Contacts of the helix formed by residues 1162 - 1178 (chain A) in PDB entry 5WS3
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 ASP1162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1050A VAL* 4.0 4.5 - - - +
1159A LYS* 3.6 38.8 + - + +
1160A ALA 3.3 1.2 - - - +
1161A GLY* 1.3 76.8 - - - +
1163A PRO* 1.3 66.9 - - - +
1164A GLY* 3.1 14.7 + - - -
1165A GLU* 3.1 26.0 + - + +
1166A LEU* 3.0 20.4 + - - +
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Residues in contact with PRO1163 (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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1050A VAL* 3.8 24.6 - - + +
1053A LYS* 3.7 42.2 - - + +
1054A ALA* 3.4 12.1 - - + +
1057A ILE* 4.1 7.6 - - + -
1161A GLY 3.2 12.1 - - - +
1162A ASP* 1.3 86.0 - - - +
1164A GLY* 1.3 58.3 + - - +
1166A LEU* 3.3 0.6 + - + -
1167A ALA* 2.9 26.2 + - - +
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Residues in contact with GLY1164 (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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1057A ILE* 4.1 13.9 - - - +
1162A ASP* 3.1 8.1 + - - -
1163A PRO* 1.3 76.8 - - - +
1165A GLU* 1.3 59.5 + - - +
1167A ALA* 3.4 4.5 + - - +
1168A ASN* 3.0 38.0 + - - -
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Residues in contact with GLU1165 (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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1158A VAL* 4.4 7.6 - - + -
1159A LYS* 4.1 32.1 - - + +
1162A ASP* 3.1 33.2 + - + +
1164A GLY* 1.3 75.5 - - - +
1166A LEU* 1.3 57.4 + - - +
1168A ASN* 3.3 18.2 + - - +
1169A ALA* 2.9 28.3 + - + +
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Residues in contact with LEU1166 (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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1050A VAL* 4.0 9.6 - - + +
1051A LEU* 3.9 31.2 - - + -
1054A ALA* 4.1 4.5 - - + -
1116A ILE* 4.0 24.0 - - + -
1118A PRO* 3.9 23.1 - - + -
1139A ILE* 4.2 20.0 - - + +
1158A VAL* 4.3 21.0 - - + +
1162A ASP 3.0 12.9 + - - +
1163A PRO* 3.7 8.7 - - + +
1165A GLU* 1.3 77.3 - - - +
1167A ALA* 1.3 58.9 + - - +
1169A ALA* 3.2 2.6 + - - -
1170A ILE* 2.9 43.9 + - + +
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Residues in contact with ALA1167 (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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1054A ALA* 3.9 12.5 - - + +
1057A ILE* 4.4 14.4 - - + -
1058A LEU* 3.7 32.2 - - + +
1061A LYS* 5.8 1.6 - - - +
1163A PRO 2.9 17.8 + - - +
1164A GLY 3.7 5.4 - - - +
1166A LEU* 1.3 78.1 - - - +
1168A ASN* 1.3 63.5 + - - +
1170A ILE* 3.2 3.5 + - - +
1171A LEU* 2.9 28.4 + - + +
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Residues in contact with ASN1168 (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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1061A LYS* 4.6 6.4 + - - -
1164A GLY 3.0 25.5 + - - +
1165A GLU* 3.3 22.1 + - - +
1167A ALA* 1.3 76.6 - - - +
1169A ALA* 1.3 56.2 + - - +
1171A LEU* 3.3 18.2 + - - +
1172A LYS* 2.9 27.5 + - - +
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Residues in contact with ALA1169 (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 ILE* 4.1 8.6 - - + +
1156A ILE* 3.8 20.5 - - + +
1158A VAL* 3.4 33.7 - - + -
1165A GLU 2.9 10.8 + - - +
1166A LEU 3.2 4.2 + - - +
1168A ASN* 1.3 76.7 - - - +
1170A ILE* 1.3 57.4 + - - +
1172A LYS* 3.3 10.0 + - - +
1173A ALA* 2.8 27.9 + - - +
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Residues in contact with ILE1170 (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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1035A PHE* 3.8 23.4 - - + -
1051A LEU* 4.5 5.6 - - + -
1054A ALA* 4.7 3.8 - - + -
1055A ILE* 5.8 0.2 - - + -
1058A LEU* 3.6 30.3 - - + -
1067A MET* 3.8 13.2 - - - -
1069A PHE* 4.3 9.0 - - + -
1116A ILE* 3.7 30.1 - - + -
