Contacts of the helix formed by residues 1141 - 1159 (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 ASP1141 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1137B TYR 4.1 1.4 + - - -
1138B SER 3.6 8.2 - - - +
1139B ALA 3.3 1.9 - - - -
1140B ILE* 1.3 88.4 - - + +
1142B PRO* 1.3 79.3 - - - +
1143B ARG* 2.8 66.9 + - - +
1144B VAL* 2.9 32.0 + - + +
1145B LYS 4.0 0.2 + - - -
1188B VAL* 4.3 10.6 - - + +
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Residues in contact with PRO1142 (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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1138B SER 5.0 2.7 - - - +
1140B ILE 4.8 0.9 - - - +
1141B ASP* 1.3 92.2 - - - +
1143B ARG* 1.3 61.2 + - + +
1145B LYS* 3.2 18.9 + - + +
1146B TYR* 3.2 36.7 + - + +
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Residues in contact with ARG1143 (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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1141B ASP* 2.8 39.1 + - - +
1142B PRO* 1.3 73.9 - - + +
1144B VAL* 1.3 61.3 + - - +
1146B TYR* 3.9 14.5 - - + +
1147B LEU* 3.0 38.8 + - + +
1181B LEU* 5.4 0.2 - - - -
1188B VAL* 3.7 38.3 + - + +
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Residues in contact with VAL1144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1052B PHE* 4.1 8.1 - - + -
1137B TYR 3.6 24.7 - - - +
1138B SER* 3.8 11.4 - - - -
1141B ASP* 2.9 22.4 + - + +
1143B ARG* 1.3 77.9 - - - +
1145B LYS* 1.3 62.8 + - - +
1147B LEU* 4.0 1.0 - - - +
1148B CYS* 3.0 26.2 + - - -
1177B VAL* 4.9 0.2 - - - +
1178B LEU* 3.9 25.6 - - + -
1181B LEU* 4.2 17.0 - - + -
1188B VAL* 4.8 2.2 - - + -
1189B ILE* 3.7 24.9 - - + -
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Residues in contact with LYS1145 (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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1009B TYR* 4.3 30.9 + - + +
1051B GLY* 3.4 32.5 + - - +
1052B PHE* 3.9 13.9 - - + -
1138B SER* 4.0 28.9 - - - +
1141B ASP 4.0 0.4 + - - -
1142B PRO* 3.2 12.7 + - + +
1144B VAL* 1.3 78.3 - - - +
1146B TYR* 1.3 67.1 + - + +
1148B CYS* 3.2 1.2 + - - -
1149B TYR* 2.8 35.1 + - + -
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Residues in contact with TYR1146 (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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1005B CYS* 3.9 17.0 - - + +
1006B ILE* 4.4 37.4 - - + +
1009B TYR* 3.8 42.0 - + + -
1142B PRO* 3.2 37.8 + - + +
1143B ARG* 3.9 13.5 - - + +
1144B VAL 3.4 0.2 - - - -
1145B LYS* 1.3 77.7 - - + +
1147B LEU* 1.3 59.6 + - + +
1149B TYR* 3.5 5.2 + - - +
1150B THR* 2.8 32.4 + - - -
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Residues in contact with LEU1147 (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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1005B CYS* 5.1 15.3 - - + -
1143B ARG* 3.0 28.0 + - + +
1144B VAL 4.0 1.1 - - - +
1146B TYR* 1.3 75.2 - - + +
1148B CYS* 1.3 61.7 + - - +
1150B THR* 3.2 7.1 + - + -
1151B MET* 2.8 30.8 + - - +
1177B VAL* 3.9 16.9 - - + +
1180B PHE* 5.1 7.6 - - + -
1181B LEU* 3.6 34.1 - - + -
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Residues in contact with CYS1148 (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* 3.6 43.5 - - + -
1144B VAL* 3.0 27.3 + - - +
1145B LYS 3.8 0.2 - - - +
1147B LEU* 1.3 76.0 - - - +
1149B TYR* 1.3 58.9 + - - +
1151B MET* 3.4 1.7 + - - +
1152B LYS* 2.9 30.5 + - - +
1174B THR* 4.0 23.0 + - + +
1177B VAL* 3.7 28.7 - - - -
1178B LEU* 4.7 2.5 - - - -
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Residues in contact with TYR1149 (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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1008B CYS* 3.8 15.5 - - - -
1009B TYR* 3.6 43.0 - + + +
1013B SER* 3.6 24.9 - - - -
1014B PRO* 4.1 2.4 - - - +
1051B GLY 3.5 22.3 + - - -
1052B PHE* 3.7 13.7 - + - -
1053B GLY 2.6 36.0 + - - -
1054B PHE* 3.3 30.4 - + - -
1145B LYS* 2.8 31.0 + - + +
1146B TYR 3.8 3.8 - - - +
1148B CYS* 1.3 75.8 - - - +
1150B THR* 1.3 57.9 + - - +
1152B LYS* 3.2 2.7 + - - +
1153B VAL* 2.9 33.4 + - - +
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Residues in contact with THR1150 (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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1004B VAL* 5.8 3.6 - - + -
