Contacts of the helix formed by residues 1082 - 1095 (chain M) in PDB entry 4G7H
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 PRO1082 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1053M LEU 3.9 11.9 - - - +
1054M THR* 4.0 3.6 - - + -
1058M ASP* 3.5 25.4 - - - +
1059M ASP* 4.3 5.8 - - + -
1080M SER 3.4 4.2 - - - +
1081M VAL* 1.3 93.7 - - + +
1083M GLU* 1.3 65.0 + - - +
1084M SER* 4.4 1.6 - - - +
1085M PHE* 3.0 22.2 + - + +
1086M ARG* 3.6 1.7 + - - +
618N LEU* 5.8 0.7 - - + -
621N LYS* 4.2 8.7 - - - +
1467N ILE 4.8 3.6 - - - +
1468N LEU 3.3 30.3 - - - +
1469N GLY* 3.9 14.6 - - - +
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Residues in contact with GLU1083 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017M THR 4.7 0.7 - - - +
1018M GLN* 4.3 9.0 - - + -
1058M ASP* 3.0 29.0 + - + +
1060M ILE* 3.8 27.1 + - + +
1081M VAL 3.5 2.3 + - - +
1082M PRO* 1.3 71.2 - - - +
1084M SER* 1.3 56.5 + - - +
1086M ARG* 2.6 38.7 + - - +
1087M VAL* 2.9 26.5 + - + +
87N ARG* 3.2 32.7 + - - +
88N TYR* 2.8 34.3 + - - -
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Residues in contact with SER1084 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017M THR* 3.0 27.4 + - - +
1019M GLN* 3.2 15.1 + - - -
1058M ASP* 3.0 20.3 + - - -
1082M PRO 3.1 1.4 - - - -
1083M GLU* 1.3 76.6 - - - +
1085M PHE* 1.3 59.6 + - - +
1087M VAL* 3.5 10.8 + - - +
1088M LEU* 2.9 25.3 + - - +
613N ARG* 4.5 4.7 - - - -
617N ASN* 3.8 7.1 - - - +
618N LEU* 3.7 20.3 - - - +
621N LYS* 5.1 0.2 - - - -
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Residues in contact with PHE1085 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1081M VAL* 4.2 12.3 - - + -
1082M PRO* 3.0 19.4 + - + +
1084M SER* 1.3 75.4 - - - +
1086M ARG* 1.3 59.5 + - - +
1087M VAL 3.1 0.2 - - - -
1088M LEU* 3.1 27.9 + - + +
1089M VAL* 2.9 42.4 + - + +
1099M VAL* 4.9 2.2 - - + -
1101M THR* 4.0 18.8 - - + -
1111M ILE* 3.7 28.9 - - + -
8N VAL* 4.7 10.8 - - + -
618N LEU* 3.9 5.1 - - - +
1435N LEU* 4.9 4.9 - - + -
1467N ILE* 3.8 29.2 - - + +
1468N LEU* 3.7 34.3 - - + -
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Residues in contact with ARG1086 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1060M ILE* 5.6 0.6 - - - +
1061M GLU* 6.0 0.4 + - - -
1080M SER* 5.6 3.4 - - - -
1081M VAL* 3.8 41.1 + - + +
1082M PRO 3.6 1.3 + - - +
1083M GLU* 2.6 46.5 + - - +
1085M PHE* 1.3 76.8 - - - +
1087M VAL* 1.3 62.6 + - - +
1089M VAL* 3.3 5.2 + - - +
1090M LYS* 3.0 29.4 + - - +
1111M ILE* 2.7 40.3 + - + -
1112M PHE* 3.8 23.2 - - + +
1113M GLU* 4.6 14.1 + - - -
87N ARG 6.0 0.4 - - - -
88N TYR* 3.5 30.2 + - + -
524N LEU* 5.6 0.2 - - - -
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Residues in contact with VAL1087 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1016M ILE* 3.4 31.9 - - + +
1017M THR* 4.9 0.4 - - - -
1083M GLU 2.9 18.8 + - - +
1084M SER* 3.5 13.0 - - - +
1085M PHE 3.1 0.2 - - - -
1086M ARG* 1.3 77.8 - - - +
1088M LEU* 1.3 56.8 + - - +
1090M LYS* 3.3 1.6 + - - +
1091M GLU* 2.9 53.3 + - - +
87N ARG* 3.7 14.4 - - - +
524N LEU* 3.8 18.5 - - + +
613N ARG* 3.5 21.8 - - - +
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Residues in contact with LEU1088 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084M SER 2.9 14.4 + - - +
1085M PHE* 3.1 30.7 + - + +
1087M VAL* 1.3 77.3 - - - +
1089M VAL* 1.3 58.0 + - + +
1091M GLU* 3.2 7.8 + - - +
1092M LEU* 2.9 45.4 + - + +
1099M VAL* 6.4 0.7 - - + -
607N LEU* 3.5 30.3 - - + -
613N ARG* 4.5 5.4 - - + -
614N PHE* 3.6 39.3 - - + -
618N LEU* 3.8 17.7 - - + -
1434N TRP* 6.1 0.4 - - + -
