Contacts of the helix formed by residues 1099 - 1114 (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 ALA1099 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1097C ASP* 2.8 3.7 + - + +
1098C SER* 1.3 74.5 - - - +
1100C ARG* 1.3 84.4 + - - +
1101C ALA 3.1 4.1 + - - -
1102C ASP* 3.2 26.6 + - - +
1103C ASP* 3.6 9.8 - - - +
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Residues in contact with ARG1100 (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 21.3 - - + -
1097C ASP* 2.7 39.3 + - - +
1099C ALA* 1.3 94.4 - - - +
1101C ALA* 1.3 55.9 + - - +
1102C ASP 3.3 0.2 - - - -
1103C ASP* 2.8 32.9 + - - +
1104C ALA* 2.9 25.1 + - - +
1129C ARG* 3.5 48.7 + - - +
1130C LEU* 3.6 11.7 - - + +
1133C ASP* 3.2 29.7 + - - +
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Residues in contact with ALA1101 (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* 3.7 28.8 - - + -
1098C SER 3.4 14.0 + - - +
1099C ALA 3.1 0.8 - - - -
1100C ARG* 1.3 78.4 - - - +
1102C ASP* 1.3 62.7 + - - +
1104C ALA* 3.3 2.9 + - - +
1105C ARG* 3.1 47.9 + - - +
1530D LEU* 4.3 2.8 - - + +
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Residues in contact with ASP1102 (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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1098C SER 4.9 1.5 - - - +
1099C ALA* 3.2 20.0 + - - +
1101C ALA* 1.3 74.6 - - - +
1103C ASP* 1.3 62.5 + - - +
1105C ARG* 3.1 27.0 + - - +
1106C GLN* 2.9 33.4 + - - +
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Residues in contact with ASP1103 (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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1099C ALA 3.6 8.0 + - - +
1100C ARG* 2.8 44.7 + - - +
1102C ASP* 1.3 78.8 - - - +
1104C ALA* 1.3 51.8 - - - +
1106C GLN* 3.1 15.4 + - - +
1107C LEU* 2.7 31.9 + - - +
1126C VAL* 3.5 18.0 - - + +
1129C ARG* 2.5 34.0 + - - -
1130C LEU* 4.0 13.5 - - + -
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Residues in contact with ALA1104 (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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1085C ILE* 4.4 9.0 - - + -
1095C PHE* 3.8 22.4 - - + -
1100C ARG 2.9 13.6 + - - +
1101C ALA 3.5 8.3 - - - +
1102C ASP 3.2 0.2 - - - -
1103C ASP* 1.3 77.2 - - - +
1105C ARG* 1.3 62.2 + - - +
1107C LEU* 3.3 10.7 + - - +
1108C PHE* 3.3 21.1 - - - -
1130C LEU* 3.8 15.2 - - + +
1530D LEU* 3.8 18.6 - - + -
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Residues in contact with ARG1105 (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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1101C ALA* 3.1 31.9 + - - +
1102C ASP* 3.1 33.1 + - - +
1104C ALA* 1.3 78.4 - - - +
1106C GLN* 1.3 64.9 + - - +
1107C LEU 3.4 0.7 + - - -
1108C PHE* 3.4 13.9 + - - +
1109C VAL* 3.5 14.3 + - - +
1526D LEU* 4.2 17.3 - - + +
1529D PHE 5.2 0.6 + - - -
1530D LEU* 3.0 52.5 + - + +
1531D GLN* 4.5 9.9 + - - -
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Residues in contact with GLN1106 (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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1102C ASP* 2.9 17.7 + - - +
1103C ASP* 3.1 23.6 + - - +
1105C ARG* 1.3 75.8 - - - +
1107C LEU* 1.3 66.6 + - - +
1109C VAL* 2.8 21.9 + - + +
1110C LEU* 2.8 28.9 + - + +
1122C GLU* 3.5 30.8 - - - +
1126C VAL* 4.0 13.4 - - + +
1129C ARG* 4.7 2.0 - - - +
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Residues in contact with LEU1107 (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* 4.6 11.7 - - + -
