Contacts of the helix formed by residues 1169 - 1184 (chain B) in PDB entry 5W0N
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 SER1169 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1161B GLY 4.7 1.1 - - - -
1163B ALA* 3.8 23.3 - - - +
1168B LEU* 1.3 75.8 - - - +
1170B SER* 1.3 63.2 + - - +
1171B TYR* 3.1 22.9 + - - +
1172B ALA* 2.9 31.9 + - - +
1173B TYR* 3.3 7.9 + - - -
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Residues in contact with SER1170 (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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1152B LYS* 4.0 32.5 + - - -
1155B THR* 5.7 2.7 - - - -
1161B GLY* 4.1 13.6 + - - -
1168B LEU 3.7 2.0 + - - -
1169B SER* 1.3 73.5 + - - +
1171B TYR* 1.3 58.3 + - - +
1173B TYR* 3.2 15.4 + - - +
1174B THR* 3.0 30.7 + - - -
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Residues in contact with TYR1171 (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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1050B ASN* 5.6 2.7 - - - -
1130B ASN* 3.3 46.6 + - - +
1133B LEU* 6.1 0.2 - - - +
1134B LEU* 3.9 27.9 - - + +
1169B SER* 3.1 15.0 + - - +
1170B SER* 1.3 82.0 + - - +
1172B ALA* 1.3 62.7 + - + +
1174B THR* 3.4 6.2 + - - -
1175B LEU* 3.2 52.4 + - + +
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Residues in contact with ALA1172 (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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1168B LEU* 4.4 21.1 - - + -
1169B SER* 2.9 23.6 + - - +
1171B TYR* 1.3 82.4 - - + +
1173B TYR* 1.3 62.0 + - - +
1175B LEU* 3.2 16.2 + - + +
1176B MET* 3.1 26.0 + - + +
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Residues in contact with TYR1173 (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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1151B MET* 3.8 24.2 - - + +
1152B LYS* 6.1 0.7 - - - -
1155B THR* 3.7 39.5 - - + +
1160B ILE* 2.7 48.5 + - + +
1161B GLY* 3.9 5.4 - - - -
1168B LEU* 3.7 34.6 + - + +
1169B SER 3.3 14.3 + - - -
1170B SER* 3.2 13.5 + - - +
1172B ALA* 1.3 73.9 - - - +
1174B THR* 1.3 65.6 + - - +
1176B MET* 3.1 25.8 + - + +
1177B VAL* 3.0 23.9 + - - +
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Residues in contact with THR1174 (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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1050B ASN* 5.7 1.0 + - - -
1052B PHE* 3.8 26.0 - - + +
1134B LEU* 3.5 32.2 - - + +
1148B CYS* 4.0 14.7 + - - +
1151B MET* 5.1 0.6 - - - +
1152B LYS* 4.9 10.6 + - - -
1170B SER 3.0 16.1 + - - -
1171B TYR* 3.6 11.3 - - - -
1173B TYR* 1.3 76.3 - - - +
1175B LEU* 1.3 61.8 + - - +
1177B VAL* 3.1 10.6 + - - +
1178B LEU* 3.0 24.7 + - + +
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Residues in contact with LEU1175 (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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1133B LEU* 6.2 2.2 - - + -
1134B LEU* 4.5 15.3 - - + -
1171B TYR* 3.2 50.5 + - + +
1172B ALA* 3.2 14.8 + - + +
1174B THR* 1.3 76.9 - - - +
1176B MET* 1.3 58.8 + - + +
1178B LEU* 3.3 9.9 + - + +
1179B TYR* 2.8 31.6 + - - +
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Residues in contact with MET1176 (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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1151B MET* 4.3 13.7 - - + -
1168B LEU* 4.9 10.1 - - - -
1172B ALA* 3.1 13.8 + - - +
1173B TYR* 3.1 36.9 + - + +
1175B LEU* 1.3 77.8 - - + +
1177B VAL* 1.3 61.8 + - - +
1179B TYR* 3.9 6.6 - - - +
1180B PHE* 3.0 24.1 + - - +