1005B CYS* 3.3 42.8 + - - +
1008B CYS* 3.9 16.5 - - - +
1146B TYR 2.8 22.6 + - - -
1147B LEU* 3.6 9.2 - - + -
1149B TYR* 1.3 76.6 - - - +
1151B MET* 1.3 58.3 + - - +
1153B VAL* 3.3 2.1 + - - +
1154B PHE* 2.9 31.5 + - + +
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Residues in contact with MET1151 (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 2.8 19.9 + - - +
1148B CYS 3.7 3.4 - - - +
1150B THR* 1.3 73.4 - - - +
1152B LYS* 1.3 57.6 + - - +
1154B PHE* 3.6 12.4 - - - +
1155B THR* 3.0 48.9 + - - +
1173B TYR* 3.8 33.4 - - + +
1174B THR* 5.1 0.4 - - - +
1176B MET* 4.3 19.1 - - + -
1177B VAL* 3.6 31.4 - - + +
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Residues in contact with LYS1152 (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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1047B SER* 3.6 20.0 + - - -
1050B ASN* 5.5 0.8 - - - +
1052B PHE* 2.7 32.0 + - + +
1053B GLY* 4.6 0.6 - - - -
1054B PHE* 3.6 35.9 - - + -
1057B SER* 4.9 4.4 + - - +
1148B CYS 2.9 18.5 + - - +
1149B TYR* 3.2 5.1 + - - +
1151B MET* 1.3 74.8 - - - +
1153B VAL* 1.3 65.0 + - - +
1155B THR* 3.4 6.4 + - - +
1156B LYS* 3.0 30.1 + - + +
1170B SER* 4.0 31.6 + - - -
1173B TYR* 6.1 1.1 - - - -
1174B THR* 4.9 10.7 + - - -
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Residues in contact with VAL1153 (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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1016A ILE* 3.7 30.7 - - + -
1017A ILE* 4.7 3.6 - - + -
1008B CYS* 3.9 22.0 - - + -
1012B PHE* 3.5 34.3 - - + -
1054B PHE* 3.6 10.5 - - + -
1149B TYR 2.9 20.3 + - - +
1150B THR 3.7 4.0 - - - +
1152B LYS* 1.3 76.4 - - - +
1154B PHE* 1.3 65.0 + - - +
1156B LYS* 3.2 5.7 + - - +
1157B MET* 2.9 32.8 + - + +
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Residues in contact with PHE1154 (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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1150B THR* 2.9 22.1 + - + +
1151B MET* 3.3 13.7 + - - +
1153B VAL* 1.3 79.0 - - - +
1155B THR* 1.3 73.8 + - + +
1157B MET* 3.3 4.3 + - - +
1158B CYS* 3.1 48.5 + - - -
1160B ILE* 5.2 5.8 - - + -
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Residues in contact with THR1155 (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* 3.0 31.0 + - - +
1152B LYS* 3.4 8.5 + - - +
1154B PHE* 1.3 78.3 - - + +
1156B LYS* 1.3 67.0 + - - +
1158B CYS 3.3 0.5 + - - -
1159B ASP 3.0 17.5 + - - -
1160B ILE* 3.1 28.2 + - + +
1161B GLY* 3.9 6.5 + - - -
1170B SER* 5.7 2.8 - - - -
1173B TYR* 3.7 56.0 - - + +
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Residues in contact with LYS1156 (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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1017A ILE* 3.9 28.9 - - + -
1020A GLN* 3.0 22.6 + - - +
1054B PHE* 5.6 7.6 - - + -
1152B LYS* 3.0 25.3 + - + +
1153B VAL* 3.2 6.9 + - - +
1155B THR* 1.3 77.8 + - - +
1157B MET* 1.3 61.1 + - - +
1159B ASP* 3.1 12.7 + - - +
1161B GLY* 5.4 9.9 + - - +
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Residues in contact with MET1157 (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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1016A ILE* 3.7 51.4 - - + +
1017A ILE* 3.7 24.2 - - + -
1020A GLN* 3.3 30.7 + - + +
1153B VAL* 2.9 23.2 + - + +
1154B PHE* 3.8 5.2 - - - +
1156B LYS* 1.3 76.3 - - - +
1158B CYS* 1.3 60.0 + - - +
1159B ASP* 4.9 0.5 - - - +
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Residues in contact with CYS1158 (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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1154B PHE* 3.1 47.3 + - - +
1155B THR 3.3 4.0 + - - +
1157B MET* 1.3 77.7 - - - +
1159B ASP* 1.3 70.8 + - - +
1160B ILE* 3.5 24.5 + - + +
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Residues in contact with ASP1159 (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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1020A GLN* 4.8 6.3 - - - +
1024A HIS* 4.6 21.8 + - + -
1155B THR 3.0 4.6 + - - -
1156B LYS 3.1 12.8 + - - +
1157B MET 3.3 0.6 - - - +
1158B CYS* 1.3 80.6 - - - +
1160B ILE* 1.3 61.2 + - - +
1161B GLY 3.6 2.7 - - - +
1165B ARG* 2.4 35.7 + - - -
1167B SER* 4.3 4.4 + - - -
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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