1081C ILE* 3.7 28.7 - - + -
1082C ILE* 3.7 22.4 - - + -
1085C ILE* 4.4 10.1 - - + -
1103C ASP 2.7 15.5 + - - +
1104C ALA 3.3 12.6 - - - +
1106C GLN* 1.3 72.0 - - - +
1108C PHE* 1.3 57.0 + - + +
1110C LEU* 3.8 3.7 - - - +
1111C ALA* 2.8 37.6 + - - +
1123C LEU* 3.9 22.0 - - + -
1126C VAL* 4.2 9.3 - - + +
1127C ILE* 4.1 16.2 - - + -
1130C LEU* 4.0 18.8 - - + -
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Residues in contact with PHE1108 (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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1082C ILE* 3.9 37.0 - - + -
1085C ILE* 4.4 11.2 - - + -
1086C ARG* 3.7 27.8 - - + -
1104C ALA 3.3 24.7 - - - -
1105C ARG 3.4 6.4 + - - +
1106C GLN 3.2 0.4 - - - -
1107C LEU* 1.3 82.4 - - + +
1109C VAL* 1.3 62.7 + - + +
1111C ALA* 4.1 5.2 - - - +
1112C GLY* 3.1 18.5 + - - -
1523D ASP 4.0 0.4 - - - -
1524D LEU* 3.2 34.4 - - - +
1525D VAL 3.9 3.1 - - - -
1526D LEU* 3.7 21.8 - - + -
1527D PRO* 3.4 28.7 - - + -
1530D LEU* 4.1 6.1 - - + -
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Residues in contact with VAL1109 (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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1105C ARG 3.5 12.5 + - - +
1106C GLN* 2.8 15.1 + - + +
1108C PHE* 1.3 76.1 - - + +
1110C LEU* 1.3 71.9 + - + +
1112C GLY* 3.1 4.0 + - - -
1113C ALA* 3.0 25.3 + - + +
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Residues in contact with LEU1110 (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* 2.8 37.5 + - + +
1107C LEU 3.8 2.7 - - - +
1109C VAL* 1.3 77.9 - - + +
1111C ALA* 1.3 52.8 + - - +
1113C ALA* 2.8 8.1 + - + +
1114C ALA* 2.6 38.3 + - - +
1120C THR* 5.2 6.5 - - - +
1122C GLU* 3.5 21.3 - - + +
1123C LEU* 3.9 33.9 - - + +
1126C VAL* 3.7 30.7 - - + -
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Residues in contact with ALA1111 (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* 3.8 33.4 - - + -
1082C ILE* 4.9 0.9 - - + -
1107C LEU* 2.8 25.5 + - + +
1108C PHE* 4.1 2.0 - - - +
1110C LEU* 1.3 73.7 - - - +
1112C GLY* 1.3 62.1 + - - +
1113C ALA 3.2 0.9 + - - -
1114C ALA* 3.4 18.8 + - - +
1123C LEU* 4.7 3.2 - - + +
1519D LEU* 3.9 15.1 - - + +
1524D LEU* 3.8 19.5 - - + +
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Residues in contact with GLY1112 (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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1108C PHE 3.1 14.7 + - - -
1109C VAL* 3.1 4.9 + - - -
1111C ALA* 1.3 76.2 - - - +
1113C ALA* 1.3 58.7 + - - +
1114C ALA 4.9 1.6 - - - +
1524D LEU* 3.3 22.2 - - - +
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Residues in contact with ALA1113 (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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1109C VAL* 3.0 18.1 + - + +
1110C LEU* 2.8 9.7 + - + +
1112C GLY* 1.3 76.5 - - - +
1114C ALA* 1.3 70.4 + - - +
1115C GLU* 4.2 7.6 - - - +
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Residues in contact with ALA1114 (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* 5.2 4.7 - - + -
1110C LEU 2.6 18.2 + - - +
1111C ALA* 3.4 13.8 + - - +
1112C GLY 4.9 1.7 - - - +
1113C ALA* 1.3 79.6 + - - +
1115C GLU* 1.3 63.1 + - - +
1116C GLU* 4.1 1.7 + - - +
1118C PHE 4.6 8.1 - - - +
1120C THR* 5.6 9.6 - - + -
1123C LEU* 4.2 21.1 - - + -
1519D LEU* 5.9 1.1 - - + -
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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