Contacts of the strand formed by residues 1467 - 1472 (chain A) in PDB entry 4C6C
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 LEU1467 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1464A LEU* 4.4 10.3 - - + -
1465A PRO* 3.2 17.7 + - + +
1466A GLY* 1.3 73.3 - - - -
1468A ILE* 1.3 60.3 + - - +
1496A GLY 3.4 24.3 + - - +
1497A ILE* 3.6 15.1 - - + -
1498A THR* 2.9 27.0 + - - -
1499A MET 3.4 5.9 + - - -
1711A LEU* 3.8 36.3 - - + -
1728A LEU* 6.0 0.4 - - + -
1729A LEU* 3.7 28.3 - - + -
1732A LEU* 3.4 28.3 - - + +
1733A HIS* 4.2 6.1 - - + -
1750A VAL* 4.9 1.8 - - + -
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Residues in contact with ILE1468 (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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1466A GLY 4.0 9.0 - - - +
1467A LEU* 1.3 78.3 - - - +
1469A ASP* 1.3 63.3 + - - +
1470A VAL* 3.9 8.8 + - + -
1497A ILE* 4.4 2.7 - - - -
1499A MET* 3.4 40.6 - - + +
1501A CYS* 5.2 1.3 - - - -
1683A PHE 4.5 1.0 - - - +
1732A LEU* 2.8 30.2 + - - +
1733A HIS* 3.9 14.1 - - + +
1736A PRO* 3.9 19.9 - - + +
1737A ARG* 3.8 36.1 - - + +
1742A LEU* 3.8 24.7 - - + -
1745A GLN* 5.1 0.9 - - - +
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Residues in contact with ASP1469 (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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1468A ILE* 1.3 72.7 - - - +
1470A VAL* 1.3 59.2 + - - +
1471A HIS 3.0 17.2 + - - +
1472A VAL* 3.6 12.6 - - + +
1497A ILE* 3.8 18.7 - - + +
1499A MET 3.0 9.0 + - - +
1500A VAL* 3.3 4.8 - - + +
1501A CYS 2.9 23.6 + - - +
1683A PHE 5.1 2.0 - - - -
1684A ALA* 3.4 2.5 - - - -
1685A SER* 2.5 47.8 + - - -
1707A LEU* 3.3 11.9 - - + +
1710A MET* 3.4 14.7 - - + +
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Residues in contact with VAL1470 (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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1468A ILE* 3.9 11.6 + - + -
1469A ASP* 1.3 71.3 + - - +
1471A HIS* 1.3 59.1 + - - +
1501A CYS* 3.8 21.1 - - - -
1503A MET* 4.1 1.7 - - - +
1534A PHE* 3.5 22.5 - - - -
1611A HIS* 4.7 1.1 - - - +
1637A GLU* 3.4 23.6 - - - +
1682A CYS* 4.8 10.8 - - + -
1683A PHE 5.0 1.1 - - - +
1684A ALA* 3.9 10.3 - - + +
1736A PRO* 3.8 24.2 - - + -
1740A PHE* 3.7 40.1 - - + -
1742A LEU* 4.3 1.8 - - + -
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Residues in contact with HIS1471 (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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1469A ASP* 3.0 8.2 + - - +
1470A VAL* 1.3 80.0 - - - +
1472A VAL* 1.3 65.6 + - - +
1473A HIS* 3.8 5.4 - + - -
1501A CYS 3.8 1.1 - - - -
1503A MET* 3.5 12.9 - - + +
1556A KCX 3.0 23.7 + - - -
1613A CYS* 3.7 1.6 - - - -
1614A HIS* 3.6 16.1 - + - -
1637A GLU* 3.0 8.4 + - - +
1684A ALA* 3.7 11.4 - - + -
1686A ASP* 2.8 39.7 + - + +
2822A ZN 2.0 36.6 - - - -
2824A ZN 2.0 36.0 - - - -
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Residues in contact with VAL1472 (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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1469A ASP* 3.6 28.7 - - + +
1471A HIS* 1.3 80.8 - - - +
1473A HIS* 1.3 60.4 + - - +
1474A LEU* 3.7 28.3 - - + -
1500A VAL* 3.8 20.0 - - + -
1501A CYS 3.1 14.7 + - - +
1502A ALA* 3.3 5.8 - - - -
1503A MET* 2.8 31.0 + - - +
1685A SER* 3.9 4.7 - - - +
1687A HIS* 3.9 11.9 - - + +
1707A LEU* 3.9 15.7 - - + -
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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