Contacts of the helix formed by residues 1133 - 1145 (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 ASP1133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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889A MET* 4.3 25.3 + - - +
890A ALA* 4.1 14.4 + - + +
891A ILE* 5.7 1.1 - - - -
1122A MET* 3.8 5.6 - - - +
1125A MET* 3.7 17.0 - - + +
1132A VAL* 1.3 74.0 - - - +
1134A ILE* 1.3 58.3 + - - +
1135A PHE* 3.6 6.4 + - - +
1136A ASN* 2.7 45.4 + - + +
1137A CYS* 3.0 26.9 + - - +
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Residues in contact with ILE1134 (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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891A ILE* 6.2 0.6 - - - +
896A LEU* 4.9 4.9 - - + -
1118A ALA* 5.5 0.4 - - + -
1122A MET* 4.0 11.2 - - + -
1132A VAL* 3.8 19.6 + - + +
1133A ASP* 1.3 69.9 - - - +
1135A PHE* 1.3 67.2 + - - +
1137A CYS* 3.4 7.2 - - + +
1138A VAL* 3.0 27.4 + - + +
1155A TYR* 4.2 6.7 - - + -
1158A VAL* 3.9 20.4 - - + -
1159A HIS* 3.4 55.0 - - + +
1162A ILE* 3.4 32.8 - - + -
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Residues in contact with PHE1135 (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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889A MET* 3.7 24.2 - - + -
909A TYR* 5.1 1.3 - - - -
914A GLU* 3.4 52.7 + - + +
917A ALA* 3.9 24.5 - - + -
918A LEU* 3.6 25.6 - - + +
919A PRO* 6.0 0.7 - - + -
1133A ASP* 3.3 5.1 + - - +
1134A ILE* 1.3 80.1 - - - +
1136A ASN* 1.3 71.9 + - - +
1138A VAL 3.4 0.2 + - - -
1139A ARG* 2.9 32.5 + - + +
1155A TYR* 3.2 20.0 + - - +
1159A HIS* 5.2 0.2 + - - -
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Residues in contact with ASN1136 (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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889A MET* 3.0 30.2 - - - +
1133A ASP* 2.7 35.2 + - - +
1135A PHE* 1.3 87.3 - - - +
1137A CYS* 1.3 60.0 + - - +
1139A ARG* 3.6 8.8 - - - +
1140A GLU* 2.8 44.8 + - + +
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Residues in contact with CYS1137 (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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1118A ALA* 4.1 27.8 - - - -
1121A THR* 4.2 11.7 - - - -
1122A MET* 3.7 31.6 - - + -
1133A ASP 3.0 16.0 + - - +
1134A ILE* 3.4 9.4 - - + +
1135A PHE 3.2 0.2 - - - -
1136A ASN* 1.3 77.2 - - - +
1138A VAL* 1.3 52.6 + - + +
1140A GLU* 3.2 12.7 + - - +
1141A LEU* 2.8 46.8 + - - +
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Residues in contact with VAL1138 (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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918A LEU* 3.7 27.8 - - + -
1118A ALA* 4.4 15.5 - - + -
1134A ILE* 3.0 21.2 + - + +
1135A PHE 4.0 2.7 - - - +
1137A CYS* 1.3 71.9 - - - +
1139A ARG* 1.3 60.9 + - - +
1141A LEU* 3.5 7.8 - - + +
1142A ARG* 2.9 32.3 + - - +
1148A LEU 3.9 18.8 - - - +
1149A VAL* 4.1 24.2 - - + -
1155A TYR* 4.0 15.7 - - + -
1158A VAL* 5.4 1.3 - - + -
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Residues in contact with ARG1139 (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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918A LEU* 3.7 12.2 - - + +
919A PRO* 4.5 17.0 - - + +
1135A PHE* 2.9 24.8 + - + +
1136A ASN* 3.6 17.5 - - - +
1138A VAL* 1.3 77.5 - - - +
1140A GLU* 1.3 63.4 + - + +
1142A ARG* 3.2 5.2 + - - +
