Contacts of the strand formed by residues 1137 - 1146 (chain A) in PDB entry 6BM0
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 GLY1137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1125A THR 3.3 10.8 - - - -
1126A CYS* 3.6 8.3 - - - -
1127A LEU* 5.5 2.5 - - - -
1136A ARG* 1.3 76.1 - - - +
1138A ARG* 1.3 58.0 + - - +
1167A GLU* 3.3 9.6 - - - +
1168A GLN 2.7 29.9 + - - +
1170A GLY 2.6 19.3 + - - +
1172A VAL* 4.0 8.3 - - - -
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Residues in contact with ARG1138 (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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1092A ILE* 6.4 0.4 - - - +
1094A LEU* 4.3 14.3 - - - +
1095A GLN* 3.2 33.1 - - - +
1098A GLU* 2.6 37.6 + - - +
1125A THR* 2.7 44.1 + - - +
1127A LEU* 6.0 2.0 - - + -
1137A GLY* 1.3 75.8 - - - +
1139A ILE* 1.3 65.0 + - - +
1140A LEU* 3.8 9.3 + - - +
1165A GLU* 3.1 40.4 + - + +
1166A LYS 3.3 28.7 - - - +
1167A GLU* 3.7 30.0 + - + +
1168A GLN* 4.2 1.3 - - - +
1172A VAL* 3.9 3.6 - - - +
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Residues in contact with ILE1139 (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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1123A ALA 3.9 5.2 - - - +
1124A GLY* 4.8 0.2 - - - -
1138A ARG* 1.3 71.1 - - - +
1140A LEU* 1.3 61.6 + - - +
1141A ILE* 4.3 7.2 - - + -
1164A TYR* 3.3 27.0 - - + +
1165A GLU* 3.6 9.2 - - - -
1166A LYS 3.4 6.3 + - - -
1168A GLN* 3.5 36.7 - - + +
1172A VAL* 3.8 20.6 - - + -
1175A LEU* 4.6 9.6 - - + -
1182A LEU* 4.0 20.6 - - + -
1184A SER* 3.9 17.3 - - - -
1186A ILE* 4.7 0.9 - - + -
1193A TRP* 3.8 23.8 - - + +
1200A LEU* 4.2 11.2 - - + -
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Residues in contact with LEU1140 (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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1076A ILE* 4.1 26.0 - - + -
1092A ILE* 4.2 15.5 - - + -
1094A LEU* 5.3 4.5 - - + -
1121A VAL 3.8 1.0 - - - +
1122A ALA* 3.3 1.2 - - - -
1123A ALA* 2.7 47.9 + - + +
1125A THR* 4.9 9.9 - - + -
1138A ARG* 4.8 14.1 - - - +
1139A ILE* 1.3 73.4 - - - +
1141A ILE* 1.3 59.9 + - - +
1142A MET* 4.0 14.3 + - + +
1162A VAL* 3.7 34.5 - - + -
1164A TYR 3.5 0.4 - - - -
1165A GLU* 3.8 27.1 - - + +
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Residues in contact with ILE1141 (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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1108A LEU* 4.0 15.7 - - + -
1120A TYR* 3.7 35.9 - - + -
1121A VAL 3.6 3.6 - - - +
1122A ALA* 4.2 13.9 - - + -
1139A ILE* 4.3 8.3 - - + -
1140A LEU* 1.3 74.2 - - - +
1142A MET* 1.3 64.1 + - - +
1162A VAL* 3.7 4.2 - - - -
1163A LEU* 3.1 33.9 + - + -
1164A TYR* 3.0 28.4 + - + +
1182A LEU* 3.8 21.8 - - + -
1195A LEU* 4.5 4.7 - - + -
1200A LEU* 4.1 20.6 - - + -
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Residues in contact with MET1142 (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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1076A ILE* 3.8 31.0 - - + -
1092A ILE* 3.8 22.7 - - - -
1103A MET* 5.0 0.7 - - + -
1120A TYR* 3.6 5.2 - - - +
1121A VAL* 2.6 63.4 + - + +
1123A ALA* 4.4 8.7 - - + -
1140A LEU* 4.2 19.7 - - + +
1141A ILE* 1.3 80.7 - - - +
1143A ASP* 1.3 60.3 + - - +
1160A PHE* 3.8 32.1 - - + -
1161A LYS 3.7 5.2 - - - +
1162A VAL* 3.7 18.4 - - + -
1163A LEU* 4.8 0.9 - - - +
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Residues in contact with ASP1143 (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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1028A HIS* 3.3 19.8 + - - -
1030A GLU* 4.7 5.2 - - - +
1118A LYS* 3.8 13.5 + - - -
1119A GLY 4.5 0.2 - - - +
1120A TYR* 3.2 32.6 - - + -
1142A MET* 1.3 76.6 - - - +
1144A VAL* 1.3 89.1 + - - +
1145A ILE* 3.7 11.4 + - + +
1160A PHE* 3.8 2.4 - - - -
1161A LYS* 3.0 37.5 + - + +
1163A LEU* 4.7 10.4 - - + +
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Residues in contact with VAL1144 (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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1028A HIS* 4.2 26.9 + - + +
1030A GLU* 5.6 1.6 - - - +
1031A SER* 4.0 23.5 + - - -
1033A VAL* 3.9 30.5 - - + -
1078A LEU* 4.5 12.8 - - + -
1121A VAL* 5.3 4.3 - - + -
1143A ASP* 1.3 89.3 + - - +
1145A ILE* 1.3 64.1 + - - +
1146A GLU 4.3 0.3 + - - -
1158A ASN* 4.0 21.8 - - + +
1159A LYS 3.8 7.6 - - - +
1160A PHE* 4.6 13.5 - - + -
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Residues in contact with ILE1145 (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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1143A ASP* 3.7 15.5 + - + +
1144A VAL* 1.3 78.5 - - - +
1146A GLU* 1.3 73.7 - - - +
1147A VAL* 3.5 18.1 + - + +
1157A LYS 3.7 0.3 - - - +
1158A ASN* 3.8 2.4 - - - -
1159A LYS 3.2 30.5 + - - +
1161A LYS* 3.7 39.7 - - + +
1163A LEU* 6.4 0.2 - - + -
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Residues in contact with GLU1146 (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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1031A SER* 3.2 33.8 + - - +
1144A VAL 4.3 0.4 - - - -
1145A ILE* 1.3 79.6 - - - +
1147A VAL* 1.3 61.7 + - - +
1157A LYS* 3.3 19.1 + - + +
1158A ASN* 3.4 13.6 - - - +
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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