Contacts of the strand formed by residues 1170 - 1177 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1096B LEU 3.6 4.0 - - - +
1097B LYS* 3.6 35.2 + - - +
1148B ASN* 3.4 17.0 + - - +
1168B PRO* 3.3 9.5 - - + +
1169B GLU* 1.3 79.1 - - - +
1171B VAL* 1.3 62.0 + - - +
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Residues in contact with VAL1171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094B VAL 3.7 0.5 - - - +
1095B ASN* 3.4 3.5 - - - +
1096B LEU* 2.8 47.4 + - + +
1098B LYS* 4.7 0.2 - - - -
1104B LEU* 3.6 34.3 - - + -
1147B VAL* 4.7 4.7 - - + -
1148B ASN* 3.4 11.0 - - - +
1167B ALA* 3.8 20.6 - - + -
1168B PRO 3.4 23.1 - - - +
1169B GLU 4.3 1.8 - - - +
1170B ASP* 1.3 75.2 - - - +
1172B THR* 1.3 61.6 - - - +
1173B LEU* 4.2 23.6 - - + -
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Residues in contact with THR1172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093B LEU* 4.3 25.6 - - + -
1094B VAL 3.4 4.5 - - - +
1095B ASN* 2.6 24.2 + - - +
1146B SER* 3.9 1.2 + - - +
1147B VAL* 3.9 0.7 - - - -
1148B ASN* 2.8 46.8 + - - -
1149B SER 4.5 1.1 + - - +
1171B VAL* 1.3 72.4 - - - +
1173B LEU* 1.3 69.1 + - - +
1174B VAL* 4.2 3.4 + - + +
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Residues in contact with LEU1173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092B THR 3.7 0.3 - - - +
1093B LEU* 3.3 7.1 - - - +
1094B VAL* 2.8 50.2 + - + +
1096B LEU* 3.8 27.8 - - + -
1104B LEU* 5.1 0.2 - - + -
1106B PHE* 4.0 19.7 - - + -
1138B LEU* 4.9 6.7 - - + -
1144B LEU* 4.0 19.3 - - + -
1146B SER 3.4 13.0 - - - +
1147B VAL* 4.0 19.3 - - + -
1164B LEU* 4.7 7.4 - - + -
1171B VAL* 4.2 18.4 - - + -
1172B THR* 1.3 77.9 - - - +
1174B VAL* 1.3 61.1 + - - +
1175B ILE* 4.2 9.2 - - + -
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Residues in contact with VAL1174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091B ILE* 3.9 25.4 - - + -
1092B THR 3.6 4.3 - - - +
1093B LEU* 4.0 23.6 - - + -
1144B LEU* 4.0 0.3 - - - +
1145B ILE* 2.8 41.5 + - + -
1146B SER* 3.2 32.4 + - - +
1149B SER* 6.3 0.2 - - - -
1172B THR* 4.2 3.8 + - + +
1173B LEU* 1.3 74.2 - - - +
1175B ILE* 1.3 65.7 + - - +
1091D ILE* 4.2 12.6 - - + -
1093D LEU* 4.9 4.7 - - + -
1174D VAL* 4.4 11.4 - - + -
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Residues in contact with ILE1175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091B ILE* 3.4 6.9 - - - +
1092B THR* 3.0 55.5 + - - +
1094B VAL* 3.8 15.0 - - + -
1123B ILE* 5.7 0.2 - - + -
1138B LEU* 3.7 24.5 - - + -
1142B ASP* 3.6 12.3 - - + +
1143B ARG 3.1 15.0 - - - +
1144B LEU* 3.9 19.1 - - + -
1145B ILE* 4.1 6.1 - - - +
1173B LEU* 4.2 10.5 - - + -
1174B VAL* 1.3 81.1 - - - +
1176B SER* 1.3 61.2 + - - +
1177B GLN* 3.6 26.9 - - + +
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Residues in contact with SER1176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089B ARG* 2.9 16.8 + - - -
1090B GLU 3.1 4.7 - - - -
1091B ILE* 3.4 17.5 - - - -
1142B ASP* 3.5 5.4 - - - +
1143B ARG* 2.9 43.0 + - - +
1145B ILE* 3.9 5.0 - - - +
1175B ILE* 1.3 72.3 - - - +
1177B GLN* 1.3 65.4 + - - +
1153D GLU* 2.7 40.0 + - - -
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Residues in contact with GLN1177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089B ARG* 3.2 10.3 - - - +
1090B GLU* 2.8 40.7 + - + +
1092B THR* 3.0 31.4 - - + +
1137B CYS* 3.0 27.7 + - - -
1139B LYS* 4.9 2.6 - - - +
1142B ASP* 2.8 33.4 + - - +
1175B ILE* 3.6 15.2 - - + +
1176B SER* 1.3 80.2 - - - +
1178B PRO* 1.3 73.4 - - + +
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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