Contacts of the strand formed by residues 1457 - 1462 (chain A) in PDB entry 5M64
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 ILE1457 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1322A ILE* 3.6 34.5 - - + -
1325A LEU* 5.7 1.6 - - + -
1326A GLU* 3.3 23.8 - - + +
1450A ILE* 4.3 22.0 - - + +
1451A ILE* 4.3 24.0 - - + +
1454A HIS* 3.8 19.0 - - + +
1455A ARG 3.2 9.3 - - - +
1456A PHE* 1.3 77.1 - - - +
1458A THR* 1.3 64.3 + - - +
1459A LYS 4.2 15.3 - - - +
1460A TYR* 5.0 6.5 - - + -
1472A PHE* 5.6 1.1 - - + -
1473A LYS 4.8 0.2 - - - +
1474A LEU* 3.7 29.4 - - + -
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Residues in contact with THR1458 (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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1447A GLN* 3.4 12.8 + - - -
1451A ILE* 3.6 16.6 - - - +
1455A ARG 5.0 2.7 - - - +
1456A PHE 3.7 9.4 - - - +
1457A ILE* 1.3 80.1 - - - +
1459A LYS* 1.3 83.5 + - - +
1473A LYS* 2.8 29.5 + - - -
1475A GLU* 3.7 32.5 - - + +
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Residues in contact with LYS1459 (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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1447A GLN* 3.5 10.8 - - - +
1457A ILE* 4.2 5.7 - - - +
1458A THR* 1.3 95.5 + - - +
1460A TYR* 1.3 62.5 + - - +
1471A GLU* 5.7 2.9 - - - +
1472A PHE* 3.3 5.8 - - - +
1473A LYS* 2.9 68.2 + - + +
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Residues in contact with TYR1460 (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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1314A GLN* 2.4 43.2 + - - -
1317A ILE* 3.4 22.0 - - + +
1318A SER* 4.5 4.8 - - - -
1322A ILE* 5.1 9.4 - - + -
1439A MET* 5.7 3.3 - - - +
1443A GLN* 4.1 9.3 + - + +
1446A ARG* 3.6 21.1 - - - -
1447A GLN* 3.6 34.5 - - + +
1450A ILE* 4.7 32.8 - - + -
1451A ILE* 6.5 0.2 - - + -
1457A ILE* 5.0 5.2 - - + -
1459A LYS* 1.3 79.1 - - - +
1461A ASN* 1.3 64.9 + - - +
1462A PHE* 4.3 5.2 - - + -
1470A CYS* 4.1 10.7 - - - -
1471A GLU* 3.8 0.4 - - - -
1472A PHE* 3.7 34.1 - + + +
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Residues in contact with ASN1461 (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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1435A ALA* 5.4 0.6 - - - +
1436A ASN* 3.8 10.5 + - - +
1439A MET* 3.3 38.0 - - + +
1443A GLN* 3.2 14.4 + - - +
1460A TYR* 1.3 81.2 - - - +
1462A PHE* 1.3 79.6 + - - +
1469A TRP* 3.2 30.1 - - - -
1470A CYS* 3.4 8.5 - - - -
1471A GLU* 2.8 49.6 + - - +
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Residues in contact with PHE1462 (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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1296A PHE* 3.7 25.6 - + - -
1310A LYS* 3.6 32.5 - - + -
1313A LEU* 4.0 17.7 - - + -
1314A GLN* 3.2 29.8 - - + +
1317A ILE* 5.4 0.9 - - + -
1436A ASN* 5.1 1.4 + - - -
1443A GLN* 3.1 11.7 + - - +
1446A ARG* 3.3 27.5 + - - +
1460A TYR* 4.3 1.8 - - + -
1461A ASN* 1.3 89.0 + - - +
1463A ASP* 1.3 87.6 + - - +
1464A ASP* 3.2 14.6 + - + +
1467A GLY* 4.7 2.9 - - - -
1469A TRP* 4.1 4.7 - - - -
1470A CYS* 3.5 25.6 - - + +
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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