Contacts of the helix formed by residues 1081 - 1095 (chain B) in PDB entry 2OOQ
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 ALA1081 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1080B TYR* 1.3 72.9 - - - +
1082B THR* 1.3 60.4 + - - +
1083B GLY 3.4 2.5 - - - -
1084B LEU* 3.2 7.1 + - - +
1085B LEU* 2.9 30.8 + - + +
1157B PHE* 4.1 15.3 - - + -
1160B ASP* 4.7 2.5 - - + +
1161B ALA* 3.6 38.1 - - + +
1164B GLU* 3.6 18.0 + - + +
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Residues in contact with THR1082 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045B GLU* 4.9 0.7 - - - -
1080B TYR* 3.5 16.8 - - - +
1081B ALA* 1.3 75.4 + - - +
1083B GLY* 1.3 58.5 + - - +
1085B LEU* 3.8 5.5 - - + +
1086B GLY* 3.0 24.6 + - - -
1164B GLU* 2.7 29.2 + - - +
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Residues in contact with GLY1083 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045B GLU* 3.5 33.4 + - - -
1046B TYR* 4.0 5.2 - - - -
1069B PHE* 3.8 9.2 - - - -
1080B TYR* 3.5 12.6 - - - -
1081B ALA 3.4 0.8 - - - -
1082B THR* 1.3 78.1 - - - +
1084B LEU* 1.3 62.5 + - - +
1086B GLY* 3.3 2.8 + - - -
1087B PHE* 3.0 23.4 + - - +
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Residues in contact with LEU1084 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008B VAL* 5.1 4.5 - - + -
1069B PHE* 3.6 33.3 - - + -
1072B TRP* 4.1 15.0 - - + -
1078B PRO* 5.5 1.3 - - + -
1080B TYR 5.4 1.5 + - - +
1081B ALA 3.2 9.4 + - - +
1083B GLY* 1.3 76.0 - - - +
1085B LEU* 1.3 58.8 + - + +
1087B PHE* 3.2 25.4 + - + +
1088B VAL* 2.9 33.5 + - + +
1115B CYS* 5.5 1.6 - - + -
1116B PHE* 4.7 13.9 - - + -
1119B ILE* 3.7 19.7 - - + -
1157B PHE* 3.6 35.2 - - + -
1161B ALA* 5.6 0.4 - - + -
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Residues in contact with LEU1085 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1081B ALA* 2.9 22.0 + - + +
1082B THR* 3.8 5.4 - - + +
1084B LEU* 1.3 78.0 - - + +
1086B GLY* 1.3 61.3 + - - +
1088B VAL* 3.4 4.8 + - + +
1089B ARG* 3.0 32.9 + - - +
1119B ILE* 4.0 27.4 - - + -
1123B LEU* 4.3 9.0 - - + -
1161B ALA* 3.5 30.3 - - + +
1164B GLU* 3.7 33.2 - - + +
1165B ALA* 3.8 21.1 - - + +
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Residues in contact with GLY1086 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046B TYR* 3.9 11.7 + - - -
1082B THR 3.0 15.5 + - - -
1083B GLY* 3.3 3.6 + - - -
1085B LEU* 1.3 74.8 - - - +
1087B PHE* 1.3 61.2 + - - +
1089B ARG* 3.2 22.4 + - - +
1090B GLN* 3.1 25.3 + - - +
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Residues in contact with PHE1087 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006B VAL* 3.5 24.2 - - + -
1007B MET 4.5 0.7 - - - -
1008B VAL* 4.7 2.0 - - + -
1046B TYR* 3.6 39.1 - + + -
1067B PHE* 3.3 46.0 - + + -
1068B HIS 3.8 2.0 - - - -
1069B PHE* 3.6 36.3 - + + -
1083B GLY 3.0 13.2 + - - +
1084B LEU* 3.3 25.1 - - + +
1086B GLY* 1.3 72.8 - - - +
1088B VAL* 1.3 66.6 + - - +
1090B GLN* 3.1 15.5 + - + +
1091B VAL* 3.2 17.7 + - + +
1116B PHE* 3.7 13.5 - + - -
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Residues in contact with VAL1088 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084B LEU* 2.9 27.9 + - + +
