Contacts of the helix formed by residues 1081 - 1095 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1080A TYR* 1.3 74.6 - - - +
1082A THR* 1.3 64.9 + - - +
1083A GLY 3.4 0.4 - - - -
1084A LEU* 3.2 7.1 + - - +
1085A LEU* 2.9 25.5 + - + +
1157A PHE* 4.0 17.1 - - + -
1160A ASP* 4.7 4.3 - - + -
1161A ALA* 3.6 39.3 - - + +
1164A GLU* 3.9 15.5 + - - +
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Residues in contact with THR1082 (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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1080A TYR* 3.3 14.9 - - - +
1081A ALA* 1.3 77.6 - - - +
1083A GLY* 1.3 62.5 + - - +
1085A LEU* 3.3 6.6 + - + +
1086A GLY* 3.1 18.2 + - - -
1089A ARG* 5.3 1.2 + - - -
1164A GLU* 2.8 27.8 + - - +
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Residues in contact with GLY1083 (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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1045A GLU* 3.6 32.4 + - - -
1046A TYR* 4.2 7.3 - - - -
1069A PHE* 3.8 7.6 - - - -
1080A TYR* 4.6 3.0 + - - +
1081A ALA 3.4 0.4 - - - -
1082A THR* 1.3 78.4 - - - +
1084A LEU* 1.3 62.3 + - - +
1086A GLY* 3.1 3.9 + - - -
1087A PHE* 3.0 21.8 + - - +
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Residues in contact with LEU1084 (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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1008A VAL* 4.9 0.9 - - + -
1045A GLU* 4.6 0.2 + - - -
1069A PHE* 3.5 27.0 - - + -
1072A TRP* 3.0 44.4 - - + -
1078A PRO* 5.1 2.5 - - + -
1080A TYR 5.0 1.0 + - - +
1081A ALA* 3.2 10.6 + - - +
1083A GLY* 1.3 75.4 - - - +
1085A LEU* 1.3 58.4 + - + +
1087A PHE* 3.2 24.8 + - + +
1088A VAL* 2.9 41.2 + - + +
1116A PHE* 4.8 6.3 - - + -
1119A ILE* 3.8 14.8 - - + -
1157A PHE* 3.5 27.1 - - + -
1161A ALA* 5.4 1.3 - - + -
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Residues in contact with LEU1085 (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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1081A ALA* 2.9 21.0 + - + +
1082A THR* 3.6 7.4 - - + +
1084A LEU* 1.3 79.8 - - + +
1086A GLY* 1.3 56.8 + - - +
1088A VAL* 3.4 4.8 + - + +
1089A ARG* 2.9 41.1 + - - +
1119A ILE* 4.0 25.1 - - + -
1123A LEU* 4.4 7.0 - - + -
1161A ALA* 3.5 31.9 - - + +
1164A GLU* 3.7 34.8 - - + +
1165A ALA* 3.8 19.3 - - + +
1168A CYS* 6.2 0.4 - - - -
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Residues in contact with GLY1086 (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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1046A TYR* 4.3 9.6 - - - -
1082A THR 3.1 13.1 + - - -
1083A GLY* 3.1 4.6 + - - -
1085A LEU* 1.3 76.3 - - - +
1087A PHE* 1.3 55.6 + - - +
1089A ARG* 3.2 28.8 + - - +
1090A GLN* 2.9 31.2 + - - +
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Residues in contact with PHE1087 (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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1006A VAL* 3.7 12.8 - - + -
1008A VAL* 4.1 9.0 - - + -
1046A TYR* 3.5 37.3 - + + -
1067A PHE* 3.5 44.6 - + + -
1068A HIS 3.9 2.0 - - - -
1069A PHE* 3.6 32.8 - + + -
1083A GLY 3.0 11.6 + - - +
1084A LEU* 3.2 22.0 - - + +
1086A GLY* 1.3 72.8 - - - +
1088A VAL* 1.3 67.0 + - - +
1090A GLN* 3.2 12.2 + - - +
1091A VAL* 3.2 20.7 + - + +
1116A PHE* 3.7 29.2 - + - -
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Residues in contact with VAL1088 (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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1084A LEU* 2.9 28.1 + - + +
