Contacts of the strand formed by residues 1680 - 1683 (chain A) in PDB entry 4C8D
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 ALA1680 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1415A VAL 3.7 0.9 - - - +
1416A LEU* 3.4 6.3 - - - -
1417A VAL* 2.8 40.0 + - + +
1420A VAL* 4.1 13.5 - - + -
1510A PRO* 4.1 10.3 - - + -
1567A VAL* 3.7 22.2 - - + -
1568A ASN 3.2 5.8 - - - -
1569A VAL* 4.0 13.0 - - + +
1678A GLY 3.7 0.2 + - - -
1679A ASP* 1.3 72.8 - - - +
1681A VAL* 1.3 62.5 + - - +
1682A PHE* 3.9 2.2 + - + -
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Residues in contact with VAL1681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1414A PRO* 5.2 0.7 - - + -
1415A VAL 3.7 4.7 - - - +
1416A LEU* 4.1 17.5 - - + +
1567A VAL* 3.4 1.7 - - - -
1568A ASN* 2.8 42.5 + - + +
1614A TRP* 4.4 14.1 - - + +
1616A ILE* 3.8 29.4 - - + -
1673A ILE* 4.6 11.2 - - + -
1675A GLN* 3.7 34.5 - - + +
1680A ALA* 1.3 75.0 - - - +
1682A PHE* 1.3 63.9 + - - +
1683A ILE* 3.7 14.5 + - + +
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Residues in contact with PHE1682 (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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1405A PHE* 3.9 16.8 - + - -
1409A TRP* 3.7 13.0 - + + -
1414A PRO* 3.2 30.0 - - - +
1415A VAL* 2.9 30.9 + - + +
1417A VAL* 3.6 28.5 - - + -
1510A PRO* 3.9 18.4 - - + -
1511A LEU* 3.5 24.7 - - + -
1514A TYR* 5.6 0.4 - - + -
1515A THR* 3.6 21.5 - - + -
1566A ALA 3.5 2.2 - - - -
1567A VAL* 3.6 26.2 - - + -
1680A ALA* 4.2 2.2 - - + -
1681A VAL* 1.3 71.8 - - - +
1683A ILE* 1.3 61.9 + - - +
1684A PRO* 3.6 0.9 - - - +
1704A PHE* 3.9 21.1 - + - -
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Residues in contact with ILE1683 (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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1409A TRP* 3.9 2.7 - - - -
1414A PRO* 5.0 0.9 - - - -
1562A ASP* 6.3 0.7 - - + -
1564A SER 4.4 1.2 - - - +
1565A ASP* 3.7 0.9 - - - -
1566A ALA* 2.9 40.5 + - + +
1568A ASN* 4.2 4.3 - - + -
1614A TRP* 3.7 21.8 - - + -
1616A ILE* 4.6 7.6 - - + -
1681A VAL* 3.8 24.7 - - + +
1682A PHE* 1.3 73.9 - - - +
1684A PRO* 1.3 80.7 - - + +
1687A ALA* 4.0 6.3 - - + +
1689A HIS* 3.6 32.1 - - + +
2722A OGA 3.6 31.2 - - - +
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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