Contacts of the strand formed by residues 1293 - 1297 (chain A) in PDB entry 6CNB
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 LEU1293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1142A ASN* 4.3 3.3 - - - +
1143A ALA* 3.0 50.1 + - + +
1145A LEU* 4.1 13.5 - - + +
1154A ALA 4.9 2.0 - - - +
1157A VAL* 3.8 29.6 - - + -
1158A LYS* 4.7 14.4 - - + +
1281A ALA* 5.8 1.6 - - + -
1282A VAL 3.0 17.3 - - - +
1283A ILE* 3.8 12.0 - - + +
1286A ARG* 5.9 0.3 + - - -
1292A GLU* 1.3 76.0 - - - +
1294A LEU* 1.3 61.9 + - - +
1295A VAL* 3.6 26.7 - - + -
1303A VAL* 5.9 2.7 - - + -
1309A VAL* 5.0 9.6 - - + -
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Residues in contact with LEU1294 (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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1117A MET* 4.2 22.7 - - - +
1140A ILE* 5.2 20.4 - - + -
1141A ILE 3.2 16.2 - - - +
1142A ASN* 4.6 8.3 - - + +
1281A ALA* 3.7 0.3 - - - -
1282A VAL* 2.9 45.6 + - + +
1284A ASN* 4.0 25.8 - - + +
1286A ARG* 6.1 2.9 - - - +
1292A GLU 4.1 0.4 + - - -
1293A LEU* 1.3 73.5 - - - +
1295A VAL* 1.3 65.7 + - - +
1296A GLU* 4.5 11.2 - - - +
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Residues in contact with VAL1295 (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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1140A ILE* 4.8 1.1 - - - -
1141A ILE* 2.8 49.1 + - + +
1143A ALA* 5.9 0.2 - - + -
1161A VAL* 5.3 5.2 - - + +
1278A ILE* 3.4 41.1 - - + -
1280A ARG 3.5 7.4 - - - +
1281A ALA* 3.5 17.7 - - + -
1293A LEU* 3.6 25.6 - - + -
1294A LEU* 1.3 81.1 - - - +
1296A GLU* 1.3 66.8 + - - +
1303A VAL* 5.4 9.0 - - + -
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Residues in contact with GLU1296 (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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1117A MET 3.7 22.2 + - - -
1118A ASN 5.0 3.9 - - - +
1138A THR* 5.4 6.1 - - - +
1139A PRO* 3.9 17.0 - - + +
1140A ILE* 4.8 12.2 - - + +
1278A ILE* 3.1 26.0 - - - +
1279A SER* 3.4 14.1 + - - -
1280A ARG* 2.8 46.8 + - + +
1281A ALA* 4.0 2.8 + - - -
1282A VAL* 5.3 0.5 - - - +
1294A LEU* 4.5 9.1 - - - +
1295A VAL* 1.3 74.2 - - - +
1297A GLY* 1.3 58.6 + - - +
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Residues in contact with GLY1297 (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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1139A PRO* 3.2 25.1 + - - +
1141A ILE* 3.5 16.8 - - - +
1277A ASP 3.8 13.9 - - - -
1278A ILE* 3.8 10.3 - - - -
1279A SER 4.8 0.4 - - - -
1295A VAL 3.5 2.2 + - - -
1296A GLU* 1.3 75.1 - - - +
1298A TYR* 1.3 67.4 + - - -
1299A GLY 3.6 2.2 - - - -
1318A HIS* 4.3 1.2 - - - -
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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