Contacts of the helix formed by residues 1079 - 1089 (chain G) in PDB entry 2NQB
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 ILE1079 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1075G LYS* 4.4 16.6 - - + +
1077G ARG* 3.8 14.4 - - + +
1078G ILE* 1.3 80.4 - - - +
1080G PRO* 1.3 76.3 - - + +
1081G ARG* 3.9 20.4 - - + +
1082G HIS* 2.9 44.8 + - + +
1083G LEU* 3.3 4.7 + - - +
1452H SER* 3.9 15.3 - - - +
1455H ALA* 3.9 6.3 - - - -
132I C 5.9 0.4 - - - +
133I A 5.7 2.7 - - - +
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Residues in contact with PRO1080 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1079G ILE* 1.3 89.5 - - + +
1081G ARG* 1.3 63.5 + - - +
1083G LEU* 2.9 10.3 + - + +
1084G GLN* 2.8 22.9 + - - +
1102G ILE* 4.0 3.0 - - + +
1103G ALA 3.3 24.7 - - - +
1104G GLN* 3.4 17.7 - - + +
1105G GLY* 4.3 1.6 - - - -
1452H SER* 4.0 10.1 - - - +
1454H LYS* 3.9 22.2 - - + -
1455H ALA* 4.0 3.8 - - + +
1458H ILE* 3.7 24.0 - - + -
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Residues in contact with ARG1081 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A GLN 3.5 10.5 + - - -
456A LYS* 3.1 28.4 + - - +
457A SER 4.8 0.4 + - - -
458A THR* 3.4 24.0 - - + +
1073G ASN* 5.9 0.2 - - - +
1079G ILE* 3.2 21.0 - - + +
1080G PRO* 1.3 78.2 - - - +
1082G HIS* 1.3 62.5 + - + +
1084G GLN* 3.1 5.0 + - - +
1085G LEU* 2.8 65.5 + - - +
1104G GLN 3.7 3.9 + - - +
1105G GLY 3.0 22.3 + - - -
1106G GLY* 3.4 1.8 - - - -
1107G VAL 2.3 49.2 + - - +
1109G PRO* 4.8 5.7 - - - +
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Residues in contact with HIS1082 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1066G ALA* 3.7 17.8 - - - +
1069G ALA* 3.7 11.5 - - + +
1070G ALA* 3.4 28.0 - - + +
1073G ASN* 3.8 27.5 + - - +
1075G LYS* 3.9 23.0 + - + +
1077G ARG 3.4 17.9 + - - -
1078G ILE* 3.5 5.3 - - + -
1079G ILE* 2.9 42.9 + - + +
1081G ARG* 1.3 81.7 - - + +
1083G LEU* 1.3 58.8 + - - +
1085G LEU* 3.5 3.1 + - + +
1086G ALA* 3.0 30.1 + - - +
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Residues in contact with LEU1083 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1062G VAL* 3.8 9.4 - - + -
1063G LEU* 5.0 2.5 - - + -
1066G ALA* 3.6 23.3 - - + -
1078G ILE* 4.2 9.4 - - + -
1079G ILE 3.3 5.1 + - - +
1080G PRO* 2.9 12.6 + - + +
1082G HIS* 1.3 76.6 - - - +
1084G GLN* 1.3 63.3 + - - +
1086G ALA* 3.3 2.2 + - - +
1087G ILE* 3.0 36.1 + - + +
1102G ILE* 4.8 5.8 - - + -
1455H ALA* 3.6 31.6 - - + +
1458H ILE* 3.6 31.0 - - + -
1459H MET* 3.7 25.8 - - + -
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Residues in contact with GLN1084 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1080G PRO 2.8 11.1 + - - +
1081G ARG* 3.4 11.9 - - - +
1083G LEU* 1.3 76.9 - - - +
1085G LEU* 1.3 58.9 + - - +
1087G ILE* 4.8 1.2 - - - +
1088G ARG* 2.8 82.2 + - + +
1102G ILE* 3.4 23.6 + - + +
1105G GLY* 3.4 29.8 - - - +
1106G GLY 2.8 22.4 + - - +
1107G VAL* 4.3 9.8 - - - +
1108G LEU* 5.3 1.5 - - + +
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Residues in contact with LEU1085 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1069G ALA* 4.3 12.8 - - + -
1073G ASN* 4.0 24.0 - - - +
1081G ARG* 2.8 62.0 + - - +
1082G HIS* 3.9 4.5 - - - +
1084G GLN* 1.3 72.1 - - - +
1086G ALA* 1.3 63.5 + - - +
1089G ASN* 3.0 38.3 + - - +
1108G LEU* 3.3 27.1 - - + -
1109G PRO* 4.7 8.5 - - + -
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Residues in contact with ALA1086 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1062G VAL* 4.4 3.8 - - + +
1065G LEU* 3.5 24.9 - - + +
1066G ALA* 3.4 30.5 - - + +
1069G ALA* 4.6 2.2 - - - +
1082G HIS 3.0 18.5 + - - +
1083G LEU* 3.6 4.5 - - - +
1085G LEU* 1.3 79.8 - - - +
1087G ILE* 1.3 64.0 + - + +
1089G ASN* 4.1 2.6 - - - +
1090G ASP* 3.5 21.8 + - - +
1093G LEU* 5.1 0.4 - - + -
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Residues in contact with ILE1087 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B TYR* 5.9 0.4 - - + -
1062G VAL* 4.5 23.1 - - + -
1083G LEU* 3.0 23.1 + - + +
1084G GLN* 4.0 2.9 - - - +
1086G ALA* 1.3 75.6 - - - +
1088G ARG* 1.3 94.6 + - + +
1090G ASP* 3.1 22.2 + - - +
1093G LEU* 3.9 31.0 - - + +
1094G ASN* 3.4 5.1 + - - -
1097G LEU* 3.6 27.1 - - + -
1102G ILE* 4.2 22.4 - - + -
1458H ILE* 6.2 0.7 - - + -
1462H PHE* 5.9 0.9 - - + -
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Residues in contact with ARG1088 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084G GLN* 2.8 62.2 + - + +
1087G ILE* 1.3 88.7 - - + +
1089G ASN* 1.3 59.3 + - - +
1090G ASP 3.6 0.9 + - - -
1094G ASN* 3.1 43.6 + - - +
1097G LEU* 2.9 31.7 + - - +
1098G SER* 4.1 4.2 + - - +
1100G VAL* 3.4 21.4 + - - +
1102G ILE* 4.5 6.7 - - - +
1108G LEU* 3.8 31.1 - - + +
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Residues in contact with ASN1089 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085G LEU* 3.0 34.3 + - - +
1086G ALA* 4.1 2.9 - - - +
1088G ARG* 1.3 75.8 - - - +
1090G ASP* 1.3 58.5 + - - +
1091G GLU 3.9 2.1 + - - -
1108G LEU* 3.4 28.3 - - - +
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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