1085A LEU* 3.6 9.9 - - - +
1087A PHE* 1.3 75.4 - - + +
1089A ARG* 1.3 62.8 + - - +
1091A VAL* 3.2 4.5 + - - +
1092A LYS* 3.0 36.0 + - + +
1116A PHE* 3.8 32.5 - - + +
1119A ILE* 4.5 15.5 - - + -
1120A ASP* 3.6 26.9 - - - +
1123A LEU* 4.2 15.9 - - + -
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Residues in contact with ARG1089 (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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1082A THR 5.3 0.8 + - - -
1085A LEU* 2.9 37.0 + - - +
1086A GLY* 3.2 24.2 + - - +
1088A VAL* 1.3 78.8 - - - +
1090A GLN* 1.3 55.3 + - + +
1092A LYS* 3.4 9.8 + - + +
1093A PHE* 2.9 31.2 + - + +
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Residues in contact with GLN1090 (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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1041A GLU* 4.8 5.8 + - - +
1043A LEU* 3.9 14.5 - - - +
1046A TYR* 2.8 39.0 + - + +
1048A ILE* 3.9 11.2 - - + +
1067A PHE* 4.2 14.8 - - + -
1086A GLY 2.9 14.6 + - - +
1087A PHE* 3.2 7.6 + - - +
1089A ARG* 1.3 72.9 - - - +
1091A VAL* 1.3 60.1 + - - +
1093A PHE* 3.3 6.4 + - - -
1094A LEU* 2.8 54.6 + - - +
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Residues in contact with VAL1091 (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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1004A SER* 5.2 0.7 - - - -
1006A VAL* 4.0 23.1 - - + -
1067A PHE* 3.6 40.8 - - + -
1087A PHE* 3.2 16.9 + - + +
1088A VAL 3.2 6.5 + - - +
1090A GLN* 1.3 75.2 - - - +
1092A LYS* 1.3 60.8 + - + +
1095A ASN* 2.9 39.4 + - + +
1102A ILE* 4.0 25.6 - - + -
1116A PHE* 4.3 18.4 - - + -
1120A ASP* 5.9 2.2 - - - +
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Residues in contact with LYS1092 (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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1088A VAL* 3.0 30.3 + - + +
1089A ARG* 3.7 7.6 - - + +
1091A VAL* 1.3 80.2 - - + +
1093A PHE* 1.3 62.1 + - - +
1095A ASN* 4.3 7.4 + - - +
1120A ASP* 2.7 48.4 + - - +
1123A LEU* 4.2 15.5 - - - -
1124A ASP* 2.6 35.6 + - - +
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Residues in contact with PHE1093 (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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1089A ARG* 2.9 18.6 + - + +
1090A GLN* 3.6 9.2 - - - +
1092A LYS* 1.3 78.9 - - - +
1094A LEU* 1.3 82.9 + - + +
1095A ASN 4.7 1.6 - - - +
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Residues in contact with LEU1094 (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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301A B3P 3.8 44.0 - - - +
1048A ILE* 4.3 1.1 - - + -
1065A ARG* 2.8 39.7 + - - +
1067A PHE* 4.0 21.3 - - + -
1090A GLN* 2.8 38.9 + - - +
1093A PHE* 1.3 100.2 - - + +
1095A ASN* 1.3 65.5 + - - +
1096A PRO* 3.2 3.6 - - - +
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Residues in contact with ASN1095 (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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978A HIS* 4.8 7.3 + - - -
1003A ALA* 4.3 2.8 + - - +
1004A SER* 2.7 36.2 + - - +
1065A ARG* 4.9 0.2 - - - +
1067A PHE* 4.9 0.6 - - - -
1091A VAL* 2.9 20.9 + - + +
1092A LYS* 4.5 7.3 - - - +
1093A PHE 3.7 1.6 - - - +
1094A LEU* 1.3 76.6 - - - +
1096A PRO* 1.3 84.3 + - - +
1097A PRO* 3.2 14.2 - - - +
1099A ALA* 4.9 1.7 - - - +
1100A GLY 5.0 6.0 + - - +
1102A ILE* 3.7 31.6 - - + +
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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