Contacts of the strand formed by residues 1263 - 1268 (chain J) in PDB entry 6C6S
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 LYS1263 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1260J MET 4.7 1.0 + - - -
1261J LEU 3.3 6.9 - - - +
1262J ARG* 1.3 87.5 - - + +
1264J ALA* 1.3 62.5 + - - +
1279J GLN* 3.7 33.0 + - + +
1280J VAL* 4.0 5.4 - - - +
1281J GLU* 3.6 40.8 - - + +
1282J TYR* 5.1 0.3 - - - +
1304J ARG* 4.0 1.4 - - - +
1305J ASP* 3.0 24.9 + - - +
1307J LEU* 3.7 15.3 - - + -
1312J ALA* 5.9 2.5 - - + +
1315J ALA* 2.7 48.2 + - + +
1316J THR* 4.1 3.4 - - - +
1317J GLU* 4.9 10.8 + - - -
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Residues in contact with ALA1264 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1263J LYS* 1.3 77.0 - - - +
1265J THR* 1.3 65.1 + - - +
1266J ILE* 6.4 0.2 - - + -
1279J GLN* 3.3 5.5 - - - +
1280J VAL* 2.8 38.6 + - + +
1282J TYR* 4.5 24.0 - - + -
1285J VAL* 5.2 2.9 - - + -
1302J TYR* 4.6 12.6 - - + -
1303J SER 3.4 14.4 - - - +
1304J ARG* 3.9 8.3 - - + -
1305J ASP 3.8 2.7 - - - +
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Residues in contact with THR1265 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1264J ALA* 1.3 78.4 - - - +
1266J ILE* 1.3 67.2 + - - +
1277J GLY 5.3 4.5 - - - +
1278J GLU 3.5 6.7 - - - -
1279J GLN* 3.9 24.0 - - + +
1302J TYR* 3.4 1.5 - - - -
1303J SER* 2.6 57.4 + - - -
1304J ARG 5.3 0.2 - - - -
1305J ASP* 3.9 21.5 + - + +
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Residues in contact with ILE1266 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1264J ALA* 6.4 0.2 - - + -
1265J THR* 1.3 77.8 + - - +
1267J VAL* 1.3 59.7 + - - +
1268J ASN* 3.3 32.1 - - - +
1269J ALA* 4.0 4.3 - - - +
1274J PHE* 3.8 22.4 - - + -
1275J LEU 3.3 23.3 - - - +
1276J GLU 2.9 19.4 - - - +
1277J GLY* 4.4 2.8 - - - -
1278J GLU* 2.9 20.7 + - + +
1280J VAL* 4.1 13.5 - - + -
1285J VAL* 4.0 27.1 - - + -
1300J ALA* 5.0 4.3 - - + -
1301J THR 3.9 5.8 - - - +
1302J TYR* 4.7 6.3 - - + -
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Residues in contact with VAL1267 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1265J THR 3.5 0.8 + - - -
1266J ILE* 1.3 76.1 - - - +
1268J ASN* 1.3 63.3 + - + +
1276J GLU* 3.7 19.4 - - - +
1301J THR* 2.8 25.6 + - - +
1302J TYR 3.4 27.4 - - - +
1303J SER* 3.8 13.7 - - - -
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Residues in contact with ASN1268 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1266J ILE* 3.3 13.1 - - - +
1267J VAL* 1.3 80.0 + - + +
1269J ALA* 1.3 77.0 + - - +
1270J GLY* 3.3 6.5 + - - +
1276J GLU* 5.2 9.6 - - - +
1300J ALA* 4.2 0.9 - - - -
1301J THR* 2.9 34.2 + - + +
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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