Contacts of the helix formed by residues 1139 - 1155 (chain B) in PDB entry 2O8C
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 GLY1139 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ADP 3.0 41.0 + - - -
1111B ASN* 5.9 0.3 + - - -
1137B MET 3.6 0.4 - - - -
1138B GLY* 1.3 79.4 - - - +
1140B LYS* 1.3 61.2 + - - +
1142B THR* 4.1 0.7 - - - -
1143B LEU* 3.1 29.5 + - - +
1267B MET* 3.4 11.1 - - - +
1287B TYR* 6.0 0.2 - - - -
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Residues in contact with LYS1140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B MG 4.6 0.7 - - - -
202B ADP 3.3 24.6 + - - +
1132B VAL* 4.2 22.9 - - + +
1133B THR* 3.9 9.2 - - - +
1134B GLY* 2.9 41.9 + - - +
1135B PRO 4.0 1.1 - - - +
1136B ASN* 4.0 3.3 + - - -
1139B GLY* 1.3 75.4 - - - +
1141B SER* 1.3 66.2 + - - +
1143B LEU* 3.4 4.9 + - - +
1144B MET* 3.4 28.4 + - - +
1213B ASP* 5.2 0.9 - - - +
1214B GLU* 3.0 15.8 + - - +
1246B SER* 4.4 16.2 - - - +
1247B THR 4.9 3.2 + - - +
1248B HIS* 2.9 30.5 + - - -
1267B MET* 3.9 13.7 - - + -
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Residues in contact with SER1141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B MG 2.3 30.3 - - - -
202B ADP 2.9 19.7 + - - -
1140B LYS* 1.3 71.5 - - - +
1142B THR* 1.3 58.3 + - - +
1144B MET* 3.4 15.9 + - - +
1145B ARG* 2.9 49.8 + - - +
1177B LEU* 4.8 2.5 - - - +
1213B ASP* 2.7 17.6 + - - -
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Residues in contact with THR1142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ADP 2.8 60.8 + - + +
1096B HIS* 4.1 18.8 - - + +
1108B PHE* 4.5 16.2 - - + -
1139B GLY 4.2 1.3 - - - -
1141B SER* 1.3 70.0 - - - +
1143B LEU* 1.3 60.6 + - - +
1145B ARG* 3.4 14.6 + - + +
1146B GLN* 2.8 29.7 + - - +
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Residues in contact with LEU1143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1111B ASN* 4.0 18.4 - - + +
1113B ILE* 3.8 30.3 - - + -
1132B VAL* 4.3 12.6 - - + -
1139B GLY 3.1 21.4 + - - +
1140B LYS 3.5 4.5 - - - +
1141B SER 3.3 0.2 - - - -
1142B THR* 1.3 76.3 - - - +
1144B MET* 1.3 58.7 + - + +
1146B GLN* 3.0 14.9 - - - +
1147B ALA* 2.9 26.3 + - - +
1244B LEU* 4.8 8.7 - - + -
1267B MET* 4.1 7.6 - - + -
1289B PHE* 3.6 55.9 - - + -
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Residues in contact with MET1144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1132B VAL* 5.3 3.6 - - + -
1140B LYS 3.4 19.5 + - - +
1141B SER* 3.4 7.7 + - - +
1143B LEU* 1.3 84.3 - - + +
1145B ARG* 1.3 57.6 + - - +
1147B ALA* 3.2 1.2 + - - +
1148B GLY 3.0 23.7 + - - -
1177B LEU* 3.9 8.3 - - + -
1211B LEU* 3.3 23.2 - - + +
1212B VAL 3.7 22.4 - - - +
1213B ASP* 3.6 25.4 - - + -
1244B LEU* 3.8 43.5 - - + +
1246B SER* 3.5 30.1 - - - +
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Residues in contact with ARG1145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742B ASN* 2.8 36.9 + - - +
