Contacts of the helix formed by residues 1120 - 1133 (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 THR1120 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1110C LEU* 5.2 5.4 - - - +
1114C ALA* 5.6 11.4 - - + -
1115C GLU 6.0 0.4 - - - +
1118C PHE* 3.8 28.3 - - + +
1119C MET* 1.3 76.7 - - - +
1121C ALA* 1.3 65.2 + - - +
1122C GLU* 3.7 6.6 + - - +
1123C LEU* 3.0 34.5 + - + +
1124C ALA* 3.1 12.7 + - - +
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Residues in contact with ALA1121 (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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1118C PHE* 5.3 0.8 - - - -
1119C MET 3.8 1.6 + - - -
1120C THR* 1.3 73.5 - - - +
1122C GLU* 1.3 62.1 + - - +
1124C ALA* 3.5 7.3 + - - +
1125C GLY* 3.2 18.0 + - - -
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Residues in contact with GLU1122 (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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1106C GLN* 3.5 22.8 - - - +
1110C LEU* 3.5 23.1 - - + +
1120C THR* 3.1 7.6 + - - +
1121C ALA* 1.3 77.3 - - - +
1123C LEU* 1.3 65.5 + - - +
1125C GLY* 3.3 2.2 + - - +
1126C VAL* 3.0 25.2 + - + +
1129C ARG* 5.2 6.4 + - - +
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Residues in contact with LEU1123 (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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1078C ILE* 4.0 22.9 - - + -
1107C LEU* 3.9 18.2 - - + -
1110C LEU* 3.9 32.5 - - + +
1111C ALA* 4.7 3.1 - - - +
1114C ALA* 4.2 21.1 - - + -
1119C MET* 3.9 22.9 - - + -
1120C THR* 3.0 23.0 + - + +
1122C GLU* 1.3 73.3 - - - +
1124C ALA* 1.3 68.1 + - - +
1126C VAL* 3.2 2.5 + - + +
1127C ILE* 3.0 40.8 + - + +
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Residues in contact with ALA1124 (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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1119C MET* 4.0 12.7 - - + +
1120C THR 3.1 10.8 + - - +
1121C ALA* 3.6 12.1 - - - +
1123C LEU* 1.3 78.9 - - - +
1125C GLY* 1.3 56.0 - - - +
1127C ILE* 3.4 2.4 + - - -
1128C LYS* 2.9 29.2 + - - +
1159C LEU* 3.7 8.8 - - + +
1163C ALA* 3.7 31.6 - - + +
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Residues in contact with GLY1125 (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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1121C ALA 3.2 11.7 + - - -
1122C GLU* 3.3 3.6 + - - -
1123C LEU 3.2 0.2 - - - -
1124C ALA* 1.3 80.4 - - - +
1126C VAL* 1.3 54.8 + - - +
1128C LYS* 3.2 9.0 + - - +
1129C ARG* 2.9 44.9 + - - +
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Residues in contact with VAL1126 (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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1103C ASP* 3.5 30.5 - - + +
1106C GLN* 4.0 15.3 - - - +
1107C LEU* 4.2 16.6 - - + +
1110C LEU* 3.7 18.4 - - + -
1122C GLU* 3.0 21.9 + - + +
1123C LEU* 3.2 7.2 + - - +
1125C GLY* 1.3 72.1 - - - +
1127C ILE* 1.3 68.0 + - - +
1129C ARG* 3.3 26.6 + - - +
1130C LEU* 3.2 31.4 + - + +
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Residues in contact with ILE1127 (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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1077C THR* 4.7 5.8 - - + -
1078C ILE* 4.3 12.8 - - + -
1081C ILE* 4.5 14.5 - - + +
1107C LEU* 4.1 11.4 - - + -
1119C MET* 3.9 31.9 - - + -
1123C LEU* 3.0 38.1 + - + +
1124C ALA 3.7 3.6 - - - +
1126C VAL* 1.3 75.7 - - - +
1128C LYS* 1.3 58.3 + - - +
1130C LEU* 3.3 9.5 + - - +
1131C TRP* 2.9 27.6 + - + +
1156C LEU* 3.6 26.5 - - + -
1159C LEU* 3.6 17.9 - - + -
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Residues in contact with LYS1128 (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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1124C ALA 2.9 17.5 + - - +
1125C GLY* 3.4 9.9 - - - +
1126C VAL 3.2 0.2 - - - -
1127C ILE* 1.3 76.2 - - - +
1129C ARG* 1.3 63.1 + - + +
1131C TRP* 3.4 6.9 + - + +
1132C LYS* 3.0 64.9 + - + +
1156C LEU 5.4 3.6 - - - +
1159C LEU* 3.6 26.2 - - + +
1160C ASP* 3.2 31.0 + - - +
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Residues in contact with ARG1129 (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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1100C ARG* 3.5 35.6 + - - +
1103C ASP* 2.5 43.9 + - - +
1106C GLN* 4.7 2.8 - - - +
1122C GLU* 5.2 6.3 + - - +
1125C GLY* 2.9 30.4 + - - +
1126C VAL* 3.3 24.5 + - - +
1128C LYS* 1.3 75.6 - - + +
1130C LEU* 1.3 63.3 + - - +
1132C LYS* 3.4 5.3 + - - +
1133C ASP 3.1 18.0 + - - -
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Residues in contact with LEU1130 (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* 4.2 13.9 - - + -
1085C ILE* 4.2 14.1 - - + -
1095C PHE* 4.2 9.9 - - + -
1100C ARG* 3.6 28.9 - - + +
1103C ASP* 4.0 7.6 - - + -
1104C ALA* 3.8 21.5 - - + +
1107C LEU* 4.0 26.2 - - + -
1126C VAL* 3.2 27.7 + - + +
1127C ILE* 3.6 7.0 - - - +
1129C ARG* 1.3 79.9 - - - +
1131C TRP* 1.3 62.7 + - - +
1133C ASP* 3.0 15.3 + - - +
1136C VAL* 3.1 23.5 - - + +
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Residues in contact with TRP1131 (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* 4.3 8.4 - - + +
1084C ILE* 3.7 26.7 - - + -
1127C ILE* 2.9 18.6 + - + +
1128C LYS* 3.9 9.4 - - + +
1130C LEU* 1.3 76.2 - - - +
1132C LYS* 1.3 73.9 + - + +
1136C VAL* 4.3 5.6 - - + -
1137C GLN* 2.6 62.3 + - - +
1140C PHE* 3.7 36.3 - + + -
1153C ALA* 4.2 7.4 - - + -
1156C LEU* 3.6 55.5 + - + -
1157C ASN* 2.8 39.2 + - - -
1159C LEU* 5.7 0.9 - - + -
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Residues in contact with LYS1132 (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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1128C LYS* 3.0 60.8 + - + +
1129C ARG* 3.8 6.7 - - - +
1131C TRP* 1.3 86.1 - - + +
1133C ASP* 1.3 67.0 + - - +
1134C SER* 3.4 2.3 + - - -
1137C GLN* 4.3 5.6 - - - +
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Residues in contact with ASP1133 (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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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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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