1435N LEU* 4.7 4.7 - - + -
1467N ILE* 4.6 2.0 - - + -
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Residues in contact with VAL1089 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085M PHE* 2.9 43.9 + - + +
1086M ARG 3.6 6.7 - - - +
1088M LEU* 1.3 77.3 - - + +
1090M LYS* 1.3 59.6 + - - +
1092M LEU* 3.1 9.0 + - - +
1093M GLN* 2.9 42.0 + - - +
1099M VAL* 3.9 34.8 - - + +
1101M THR* 5.7 1.1 - - + -
1111M ILE* 4.3 6.7 - - + -
1112M PHE* 3.7 25.8 - - + -
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Residues in contact with LYS1090 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1086M ARG 3.0 17.1 + - - +
1089M VAL* 1.3 76.8 - - - +
1091M GLU* 1.3 56.6 + - - +
1093M GLN* 3.0 33.7 + - - +
1094M ALA* 2.9 23.2 + - - +
1112M PHE* 3.5 34.2 - - + -
1116M ALA* 3.6 17.9 + - - +
21N TRP* 5.8 3.0 - - - +
87N ARG 3.8 16.8 - - - +
88N TYR 3.1 26.7 + - - +
90N MET* 3.9 14.2 - - + +
520N LEU* 3.5 12.3 - - + +
521N PRO* 4.3 2.2 - - + -
524N LEU* 3.7 21.1 - - + -
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Residues in contact with GLU1091 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1016M ILE* 4.8 2.1 - - - +
1087M VAL* 2.9 28.1 + - + +
1088M LEU* 3.6 6.5 - - - +
1090M LYS* 1.3 77.1 - - - +
1092M LEU* 1.3 61.6 + - - +
1094M ALA* 3.3 6.2 + - - +
1095M LEU* 3.3 25.5 + - - +
520N LEU* 3.8 21.2 - - + +
524N LEU* 4.8 7.6 - - + +
603N LEU* 4.2 15.3 - - + +
606N ILE* 3.2 21.9 - - + +
607N LEU* 4.4 12.8 - - + +
613N ARG* 2.6 48.9 + - - +
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Residues in contact with LEU1092 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088M LEU* 2.9 43.9 + - + +
1089M VAL* 3.6 5.6 - - - +
1091M GLU* 1.3 75.7 - - - +
1093M GLN* 1.3 60.2 + - - +
1095M LEU* 3.1 12.0 + - + +
1096M ALA 3.4 0.2 + - - -
1097M LEU* 2.9 49.5 + - + +
1099M VAL* 3.7 30.7 - - + -
10N ILE* 4.8 0.7 - - + -
607N LEU* 3.4 28.3 - - + -
614N PHE* 5.2 3.1 - - + -
1434N TRP* 5.1 10.8 - - + -
1447N LEU* 3.9 18.4 - - + -
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Residues in contact with GLN1093 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089M VAL* 2.9 29.4 + - + +
1090M LYS* 3.0 42.0 + - - +
1092M LEU* 1.3 74.6 - - - +
1094M ALA* 1.3 58.0 + - - +
1095M LEU 3.0 1.6 - - - -
1096M ALA* 2.8 18.4 + - - -
1097M LEU 3.4 10.3 - - - +
1098M ASP* 4.6 5.5 + - - -
1099M VAL 4.9 5.6 + - - +
1112M PHE* 5.4 2.0 - - - -
21N TRP* 3.5 50.4 - - + +
90N MET* 3.3 16.1 - - - +
518N PRO* 3.3 16.2 - - - +
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Residues in contact with ALA1094 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090M LYS 2.9 13.6 + - - +
1091M GLU 3.5 10.3 - - - +
1092M LEU 3.3 0.4 - - - -
1093M GLN* 1.3 75.5 - - - +
1095M LEU* 1.3 56.9 + - - +
1096M ALA 3.2 1.6 + - - -
90N MET* 4.0 4.0 - - + +
517N VAL* 5.5 0.3 - - - +
518N PRO* 4.0 25.1 - - - +
520N LEU* 3.9 20.9 - - + -
544N TYR* 4.1 5.8 - - - +
581N LEU* 5.6 0.7 - - - +
582N LEU* 3.8 8.8 - - - +
603N LEU* 3.5 33.2 - - + +
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Residues in contact with LEU1095 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091M GLU 3.3 10.6 + - - +
1092M LEU* 3.1 11.6 + - + +
1093M GLN 3.0 1.2 - - - -
1094M ALA* 1.3 75.5 - - - +
1096M ALA* 1.3 65.2 + - - +
1097M LEU* 3.2 12.0 + - + +
101N HIS* 2.7 34.1 + - - +
103N TRP* 3.7 28.3 - - + -
582N LEU* 3.8 42.4 - - + +
603N LEU* 3.8 24.2 - - + -
604N THR* 4.1 0.4 - - - +
607N LEU* 3.6 32.8 - - + -
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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