Contacts of the strand formed by residues 1170 - 1177 (chain A) in PDB entry 5GLJ
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 ASP1170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1096A LEU 3.6 3.6 - - - +
1097A LYS* 3.2 36.4 - - + +
1148A ASN* 3.2 19.1 + - - +
1168A PRO* 3.7 7.8 - - + +
1169A GLU* 1.3 86.5 - - - +
1171A VAL* 1.3 59.9 + - - +
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Residues in contact with VAL1171 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1094A VAL 3.7 0.7 - - - +
1095A ASN* 3.5 3.6 - - - +
1096A LEU* 2.9 39.1 + - + +
1098A LYS* 4.4 0.9 - - - -
1104A LEU* 3.9 29.4 - - + -
1147A VAL* 3.9 14.4 - - + -
1148A ASN* 3.2 8.5 - - - +
1167A ALA* 3.9 16.2 - - + -
1168A PRO 3.2 24.5 - - - +
1169A GLU 4.0 1.3 - - - +
1170A ASP* 1.3 73.4 - - - +
1172A THR* 1.3 65.5 + - - +
1173A LEU* 3.5 31.6 - - + -
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Residues in contact with THR1172 (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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1093A LEU* 3.9 27.6 - - + -
1094A VAL 3.4 5.4 - - - +
1095A ASN* 2.7 25.2 + - - +
1146A SER* 3.9 1.4 + - - +
1147A VAL* 3.8 1.6 - - - -
1148A ASN* 2.6 41.0 + - - -
1149A SER 4.7 0.5 + - - -
1171A VAL* 1.3 73.5 - - - +
1173A LEU* 1.3 66.6 + - - +
1174A VAL* 4.2 3.2 + - + +
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Residues in contact with LEU1173 (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 THR 3.7 0.5 - - - +
1093A LEU* 3.3 8.5 - - - +
1094A VAL* 2.7 47.6 + - + +
1096A LEU* 4.2 15.3 - - + -
1104A LEU* 4.9 0.4 - - + -
1106A PHE* 3.8 29.6 - - + -
1138A LEU* 4.5 16.6 - - + -
1144A LEU* 4.0 10.3 - - + -
1146A SER 3.4 12.8 - - - +
1147A VAL* 3.9 16.6 - - + -
1164A LEU* 4.7 7.4 - - + -
1171A VAL* 3.5 26.7 - - + -
1172A THR* 1.3 73.7 - - - +
1174A VAL* 1.3 62.1 + - - +
1175A ILE* 4.0 9.9 - - + -
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Residues in contact with VAL1174 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1091A ILE* 4.0 23.8 - - + -
1092A THR 3.5 4.3 - - - +
1093A LEU* 3.6 24.9 - - + -
1144A LEU* 4.0 0.2 - - - +
1145A ILE* 2.8 38.6 + - + -
1146A SER* 3.1 31.5 + - - +
1172A THR* 5.3 3.6 - - + +
1173A LEU* 1.3 73.6 - - - +
1175A ILE* 1.3 66.1 + - - +
1091C ILE* 4.4 4.3 - - + -
1093C LEU* 4.3 13.2 - - + -
1174C VAL* 4.2 16.2 - - + -
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Residues in contact with ILE1175 (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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1091A ILE* 3.5 7.4 - - - +
1092A THR* 2.9 47.3 + - - +
1094A VAL* 3.8 16.6 - - + -
1123A ILE* 5.6 0.4 - - + -
1138A LEU* 3.6 28.7 - - + -
1142A ASP* 3.5 26.9 - - + +
1143A ARG 3.1 14.4 - - - +
1144A LEU* 4.0 17.3 - - + -
1145A ILE* 4.0 4.9 - - - +
1173A LEU* 4.2 10.1 - - + -
1174A VAL* 1.3 79.9 - - - +
1176A SER* 1.3 62.7 + - - +
1177A GLN* 3.7 18.6 - - + +
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Residues in contact with SER1176 (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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1089A ARG* 2.8 12.9 + - - -
1090A GLU 3.2 4.9 - - - -
1091A ILE* 3.5 17.0 - - - -
1142A ASP* 3.4 6.2 - - - +
1143A ARG* 2.8 40.4 + - - +
1145A ILE* 3.9 5.1 - - - +
1175A ILE* 1.3 71.0 - - - +
1177A GLN* 1.3 65.6 + - - +
1153C GLU* 2.6 41.1 + - - -
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Residues in contact with GLN1177 (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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1089A ARG* 3.3 9.0 - - - +
1090A GLU* 2.7 46.4 + - + +
1092A THR* 2.7 29.8 + - - +
1137A CYS* 3.1 26.2 + - - -
1139A LYS* 5.0 2.2 - - - +
1142A ASP* 2.8 30.9 + - - +
1175A ILE* 3.7 16.8 - - + +
1176A SER* 1.3 78.9 - - - +
1178A PRO* 1.3 76.2 - - + +
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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