743B LEU* 3.8 25.2 - - + +
744B GLU* 4.9 12.3 + - - +
1096B HIS* 4.0 20.4 - - - +
1141B SER* 2.9 40.2 + - - +
1142B THR* 3.4 16.7 + - - +
1144B MET* 1.3 78.3 - - - +
1146B GLN* 1.3 56.6 + - - +
1148B GLY 3.5 1.0 + - - -
1149B LEU* 3.1 31.9 + - - +
1177B LEU* 3.8 23.9 - - + +
1178B GLY 5.8 0.2 - - - +
1213B ASP* 5.2 0.4 + - - -
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Residues in contact with GLN1146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1094B SER* 3.4 18.4 + - - +
1095B ARG 3.1 22.9 - - - +
1096B HIS* 3.6 32.5 - - + -
1097B PRO* 4.5 0.4 - - + -
1108B PHE* 4.0 15.9 - - - -
1111B ASN* 3.4 28.3 - - - +
1113B ILE* 3.9 10.8 - - + -
1142B THR* 2.8 16.4 + - - +
1143B LEU* 3.0 30.8 - - - +
1145B ARG* 1.3 74.0 - - - +
1147B ALA* 1.3 64.9 + - - +
1149B LEU* 4.0 4.2 - - - +
1150B LEU* 3.0 33.5 + - - +
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Residues in contact with ALA1147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1089B LEU* 4.9 9.6 - - + +
1091B LEU* 4.8 7.1 - - - +
1113B ILE* 3.9 22.7 - - + -
1115B ILE* 5.6 0.7 - - + -
1143B LEU 2.9 13.2 + - - +
1144B MET 3.2 9.4 + - - +
1146B GLN* 1.3 77.0 - - - +
1148B GLY* 1.3 61.5 + - - +
1150B LEU* 3.6 2.1 + - - +
1151B ALA* 3.3 21.1 + - - +
1209B LEU* 4.3 6.0 - - + +
1211B LEU* 4.5 4.3 - - + -
1244B LEU* 3.8 23.6 - - + -
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Residues in contact with GLY1148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733B MET* 5.0 0.3 - - - +
743B LEU* 4.0 15.0 - - - +
1144B MET 3.0 10.6 + - - -
1145B ARG 3.9 1.6 - - - -
1146B GLN 3.2 0.2 - - - -
1147B ALA* 1.3 75.4 - - - +
1149B LEU* 1.3 63.7 - - - +
1151B ALA* 3.2 5.2 + - - +
1152B VAL* 3.1 24.8 + - - +
1173B VAL* 4.9 2.4 - - - +
1209B LEU* 4.4 8.3 - - - -
1211B LEU* 3.8 21.2 - - - +
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Residues in contact with LEU1149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743B LEU* 3.4 31.8 - - + +
744B GLU* 5.7 0.7 - - + +
745B ILE* 4.0 15.0 - - + -
758B LEU* 3.8 27.1 - - + -
1096B HIS* 3.4 36.8 - - + +
1097B PRO* 3.9 23.8 - - + -
1098B CYS* 4.5 8.7 - - - -
1145B ARG* 3.1 18.5 + - + +
1146B GLN 4.0 2.9 - - - +
1148B GLY* 1.3 75.6 - - - +
1150B LEU* 1.3 56.8 + - - +
1152B VAL* 3.3 6.6 + - + +
1153B MET* 2.9 33.6 + - - +
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Residues in contact with LEU1150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1091B LEU* 3.8 28.3 - - + -
1094B SER* 3.6 31.4 - - - +
1095B ARG 3.7 18.4 - - - +
1097B PRO* 3.8 11.0 - - + -
1113B ILE* 5.0 0.4 - - + -
1146B GLN* 3.0 26.6 + - - +
1147B ALA 4.0 3.6 - - - +
1149B LEU* 1.3 72.6 - - - +
1151B ALA* 1.3 61.2 + - - +
1153B MET* 3.6 4.0 - - + +
1154B ALA* 2.8 32.9 + - - +
1160B VAL* 3.9 11.4 - - + +
