - - - +
1509A LEU* 5.7 0.4 - - + -
1536A LEU* 4.2 8.3 - - + -
1537A VAL 3.5 24.9 - - - +
1538A TYR* 3.6 31.8 + - + -
1539A ARG 4.9 1.4 - - - +
1554A ILE* 3.8 28.3 - - + -
1555A GLY 3.4 17.9 - - - +
1556A LEU* 4.6 9.4 - - + -
1557A PRO* 4.4 0.9 - - - -
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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