Contacts of the helix formed by residues 1077 - 1092 (chain B) in PDB entry 3GIJ
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 ARG1077 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1016B GLU* 2.5 35.4 + - - +
1019B LEU* 3.5 37.4 - - - +
1020B ASN* 6.2 0.8 - - - +
1075B PRO* 3.7 18.2 - - + +
1076B MET* 1.3 72.1 - - - +
1078B LYS* 1.3 62.4 + - - +
1079B GLU* 3.2 12.8 - - - +
1080B VAL* 2.9 37.1 + - + +
1081B TYR* 3.0 23.7 + - + +
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Residues in contact with LYS1078 (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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1012B TYR* 3.6 23.1 - - - +
1076B MET* 3.4 30.9 + - + -
1077B ARG* 1.3 71.8 - - - +
1079B GLU* 1.3 63.7 + - - +
1081B TYR* 3.0 11.7 + - - +
1082B GLN* 2.6 46.1 + - + +
1104B ILE* 4.3 17.0 - - + +
1242B ARG* 5.4 7.3 - - - +
1814H 2DA 6.5 0.9 - - - -
1906J 8OG 5.7 3.4 - - - -
1907J C 4.6 28.3 + - - -
1908J T 5.8 2.8 + - - -
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Residues in contact with GLU1079 (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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1076B MET 4.8 2.4 - - - +
1077B ARG* 3.5 20.3 - - - +
1078B LYS* 1.3 86.8 + - + +
1080B VAL* 1.3 59.0 + - + +
1082B GLN* 3.6 8.0 - - - +
1083B GLN* 2.8 34.4 + - - +
1274B TYR* 6.5 0.4 - - + -
1275B LYS* 5.8 6.0 + - - -
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Residues in contact with VAL1080 (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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1015B VAL* 4.1 5.6 - - + -
1019B LEU* 3.2 35.7 - - + -
1077B ARG* 2.9 41.9 + - + +
1079B GLU* 1.3 77.9 - - + +
1081B TYR* 1.3 62.8 + - + +
1083B GLN* 3.2 17.1 + - - +
1084B VAL* 3.0 33.4 + - + +
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Residues in contact with TYR1081 (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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1011B PHE* 3.1 32.1 - - + -
1012B TYR* 3.3 59.2 - + + -
1015B VAL* 3.7 21.8 - - + -
1016B GLU* 2.4 35.4 + - - -
1030B VAL* 3.4 13.7 - - - +
1075B PRO 3.5 1.2 + - - -
1076B MET* 3.6 5.8 - - + -
1077B ARG* 3.0 39.2 + - + -
1078B LYS* 3.0 11.4 + - - +
1080B VAL* 1.3 78.4 - - + +
1082B GLN* 1.3 52.7 + - - +
1084B VAL* 3.3 3.5 + - - -
1085B SER* 2.7 30.8 + - - -
1104B ILE* 4.1 1.6 - - + -
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Residues in contact with GLN1082 (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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1078B LYS* 2.6 30.4 + - + +
1079B GLU* 3.6 10.5 - - - +
1081B TYR* 1.3 70.9 - - - +
1083B GLN* 1.3 65.9 + - - +
1085B SER* 3.8 13.1 + - - -
1086B SER* 2.8 51.8 + - - +
1104B ILE* 3.6 25.0 - - + +
1242B ARG* 5.6 4.2 + - - -
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Residues in contact with GLN1083 (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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1079B GLU* 2.8 19.7 + - - +
1080B VAL* 3.2 22.4 + - - +
1082B GLN* 1.3 78.7 - - - +
1084B VAL* 1.3 62.7 + - + +
1086B SER* 3.3 4.8 + - - -
1087B ARG* 3.2 42.7 + - - +
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Residues in contact with VAL1084 (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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1011B PHE* 3.9 14.8 - - + -
1015B VAL* 3.7 22.9 - - + -
1018B VAL* 6.5 0.9 - - + -
1019B LEU* 5.3 4.3 - - + -
1080B VAL* 3.0 18.9 + - + +
1081B TYR 3.6 6.3 - - - +
1083B GLN* 1.3 75.3 - - + +
1085B SER* 1.3 63.1 + - - +
1087B ARG* 3.4 24.7 + - - +
1088B ILE* 3.1 45.4 + - + +
1136B GLU* 3.9 11.2 - - - +
1138B ILE* 3.9 15.7 - - + -