1161B PRO* 3.5 33.4 - - + -
1162B ALA* 5.6 1.1 - - + -
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Residues in contact with ALA1151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733B MET* 4.3 9.7 - - + +
1089B LEU* 5.6 6.2 - - + +
1091B LEU* 5.8 0.4 - - - +
1147B ALA 3.3 12.1 + - - +
1148B GLY 3.2 10.6 + - - +
1150B LEU* 1.3 78.0 - - - +
1152B VAL* 1.3 63.2 + - - +
1154B ALA* 3.6 4.6 + - - +
1155B GLN* 3.2 30.0 + - - +
1167B LEU* 4.8 7.4 - - + -
1170B ILE* 3.7 29.4 - - + -
1173B VAL* 4.8 0.2 - - + -
1209B LEU* 3.9 9.0 - - + -
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Residues in contact with VAL1152 (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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733B MET* 3.7 24.2 - - + -
735B LEU* 4.3 6.7 - - + -
743B LEU* 4.4 4.0 - - + -
745B ILE* 3.9 26.9 - - + -
758B LEU* 4.5 13.5 - - + -
778B LEU* 4.0 21.8 - - + +
781B PRO* 4.0 17.9 - - + +
1148B GLY 3.1 16.5 + - - +
1149B LEU* 3.3 10.3 - - - +
1151B ALA* 1.3 78.4 - - - +
1153B MET* 1.3 63.8 + - - +
1155B GLN 3.5 7.3 + - - -
1156B MET* 3.5 13.4 + - - +
1173B VAL* 5.4 0.2 - - + -
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Residues in contact with MET1153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758B LEU* 3.8 30.7 - - + -
762B VAL* 4.1 14.8 - - + -
778B LEU* 4.5 10.8 - - + -
1063B LEU* 5.4 1.6 - - + -
1066B TYR* 3.7 30.1 - - + -
1097B PRO* 4.4 14.4 - - + -
1149B LEU 2.9 23.6 + - - +
1150B LEU* 3.6 9.0 - - + +
1152B VAL* 1.3 75.7 - - - +
1154B ALA* 1.3 61.9 + - - +
1156B MET* 3.1 22.5 + - - +
1158B CYS* 3.7 35.8 + - + +
1159B TYR 4.9 0.4 - - - +
1160B VAL* 3.8 16.4 - - + -
1161B PRO* 5.3 2.0 - - + -
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Residues in contact with ALA1154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788B ILE* 3.4 17.5 - - - +
1077B PRO* 3.8 32.9 - - + +
1079B ILE* 4.1 2.5 - - - +
1150B LEU 2.8 20.4 + - - +
1151B ALA* 4.1 4.5 - - - +
1153B MET* 1.3 71.3 - - - +
1155B GLN* 1.3 59.3 + - + +
1156B MET 3.1 3.6 + - - -
1157B GLY 3.6 3.3 + - - -
1158B CYS 4.2 0.7 - - - -
1160B VAL* 3.7 14.1 - - + +
1165B CYS* 4.0 11.7 - - - -
1167B LEU* 4.1 13.7 - - + -
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Residues in contact with GLN1155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733B MET* 3.7 13.7 - - - +
781B PRO* 4.0 7.9 - - + -
782B LEU* 2.8 55.3 + - - +
783B CYS* 3.6 8.8 - - - +
788B ILE* 3.9 15.3 - - + -
1079B ILE* 4.4 7.9 - - + -
1151B ALA 3.2 17.4 + - - +
1152B VAL 3.9 2.0 - - - -
1153B MET 3.3 0.2 - - - -
1154B ALA* 1.3 75.2 - - - +
1156B MET* 1.3 58.5 + - - +
1157B GLY 3.4 1.3 - - - -
1167B LEU* 4.3 8.0 - - + +
1168B THR 4.1 1.4 - - - +
1169B PRO* 3.4 7.7 - - - +
1170B ILE* 2.5 59.1 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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