Contacts of the helix formed by residues 1056 - 1063 (chain A) in PDB entry 2OJ9
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 ASP1056 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A BMI 4.0 24.8 - - + -
1054A ARG 4.1 0.2 - - - +
1055A GLY* 1.3 75.5 - - - +
1057A LEU* 1.3 58.5 + - - +
1058A LYS* 3.1 13.5 + - - +
1059A SER* 2.7 29.7 + - - -
1060A TYR* 3.0 25.1 + - - +
1109A ARG* 3.6 19.9 - - - +
1111A CYS 3.3 7.9 - - - +
1112A MET* 4.1 5.1 - - + +
1126A MET* 6.2 0.7 - - + -
1127A THR* 4.7 0.4 - - - +
1130A ILE* 5.4 0.9 - - - +
1131A TYR* 2.7 39.8 + - - -
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Residues in contact with LEU1057 (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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1055A GLY 3.8 0.8 + - - -
1056A ASP* 1.3 69.4 - - - +
1058A LYS* 1.3 59.3 + - - +
1060A TYR* 4.1 9.2 - - + -
1061A LEU* 2.9 42.7 + - + +
1085A MET* 4.2 17.0 - - - -
1089A ILE* 4.0 26.7 - - + -
1108A ALA* 3.3 28.0 + - + +
1111A CYS* 2.8 25.9 + - + +
1113A VAL* 3.8 26.7 - - + +
1119A VAL* 4.3 7.4 - - + -
1171A VAL* 4.4 2.0 - - + -
1175A ILE* 4.4 13.9 - - + -
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Residues in contact with LYS1058 (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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1056A ASP* 3.1 11.2 + - - +
1057A LEU* 1.3 77.9 - - - +
1059A SER* 1.3 62.8 + - - +
1061A LEU* 3.4 1.7 + - - +
1062A ARG* 3.1 61.9 + - - +
1108A ALA* 3.3 13.1 + - + -
1109A ARG* 3.7 21.3 - - + +
1131A TYR* 3.8 26.0 - - + -
1134A ASP* 2.9 26.7 + - - +
1148A TRP* 4.2 7.7 - - - -
1174A GLU* 4.3 9.8 + - - +
1179A ALA* 3.8 17.5 + - + +
1180A GLU 5.0 1.8 + - - -
1181A GLN* 2.7 24.6 + - - -
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Residues in contact with SER1059 (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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1054A ARG 5.6 1.8 - - - -
1055A GLY* 5.9 0.7 - - - -
1056A ASP* 2.7 22.7 + - - -
1058A LYS* 1.3 73.0 - - - +
1060A TYR* 1.3 68.4 + - - +
1062A ARG* 3.4 7.9 + - - +
1063A SER* 3.0 23.0 + - - -
1131A TYR* 2.3 31.1 + - - -
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Residues in contact with TYR1060 (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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1054A ARG* 4.2 22.4 + - + +
1056A ASP 3.0 17.2 + - - +
1057A LEU* 3.7 20.2 - - + +
1058A LYS 3.3 0.2 - - - -
1059A SER* 1.3 77.6 - - - +
1061A LEU* 1.3 62.9 + - + +
1063A SER* 2.6 28.6 + - - -
1064A LEU* 3.3 45.2 - - + +
1085A MET* 4.5 18.4 - - + +
1113A VAL* 4.1 23.8 - - + -
1117A PHE* 3.5 40.6 - + - -
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Residues in contact with LEU1061 (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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1057A LEU* 2.9 41.1 + - + +
1058A LYS 3.7 3.8 - - - +
1059A SER 3.2 0.2 - - - -
1060A TYR* 1.3 79.5 - - + +
1062A ARG* 1.3 62.6 + - - +
1064A LEU* 3.0 29.9 + - + +
1065A ARG 3.9 0.2 + - - -
1077A PRO* 5.0 1.8 - - + -
1085A MET* 4.8 7.2 - - + -
1108A ALA* 4.4 7.2 - - + -
1174A GLU 3.6 24.2 - - - +
1175A ILE* 3.6 34.3 - - + +
1178A LEU* 3.5 34.2 - - + +
1179A ALA* 4.0 14.6 - - + +
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Residues in contact with ARG1062 (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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1058A LYS* 3.1 37.8 + - - +
1059A SER* 3.4 7.2 + - - +
1061A LEU* 1.3 75.4 - - - +
1063A SER* 1.3 60.5 + - - +
1064A LEU 3.0 0.2 - - - -
1065A ARG* 3.1 48.5 + - - +
1131A TYR* 4.9 10.0 - - - -
1178A LEU 3.8 15.0 - - - +
1179A ALA* 3.0 24.7 + - + -
1180A GLU 4.4 1.2 - - - -
1181A GLN* 3.2 33.5 + - - +
1184A GLN* 5.7 0.6 - - - +
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Residues in contact with SER1063 (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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1059A SER 3.0 13.8 + - - -
1060A TYR* 2.6 27.3 + - - -
1061A LEU 3.1 0.6 - - - -
1062A ARG* 1.3 75.7 - - - +
1064A LEU* 1.3 66.3 + - - +
1065A ARG 3.3 5.1 + - - +
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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
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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