1085B LEU* 3.7 7.0 - - - +
1087B PHE* 1.3 75.1 - - - +
1089B ARG* 1.3 58.7 + - - +
1091B VAL* 3.2 4.2 + - - +
1092B LYS* 2.9 40.2 + - + +
1116B PHE* 3.6 33.0 - - + +
1119B ILE* 4.4 18.8 - - + -
1120B ASP* 3.4 29.4 - - - +
1123B LEU* 4.2 14.6 - - + -
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Residues in contact with ARG1089 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085B LEU* 3.0 20.2 + - - +
1086B GLY* 3.4 24.5 + - - +
1087B PHE 3.2 0.2 - - - -
1088B VAL* 1.3 78.4 - - - +
1090B GLN* 1.3 57.5 + - + +
1092B LYS* 3.4 10.2 + - + +
1093B PHE* 2.9 41.2 + - + -
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Residues in contact with GLN1090 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041B GLU* 4.6 11.0 + - - +
1043B LEU* 4.4 8.1 - - - +
1046B TYR* 3.0 41.1 + - + +
1048B ILE* 3.6 26.4 - - + +
1067B PHE* 3.9 7.0 - - + -
1086B GLY 3.1 13.1 + - - +
1087B PHE* 3.1 8.9 + - + +
1089B ARG* 1.3 76.2 - - + +
1091B VAL* 1.3 58.6 + - - +
1093B PHE* 3.4 4.4 + - - +
1094B LEU* 2.9 48.7 + - - +
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Residues in contact with VAL1091 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004B SER* 5.0 0.2 - - - -
1006B VAL* 3.9 24.2 - - + -
1067B PHE* 3.7 39.5 - - + -
1087B PHE* 3.2 15.7 + - + +
1088B VAL 3.2 6.3 + - - +
1090B GLN* 1.3 76.2 - - - +
1092B LYS* 1.3 60.7 + - + +
1095B ASN* 2.9 35.1 + - + +
1102B ILE* 4.1 27.1 - - + +
1116B PHE* 4.1 20.0 - - + -
1120B ASP* 6.0 2.0 - - - +
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Residues in contact with LYS1092 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501B NA 4.5 5.6 - - - -
1088B VAL* 2.9 33.3 + - + +
1089B ARG* 3.6 9.2 - - + +
1091B VAL* 1.3 79.3 - - + +
1093B PHE* 1.3 61.9 + - + +
1095B ASN* 4.4 7.0 + - - +
1120B ASP* 2.7 44.6 + - - +
1123B LEU* 4.1 17.3 - - + -
1124B ASP* 2.6 34.4 + - - +
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Residues in contact with PHE1093 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089B ARG* 2.9 36.9 + - + +
1090B GLN* 3.8 6.3 - - - +
1092B LYS* 1.3 73.5 - - + +
1094B LEU* 1.3 71.0 + - + +
1095B ASN 4.6 2.1 - - - +
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Residues in contact with LEU1094 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B B3P 3.9 42.8 - - - +
1048B ILE* 4.4 1.3 - - + -
1065B ARG* 3.0 35.3 + - - +
1067B PHE* 3.9 22.9 - - + -
1090B GLN* 2.9 38.6 + - - +
1093B PHE* 1.3 87.5 - - + +
1095B ASN* 1.3 69.9 + - - +
1096B PRO* 3.2 3.6 - - - +
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Residues in contact with ASN1095 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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978B HIS* 5.0 7.1 - - - -
1003B ALA* 4.3 2.8 + - - +
1004B SER* 2.7 36.7 + - - +
1065B ARG* 5.0 0.2 - - - +
1067B PHE* 4.7 0.6 - - - -
1091B VAL* 2.9 20.3 + - + +
1092B LYS* 4.6 7.1 - - - +
1093B PHE 4.6 1.9 - - - +
1094B LEU* 1.3 77.0 - - - +
1096B PRO* 1.3 86.9 + - - +
1097B PRO* 3.3 13.1 - - - +
1099B ALA* 5.0 0.2 - - - +
1100B GLY 4.9 7.5 + - - +
1102B ILE* 3.6 34.0 - - + +
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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