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Residues in contact with VAL1177 (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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1144B VAL 4.9 0.2 - - - +
1147B LEU* 3.9 26.0 - - + +
1148B CYS* 3.7 24.9 - - - -
1151B MET* 3.6 36.8 - - + -
1173B TYR 3.0 15.7 + - - +
1174B THR* 3.5 7.6 - - - +
1176B MET* 1.3 76.2 - - - +
1178B LEU* 1.3 64.1 + - + +
1180B PHE* 3.2 9.3 + - + +
1181B LEU* 3.0 39.3 + - + +
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Residues in contact with LEU1178 (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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1052B PHE* 5.2 1.8 - - + -
1134B LEU* 3.9 32.1 - - + -
1137B TYR* 3.9 33.7 - - + -
1144B VAL* 3.9 19.3 - - + -
1148B CYS* 4.7 6.5 - - - -
1174B THR* 3.0 20.0 + - + +
1175B LEU* 3.8 12.6 - - + +
1177B VAL* 1.3 76.2 - - - +
1179B TYR* 1.3 57.4 + - - +
1181B LEU* 3.2 3.6 + - + -
1182B GLN* 2.9 40.7 + - - +
1189B ILE* 3.5 25.5 - - + +
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Residues in contact with TYR1179 (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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1175B LEU 2.8 20.5 + - - +
1176B MET* 3.9 8.1 - - - +
1178B LEU* 1.3 73.2 - - - +
1180B PHE* 1.3 65.2 + - + +
1182B GLN* 3.2 16.7 + - - +
1183B GLN* 3.0 59.3 + - + +
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Residues in contact with PHE1180 (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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1147B LEU* 5.1 8.3 - - + -
1176B MET 3.0 17.6 + - - +
1177B VAL* 3.2 7.4 + - + +
1179B TYR* 1.3 81.4 - - + +
1181B LEU* 1.3 80.8 + - + +
1183B GLN* 3.3 4.6 + - + +
1184B ARG* 2.9 75.6 + - + +
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Residues in contact with LEU1181 (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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1144B VAL* 4.2 31.2 - - + -
1147B LEU* 3.6 28.7 - - + -
1177B VAL* 3.0 36.1 + - + +
1178B LEU* 3.7 1.3 - - - +
1180B PHE* 1.3 94.0 - - + +
1182B GLN* 1.3 61.9 + - - +
1184B ARG* 3.7 5.0 + - + +
1187B PRO* 3.5 3.6 - - - +
1188B VAL* 3.0 53.7 + - + -
1189B ILE* 3.7 21.7 + - + -
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Residues in contact with GLN1182 (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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1137B TYR* 3.0 33.3 + - - -
1178B LEU* 2.9 25.4 + - - +
1179B TYR* 3.2 19.3 + - - +
1181B LEU* 1.3 78.4 - - - +
1183B GLN* 1.3 68.6 + - - +
1184B ARG 4.0 0.5 - - - +
1187B PRO* 3.5 16.3 - - - +
1189B ILE* 3.7 16.1 - - + +
1190B PRO 3.1 22.2 + - - +
1191B VAL* 3.7 25.2 - - + +
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Residues in contact with GLN1183 (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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1179B TYR* 3.0 60.4 + - + +
1180B PHE* 3.6 4.5 - - + +
1182B GLN* 1.3 81.7 + - - +
1184B ARG* 1.3 66.8 - - - +
1185B ASN* 3.6 3.3 + - - +
1191B VAL* 6.1 2.8 - - - +
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Residues in contact with ARG1184 (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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1180B PHE* 2.9 52.9 + - + +
1181B LEU* 3.8 12.6 - - - +
1182B GLN 3.3 2.1 - - - +
1183B GLN* 1.3 80.6 - - - +
1185B ASN* 1.3 68.9 + - - +
1186B PRO* 3.4 14.4 - - + +
1187B PRO* 2.9 24.3 - - - +
1188B VAL* 4.6 10.3 - - + +
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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