1139A ILE* 4.6 4.7 - - + -
1166A LEU* 2.9 37.0 + - + +
1167A ALA* 3.2 6.3 + - - +
1169A ALA* 1.3 74.8 - - - +
1171A LEU* 1.3 61.9 + - - +
1173A ALA* 3.2 7.8 + - - +
1174A LEU* 2.9 26.5 + - - +
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Residues in contact with LEU1171 (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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1058A LEU* 3.7 14.1 - - + -
1061A LYS* 3.6 31.4 - - + +
1063A GLU* 3.8 28.9 - - + +
1067A MET* 3.7 21.1 - - + -
1167A ALA 2.9 20.2 + - - +
1168A ASN* 3.6 17.5 - - - +
1170A ILE* 1.3 72.3 - - - +
1172A LYS* 1.3 68.2 + - - +
1174A LEU* 3.2 7.8 + - + +
1175A GLU* 3.0 29.0 + - + +
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Residues in contact with LYS1172 (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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1156A ILE* 4.0 19.3 - - + -
1168A ASN 2.9 14.9 + - - +
1169A ALA* 3.4 11.2 - - - +
1171A LEU* 1.3 75.9 - - - +
1173A ALA* 1.3 57.2 + - - +
1175A GLU* 3.2 9.6 + - + +
1176A LEU* 2.9 48.6 + - + +
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Residues in contact with ALA1173 (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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1035A PHE* 3.8 7.2 - - + -
1114A PHE* 3.5 26.7 - - + -
1139A ILE* 3.6 24.2 - - + -
1156A ILE* 4.2 8.5 - - + -
1169A ALA 2.8 15.1 + - - +
1170A ILE 3.2 8.5 + - - +
1172A LYS* 1.3 75.6 - - - +
1174A LEU* 1.3 57.6 + - - +
1176A LEU* 3.3 3.8 + - - +
1177A SER* 2.8 30.4 + - - -
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Residues in contact with LEU1174 (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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1033A VAL* 3.6 34.1 - - + -
1035A PHE* 4.4 2.6 - - + -
1063A GLU* 3.6 31.0 - - + +
1066A GLU* 3.2 37.2 - - + +
1067A MET* 4.0 15.5 - - + -
1170A ILE 2.9 13.0 + - - +
1171A LEU* 3.2 11.0 + - + +
1173A ALA* 1.3 76.6 - - - +
1175A GLU* 1.3 63.7 + - - +
1177A SER* 2.5 20.8 + - - -
1178A ARG* 3.1 29.8 + - + +
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Residues in contact with GLU1175 (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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1063A GLU* 4.9 6.2 - - - +
1171A LEU* 3.0 18.3 + - + +
1172A LYS* 3.6 11.0 - - + +
1174A LEU* 1.3 78.2 - - - +
1176A LEU* 1.3 65.7 + - + +
1178A ARG* 2.9 59.4 + - - +
1179A SER* 4.2 1.7 + - - -
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Residues in contact with LEU1176 (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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1114A PHE* 5.0 4.9 - - + -
1137A ILE* 6.5 0.7 - - + -
1156A ILE* 4.2 24.7 - - + -
1172A LYS* 2.9 37.5 + - - +
1173A ALA* 3.6 9.0 - - - +
1175A GLU* 1.3 78.6 - - + +
1177A SER* 1.3 55.9 + - - +
1179A SER* 3.0 35.4 + - - +
1181A LEU* 3.5 18.5 - - + +
1184A PHE* 5.0 26.7 - - + -
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Residues in contact with SER1177 (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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1033A VAL* 3.2 38.5 - - - +
1113A ASP* 5.6 1.8 - - - -
1114A PHE* 4.1 1.6 - - - -
1173A ALA 2.8 12.5 + - - -
1174A LEU* 2.5 26.2 + - - +
1176A LEU* 1.3 75.3 - - - +
1178A ARG* 1.3 61.6 + - - +
1179A SER 3.0 7.9 + - - +
1181A LEU* 3.5 26.8 - - - +
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Residues in contact with ARG1178 (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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1063A GLU* 4.3 6.3 - - - +
1066A GLU* 2.5 45.2 + - - -
1174A LEU* 3.1 28.5 + - + +
1175A GLU* 2.9 49.3 + - - +
1176A LEU 3.0 1.0 - - - -
1177A SER* 1.3 77.8 - - - +
1179A SER* 1.3 56.2 + - - +
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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