Contacts of the strand formed by residues 1462 - 1467 (chain B) 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 GLN1462 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1459B ALA* 2.8 44.8 + - + +
1460B ILE 3.2 6.4 - - - +
1461B ASP* 1.3 84.5 - - - +
1463B VAL* 1.3 68.0 + - - +
1476B TRP* 3.6 41.6 - - + +
1477B LEU 3.4 12.8 - - - +
1478B PRO* 5.0 2.7 - - + -
1479B VAL 3.4 1.4 + - - -
1481B SER* 4.6 0.4 - - - -
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Residues in contact with VAL1463 (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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1455B VAL* 4.1 4.3 - - + -
1457B ALA 3.7 9.9 - - - +
1458B THR* 4.3 3.8 - - + -
1462B GLN* 1.3 78.8 - - - +
1464B GLN* 1.3 68.6 + - - +
1465B VAL* 4.2 3.1 - - + -
1476B TRP* 3.8 3.1 - - - -
1477B LEU* 2.8 38.4 + - - +
1479B VAL* 3.7 25.3 + - + +
1480B GLU 3.9 2.0 - - - +
1481B SER* 3.8 23.1 - - - -
1484B VAL* 3.8 26.9 - - + -
1563B LEU* 3.7 21.5 - - + -
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Residues in contact with GLN1464 (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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1455B VAL* 3.6 6.6 - - - +
1456B THR* 2.5 47.3 + - - +
1457B ALA* 2.7 30.9 + - + +
1463B VAL* 1.3 72.9 - - - +
1465B VAL* 1.3 65.6 + - - +
1474B GLN* 3.5 28.8 + - + +
1475B VAL 3.3 17.7 - - - +
1476B TRP* 3.0 48.3 + - + -
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Residues in contact with VAL1465 (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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1453B VAL* 3.8 26.9 - - + -
1454B LYS 3.4 4.0 - - - +
1455B VAL* 4.1 15.3 - - + -
1456B THR* 4.3 3.8 - - - -
1463B VAL* 4.2 2.5 - - + +
1464B GLN* 1.3 78.4 - - - +
1466B GLU* 1.3 59.7 + - - +
1473B GLN 3.9 0.5 - - - +
1474B GLN* 3.4 3.3 - - - +
1475B VAL* 3.0 40.9 + - + +
1477B LEU* 3.9 12.8 - - + -
1492B LEU* 3.8 28.0 - - + -
1563B LEU* 3.9 25.6 - - + -
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Residues in contact with GLU1466 (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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1453B VAL* 3.5 9.0 - - - +
1454B LYS* 2.7 46.1 + - + +
1456B THR* 3.6 15.5 - - + +
1465B VAL* 1.3 74.6 - - - +
1467B LEU* 1.3 65.1 + - - +
1468B PRO* 3.8 0.9 - - - +
1472B ARG* 3.1 40.5 + - + +
1473B GLN 3.3 16.6 - - - +
1474B GLN* 3.5 28.1 + - + +
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Residues in contact with LEU1467 (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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1451B LEU* 3.9 26.9 - - + -
1453B VAL* 3.7 21.1 - - + -
1465B VAL* 5.4 0.7 - - + +
1466B GLU* 1.3 73.4 - - - +
1468B PRO* 1.3 65.7 - - + +
1469B MET* 2.9 21.6 + - + -
1471B ASN 5.3 0.2 - - - +
1472B ARG* 3.6 20.0 + - - -
1473B GLN* 2.8 38.4 + - + +
1475B VAL* 4.7 10.8 - - + -
1492B LEU* 4.9 4.0 - - + -
1507B VAL* 4.0 19.3 - - + -
1509B LEU* 3.8 24.0 - - + -
1556B LEU* 4.5 10.5 - - + -
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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