Contacts of the helix formed by residues 1133 - 1141 (chain C) in PDB entry 2OM2
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 ASP1133 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1095C PHE* 3.6 9.5 - - - -
1096C GLY* 3.0 23.0 + - - -
1097C ASP* 3.2 10.0 + - - +
1100C ARG* 3.2 31.0 + - + +
1129C ARG 3.1 13.1 + - - +
1130C LEU 3.0 14.7 + - - +
1132C LYS* 1.3 79.0 - - - +
1134C SER* 1.3 66.5 + - - +
1135C GLY* 3.0 17.0 + - - -
1136C VAL* 3.1 14.7 + - + +
1137C GLN* 3.0 23.2 + - - +
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Residues in contact with SER1134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096C GLY* 3.0 24.4 - - - -
1132C LYS 3.4 4.0 + - - -
1133C ASP* 1.3 74.4 + - - +
1135C GLY* 1.3 55.6 + - - +
1137C GLN* 3.6 6.9 + - - +
1138C ALA* 3.1 24.9 + - - +
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Residues in contact with GLY1135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088C MET* 3.9 6.5 - - - -
1093C ILE* 4.0 4.8 - - - +
1094C ASP 3.6 22.2 - - - -
1095C PHE* 4.3 0.7 - - - -
1096C GLY* 3.5 3.0 - - - +
1133C ASP* 3.0 9.9 + - - -
1134C SER* 1.3 79.6 + - - +
1136C VAL* 1.3 58.5 + - - +
1137C GLN 3.0 1.3 - - - -
1138C ALA* 2.7 29.5 + - - +
1139C CYS* 2.9 10.0 + - - +
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Residues in contact with VAL1136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1081C ILE* 4.1 13.7 - - + -
1084C ILE* 3.7 19.3 - - + +
1085C ILE* 4.4 6.5 - - + -
1088C MET* 3.7 25.9 - - - +
1095C PHE* 3.9 12.3 - - + -
1130C LEU* 3.1 38.1 - - - +
1131C TRP* 4.3 11.9 - - + -
1133C ASP* 3.1 13.9 + - + +
1135C GLY* 1.3 73.7 - - - +
1137C GLN* 1.3 58.2 + - - +
1139C CYS* 3.2 4.3 + - - +
1140C PHE* 2.9 24.9 + - - +
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Residues in contact with GLN1137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1131C TRP* 2.6 63.1 + - - +
1132C LYS 4.3 5.4 - - - +
1133C ASP 3.0 21.1 + - - +
1134C SER* 3.8 7.4 - - - +
1136C VAL* 1.3 73.6 - - - +
1138C ALA* 1.3 66.4 + - - +
1140C PHE* 3.4 19.4 - - - +
1141C ASN* 2.9 39.2 + - - +
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Residues in contact with ALA1138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093C ILE* 4.4 13.7 - - + -
1134C SER 3.1 13.8 + - - +
1135C GLY* 2.7 22.6 + - - +
1137C GLN* 1.3 74.1 - - - +
1139C CYS* 1.3 58.0 + - - +
1141C ASN* 3.4 14.3 + - - +
1142C ARG* 3.4 20.5 + - - +
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Residues in contact with CYS1139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084C ILE* 3.4 24.9 - - + -
1087C ALA* 3.5 23.6 - - - -
1088C MET* 3.6 29.2 - - + -
1091C LEU* 4.3 1.1 - - - -
1093C ILE* 3.7 20.3 - - + +
1135C GLY 2.9 6.1 + - - +
1136C VAL 3.5 8.1 - - - +
1138C ALA* 1.3 76.2 - - - +
1140C PHE* 1.3 61.7 + - - +
1142C ARG* 3.0 13.8 + - - +
1143C SER 3.4 2.9 + - - -
1146C TYR* 2.7 25.6 + - - -
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Residues in contact with PHE1140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084C ILE* 4.1 5.8 - - + +
1131C TRP* 3.7 32.5 - + + -
1136C VAL 2.9 14.8 + - - +
1137C GLN* 3.4 26.0 - - - +
1139C CYS* 1.3 76.3 - - - +
1141C ASN* 1.3 75.1 + - - +
1142C ARG 3.0 0.2 - - - -
1143C SER* 3.2 28.6 + - - -
1146C TYR* 3.7 7.0 - - - -
1148C LEU* 3.8 26.9 - - + -
1152C ALA* 5.2 0.4 - - + -
1153C ALA* 3.8 28.9 - - + -
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Residues in contact with ASN1141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1137C GLN* 2.9 35.0 + - - +
1138C ALA* 3.9 7.3 - - - +
1139C CYS 3.2 0.4 - - - -
1140C PHE* 1.3 93.1 - - - +
1142C ARG* 1.3 60.6 + - + +
1143C SER* 3.4 2.5 - - - -
1144C ARG* 5.3 2.9 - - - +
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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