Contacts of the helix formed by residues 1084 - 1094 (chain A) in PDB entry 4IGI
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 ASP1084 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1057A VAL* 3.6 16.9 - - - +
1061A ARG* 6.1 0.7 - - - +
1082A HIS 3.7 0.6 - - - -
1083A MET* 1.3 104.7 - - + +
1085A GLN* 1.3 65.7 + - - +
1086A GLN* 3.4 14.1 + - - +
1087A GLY* 3.0 27.5 + - - -
1088A VAL* 3.2 16.3 + - - +
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Residues in contact with GLN1085 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1052A VAL* 4.2 10.8 - - + +
1053A GLU* 3.6 44.7 + - - +
1055A LEU 4.2 6.9 - - - +
1057A VAL* 3.8 18.4 + - + +
1084A ASP* 1.3 76.0 - - - +
1086A GLN* 1.3 65.7 + - - +
1088A VAL* 3.1 3.9 + - - +
1089A ILE* 2.8 38.5 + - + +
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Residues in contact with GLN1086 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084A ASP* 3.3 14.2 + - - +
1085A GLN* 1.3 77.9 - - - +
1087A GLY* 1.3 60.0 + - - +
1089A ILE* 4.1 4.2 - - - +
1090A SER* 2.8 45.7 + - - +
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Residues in contact with GLY1087 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1082A HIS* 3.5 24.1 - - - -
1084A ASP* 3.0 17.8 + - - -
1086A GLN* 1.3 78.6 - - - +
1088A VAL* 1.3 61.4 + - - +
1090A SER* 3.6 4.4 + - - -
1091A ALA* 3.2 23.2 + - - +
1094A ARG* 5.0 0.7 + - - -
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Residues in contact with VAL1088 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1052A VAL* 3.8 24.5 - - + -
1057A VAL* 4.0 17.3 - - + -
1064A VAL* 4.0 24.7 - - + +
1077A PHE* 4.0 15.0 - - + -
1082A HIS* 3.7 26.7 - - + +
1084A ASP 3.5 12.1 - - - +
1085A GLN 3.1 6.1 + - - +
1087A GLY* 1.3 78.3 - - - +
1089A ILE* 1.3 63.6 + - - +
1091A ALA* 3.2 4.3 + - - +
1092A ILE* 3.0 33.7 + - + +
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Residues in contact with ILE1089 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049A GLN* 3.8 44.6 - - + +
1052A VAL* 3.9 16.6 - - + -
1053A GLU* 4.1 11.0 - - + +
1085A GLN* 2.8 42.0 + - + +
1086A GLN* 4.1 4.5 - - - +
1088A VAL* 1.3 71.9 - - - +
1090A SER* 1.3 63.9 + - - +
1092A ILE* 3.2 6.8 + - + +
1093A ARG* 3.0 58.4 + - - +
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Residues in contact with SER1090 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1086A GLN* 2.8 37.2 + - - +
1087A GLY* 3.9 4.5 - - - -
1089A ILE* 1.3 79.6 - - - +
1091A ALA* 1.3 59.2 + - - +
1093A ARG* 3.4 12.8 + - - +
1094A ARG* 3.0 46.4 + - - +
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Residues in contact with ALA1091 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1077A PHE* 3.8 18.4 - - + -
1082A HIS* 3.6 20.9 - - + +
1087A GLY 3.2 18.6 + - - +
1088A VAL 3.5 4.5 - - - +
1090A SER* 1.3 74.1 - - - +
1092A ILE* 1.3 65.1 + - - +
1094A ARG* 3.4 32.3 + - - +
1095A LEU* 3.5 16.5 + - - +
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Residues in contact with ILE1092 (chain A).
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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1045A LYS* 3.3 40.6 - - - +
1048A VAL* 3.6 30.3 - - + -
1049A GLN* 3.8 15.7 - - + +
1052A VAL* 4.0 9.9 - - + -
1064A VAL* 5.7 0.2 - - + -
1066A LEU* 4.4 2.7 - - + -
1077A PHE* 4.0 16.6 - - + -
1088A VAL* 3.0 37.8 + - + +
1089A ILE* 3.2 10.5 + - + +
1091A ALA* 1.3 74.4 - - - +
1093A ARG* 1.3 65.1 + - - +
1095A LEU* 3.1 30.3 + - + +
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Residues in contact with ARG1093 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045A LYS* 2.9 25.2 + - - +
1049A GLN* 3.0 33.0 + - - +
1053A GLU* 5.6 2.8 + - - -
1089A ILE* 3.0 37.7 + - - +
1090A SER* 3.8 12.5 + - - +
1091A ALA 3.3 0.2 - - - -
1092A ILE* 1.3 76.4 - - - +
1094A ARG* 1.3 59.7 + - + +
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Residues in contact with ARG1094 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1082A HIS* 5.4 5.1 - - - -
1087A GLY 5.0 1.0 + - - -
1090A SER* 3.0 37.0 + - - +
1091A ALA* 3.6 26.0 + - - +
1092A ILE 3.1 0.8 - - - -
1093A ARG* 1.3 78.3 - - + +
1095A LEU* 1.3 67.8 + - - +
1096A THR* 3.5 9.9 + - - +
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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