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Residues in contact with SER1085 (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 PHE* 4.1 6.5 - - - -
1011B PHE* 3.7 7.8 - - - -
1081B TYR 2.7 21.2 + - - -
1082B GLN* 3.6 14.4 + - - -
1084B VAL* 1.3 71.1 - - - +
1086B SER* 1.3 54.6 + - - +
1088B ILE* 3.1 2.3 + - - +
1089B MET* 2.7 48.2 + - - +
1101B ILE* 5.8 0.3 - - - +
1104B ILE* 2.5 41.8 + - - -
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Residues in contact with SER1086 (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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1082B GLN* 2.8 38.9 + - - +
1083B GLN* 3.7 5.2 - - - -
1085B SER* 1.3 74.3 + - - +
1087B ARG* 1.3 63.7 + - - +
1089B MET* 3.4 8.0 + - - +
1090B ASN* 3.0 34.7 + - - -
1093B ARG* 5.4 0.3 + - - -
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Residues in contact with ARG1087 (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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1083B GLN* 3.2 38.0 + - - +
1084B VAL* 3.7 25.2 - - - +
1085B SER 3.2 0.2 - - - -
1086B SER* 1.3 77.6 - - - +
1088B ILE* 1.3 59.0 + - - +
1090B ASN* 3.7 8.2 + - - +
1091B LEU* 3.3 28.6 + - - +
1136B GLU* 2.9 45.9 + - - +
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Residues in contact with ILE1088 (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 PHE* 3.4 39.9 - - + -
1011B PHE* 4.5 0.2 - - + -
1084B VAL* 3.1 32.3 - - + +
1085B SER 3.1 5.4 + - - +
1087B ARG* 1.3 75.8 - - - +
1089B MET* 1.3 55.6 + - - +
1090B ASN 2.9 5.2 - - - -
1091B LEU* 3.0 5.5 + - + +
1092B LEU* 2.9 30.5 + - + +
1132B ILE* 3.6 46.9 - - + -
1136B GLU* 3.6 18.6 - - + -
1138B ILE* 4.2 11.9 - - + -
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Residues in contact with MET1089 (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 PHE* 3.7 17.0 - - + -
1085B SER* 2.7 32.0 + - - +
1086B SER* 3.4 8.5 + - - +
1088B ILE* 1.3 72.0 - - - +
1090B ASN* 1.3 58.1 - - - +
1092B LEU* 4.0 6.1 - - - -
1093B ARG* 3.1 37.4 + - - +
1099B ILE* 4.0 4.3 - - - +
1101B ILE* 3.6 33.7 - - + -
1103B SER 3.3 26.5 - - - +
1104B ILE 3.7 12.1 - - - +
1106B GLU 3.4 29.8 - - - +
1107B ALA* 3.7 11.9 - - - -
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Residues in contact with ASN1090 (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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1086B SER* 3.0 24.1 + - - +
1087B ARG* 3.9 8.0 - - - +
1088B ILE 2.9 0.8 - - - -
1089B MET* 1.3 78.8 - - - +
1091B LEU* 1.3 64.9 + - + +
1092B LEU 3.1 1.3 - - - -
1093B ARG* 2.8 45.5 + - - +
1094B GLU* 3.1 27.8 + - - +
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Residues in contact with LEU1091 (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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1087B ARG 3.3 15.4 + - - +
1088B ILE* 3.0 12.2 + - + +
1090B ASN* 1.3 78.2 - - - +
1092B LEU* 1.3 60.1 + - - +
1094B GLU* 3.4 18.9 - - + +
1095B TYR* 3.1 25.9 - - + -
1131B LYS* 4.5 24.0 - - + -
1132B ILE* 4.7 12.6 - - + -
1135B LYS* 3.8 32.3 - - + -
1136B GLU* 4.3 15.5 - - + +
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Residues in contact with LEU1092 (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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1006B VAL* 3.7 26.9 - - + -
1008B PHE* 4.5 4.7 - - + -
1088B ILE* 2.9 20.4 + - + +
1089B MET* 4.3 8.3 - - - +
1090B ASN 3.1 0.2 - - - -
1091B LEU* 1.3 81.3 - - - +
1093B ARG* 1.3 61.8 + - - +
1094B GLU 3.3 0.4 - - - -
1095B TYR* 3.6 4.2 + - + -
1096B SER 3.5 6.8 + - - +
1099B ILE* 3.5 16.8 - - + +
1107B ALA* 3.5 27.8 - - + -
1109B LEU* 3.3 27.2 - - + +
1128B ILE* 3.7 39.3 - - + -
1132B ILE* 3.9 11.9 - - + -
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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