1143A ALA* 3.1 20.3 + - - +
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Residues in contact with GLU1140 (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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1136A ASN* 2.8 33.1 + - + +
1137A CYS* 3.5 9.2 - - - +
1139A ARG* 1.3 74.0 - - + +
1141A LEU* 1.3 63.0 + - + +
1143A ALA* 3.2 17.9 + - - +
1144A GLN* 3.0 27.3 + - - +
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Residues in contact with LEU1141 (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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970A ILE* 3.5 30.1 - - + -
971A ASP 4.9 2.7 - - - +
1114A GLY* 3.8 24.5 - - - +
1117A ILE* 3.7 14.1 - - + -
1118A ALA* 3.9 24.9 - - + +
1121A THR* 5.6 0.9 - - + +
1137A CYS* 2.8 29.6 + - - +
1138A VAL* 3.5 13.9 - - + +
1140A GLU* 1.3 72.3 - - + +
1142A ARG* 1.3 62.5 + - - +
1144A GLN* 3.1 19.1 + - - +
1145A ARG 3.1 13.2 + - - +
1148A LEU* 4.0 24.9 - - + +
1149A VAL* 4.8 2.9 - - + -
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Residues in contact with ARG1142 (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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915A TYR* 3.2 24.4 + - - -
918A LEU* 3.4 26.5 + - - +
919A PRO* 3.0 46.8 + - + +
920A GLU* 4.1 8.9 - - - +
923A THR* 4.2 5.1 + - + +
946A TYR* 3.4 16.8 + - - -
1138A VAL* 2.9 22.7 + - - +
1139A ARG 3.2 4.9 + - - +
1141A LEU* 1.3 75.3 - - - +
1143A ALA* 1.3 62.1 + - - +
1145A ARG 3.3 15.5 - - - +
1146A VAL* 4.0 0.9 + - - -
1147A ASN* 3.8 21.6 + - - +
1148A LEU 3.0 27.7 + - - +
1149A VAL 2.6 27.0 + - - -
1150A GLN* 4.3 1.6 - - - +
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Residues in contact with ALA1143 (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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919A PRO* 5.6 0.9 - - - +
923A THR* 4.6 8.5 + - - -
924A ALA* 5.1 0.2 - - - +
946A TYR* 3.6 4.9 - - - -
948A HIS* 2.9 28.1 + - - +
1139A ARG 3.1 11.8 + - - +
1140A GLU* 3.2 14.5 + - - +
1142A ARG* 1.3 77.2 - - - +
1144A GLN* 1.3 61.5 + - + +
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Residues in contact with GLN1144 (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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946A TYR* 3.7 3.8 - - - -
948A HIS* 4.0 9.2 - - + +
949A SER* 2.6 28.1 + - - -
968A ASN* 3.3 7.1 + - - +
969A TYR 3.9 8.0 - - - +
970A ILE* 3.4 26.1 - - + +
971A ASP* 2.8 45.7 + - - +
1140A GLU* 3.0 30.8 + - - +
1141A LEU* 3.1 12.9 + - - +
1143A ALA* 1.3 83.2 - - + +
1145A ARG* 1.3 60.7 + - - +
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Residues in contact with ARG1145 (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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943A ILE* 3.8 10.3 - - - +
944A ILE 4.5 2.7 - - - +
945A SER* 4.2 3.6 - - - +
946A TYR* 3.9 5.4 - - - +
966A ASN* 3.0 47.8 + - - +
967A ALA* 3.8 4.2 - - - +
968A ASN* 2.7 37.9 + - - +
970A ILE* 4.1 12.8 - - + -
981A ALA* 3.6 32.5 + - - -
982A THR* 4.3 0.2 - - - -
983A GLN 3.9 5.1 - - - +
1108A ALA 3.1 25.3 + - - -
1109A GLY 3.0 17.9 + - - -
1141A LEU 3.1 5.6 + - - +
1142A ARG* 3.3 20.5 + - - -
1144A GLN* 1.3 80.5 - - - +
1146A VAL* 1.3 77.8 + - + +
1147A ASN 3.5 0.2 + - - -
1148A LEU* 3.7 12.6 + - + +
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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