Contacts of the helix formed by residues 1151 - 1168 (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 THR1151 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502B EDO 4.8 2.9 + - - +
915B TYR* 3.3 14.8 - - - -
1149B VAL* 4.3 0.5 - - - +
1150B GLN* 1.3 86.7 - - + +
1152B GLU* 1.3 66.4 + - - +
1153B GLU* 3.5 9.8 + - - +
1154B GLN* 3.0 40.4 + - - +
1155B TYR* 3.0 17.3 + - - +
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Residues in contact with GLU1152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908B GLY* 4.6 3.5 - - - +
911B PHE* 4.5 8.3 - - - +
912B LYS* 3.9 36.7 + - - +
915B TYR* 3.6 39.9 - - + -
916B GLU* 5.3 1.0 - - - +
1151B THR* 1.3 75.1 - - - +
1153B GLU* 1.3 63.6 + - - +
1155B TYR* 3.1 4.8 + - + +
1156B VAL* 3.0 30.5 + - + +
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Residues in contact with GLU1153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B EDO 5.0 1.6 + - - -
1076B GLY* 3.4 31.7 - - - -
1077B VAL* 3.6 24.8 + - + +
1151B THR* 3.8 8.7 + - - +
1152B GLU* 1.3 80.0 - - - +
1154B GLN* 1.3 57.6 + - - +
1156B VAL* 3.3 8.1 + - - +
1157B PHE* 2.9 28.1 + - - +
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Residues in contact with GLN1154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B EDO 3.0 45.8 + - - +
1072B TRP* 4.5 1.3 - - + -
1077B VAL* 3.9 11.0 - - + -
1111B GLY* 3.1 28.1 - - - +
1112B ARG* 4.1 0.4 - - - +
1115B CYS* 3.5 17.3 - - - -
1149B VAL* 3.9 4.9 - - + -
1150B GLN* 2.8 34.1 + - - +
1151B THR* 3.0 31.2 + - - +
1153B GLU* 1.3 75.2 - - - +
1155B TYR* 1.3 59.6 + - - +
1157B PHE* 3.2 3.5 + - - +
1158B VAL* 2.9 33.4 + - - +
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Residues in contact with TYR1155 (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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911B PHE* 4.1 17.7 - + - -
914B GLU* 2.5 40.3 + - + +
915B TYR* 3.5 34.3 - + + -
918B LEU* 3.8 26.2 - - + -
1134B ILE* 4.2 4.3 - - + -
1135B PHE* 3.3 21.2 + - - +
1138B VAL* 4.0 26.2 - - + -
1149B VAL* 3.6 10.3 - - + +
1151B THR 3.0 6.9 + - - +
1152B GLU* 3.1 9.8 + - + +
1154B GLN* 1.3 74.4 - - - +
1156B VAL* 1.3 61.0 + - + +
1158B VAL* 3.3 12.0 + - + +
1159B HIS* 2.9 43.8 + + - -
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Residues in contact with VAL1156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904B LYS* 4.2 10.8 - - + -
911B PHE* 3.6 50.9 - - + -
1152B GLU* 3.0 22.6 + - + +
1153B GLU* 3.8 8.3 - - - +
1154B GLN 3.2 0.2 - - - -
1155B TYR* 1.3 76.4 - - + +
1157B PHE* 1.3 63.2 + - - +
1159B HIS* 3.0 10.2 + - - +
1160B ASP* 2.9 33.9 + - - +
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Residues in contact with PHE1157 (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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1072B TRP* 4.0 23.3 - + - -
1077B VAL* 4.0 19.7 - - + -
1078B PRO* 3.7 44.0 - - + -
1080B TYR 4.2 1.3 - - - -
1081B ALA* 4.1 30.3 - - + -
1084B LEU* 3.6 30.5 - - + -
1115B CYS* 4.8 4.0 - - - -
1119B ILE* 4.1 11.2 - - + -
1153B GLU 2.9 17.6 + - - +
1154B GLN 3.2 6.3 + - - +
1156B VAL* 1.3 76.9 - - - +
1158B VAL* 1.3 56.3 + - - +
1160B ASP* 3.2 12.3 + - + +
1161B ALA* 2.8 31.6 + - + +
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Residues in contact with VAL1158 (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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1115B CYS* 3.8 38.1 - - + +
1118B ALA* 4.0 20.2 - - + +
1119B ILE* 4.2 12.6 - - + -
1134B ILE* 3.9 20.2 - - + -
1138B VAL* 5.5 0.7 - - + -
1149B VAL* 4.5 8.1 - - + -
1154B GLN 2.9 19.1 + - - +
1155B TYR* 3.6 10.1 - - + +
1156B VAL 3.2 0.2 - - - -
1157B PHE* 1.3 74.6 - - + +
1159B HIS* 1.3 63.3 + - - +
1161B ALA* 3.8 1.2 - - - +
1162B ILE* 3.1 48.1 + - + +
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Residues in contact with HIS1159 (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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896B LEU* 5.0 1.0 - - + +
899B HIS* 4.6 14.7 + + - -
900B ILE* 3.6 22.8 - - + +
911B PHE* 3.5 33.2 - + + -
914B GLU* 4.3 7.9 + - - -
1134B ILE* 3.4 48.0 - - + +
1155B TYR* 2.9 50.7 + + - -
1156B VAL 3.0 8.4 + - - +
1158B VAL* 1.3 76.6 - - - +
1160B ASP* 1.3 58.6 + - - +
1162B ILE* 3.3 2.3 + - - +
1163B LEU* 2.9 30.7 + - - +
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Residues in contact with ASP1160 (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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900B ILE* 4.2 6.6 - - - +
904B LYS* 3.0 31.2 + - - -
1081B ALA* 4.7 3.3 - - + +
1156B VAL* 2.9 30.1 + - - +
1157B PHE* 3.6 16.7 - - + +
1159B HIS* 1.3 74.6 - - - +
1161B ALA* 1.3 56.8 + - - +
1163B LEU* 3.5 10.2 + - - +
1164B GLU* 3.0 28.2 + - - +
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Residues in contact with ALA1161 (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* 3.6 26.6 - - + +
1084B LEU* 5.6 1.1 - - + -
1085B LEU* 3.5 19.1 - - + +
1119B ILE* 3.8 26.7 - - + -
1157B PHE* 2.8 25.1 + - + +
1158B VAL 3.8 1.6 - - - +
1160B ASP* 1.3 70.6 - - - +
1162B ILE* 1.3 65.8 + - - +
1164B GLU 3.2 1.6 + - - -
1165B ALA* 3.0 19.9 + - - +
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Residues in contact with ILE1162 (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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896B LEU* 3.9 19.1 - - + -
1118B ALA 4.4 1.6 - - - +
1119B ILE* 4.4 13.7 - - + -
1122B MET* 3.2 40.8 - - + +
1123B LEU* 4.6 13.7 - - + -
1126B ALA* 5.5 0.4 - - + -
1132B VAL* 4.1 19.5 - - + -
1134B ILE* 3.7 17.0 - - + -
1158B VAL* 3.1 31.5 + - + +
1159B HIS 3.8 2.9 - - - +
1161B ALA* 1.3 75.2 - - - +
1163B LEU* 1.3 65.1 + - - +
1165B ALA* 3.1 9.4 + - - +
1166B CYS* 2.9 26.0 + - - -
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Residues in contact with LEU1163 (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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893B VAL 5.7 0.9 - - - +
896B LEU* 3.9 16.0 - - + +
897B LEU* 3.7 52.9 - - + +
900B ILE* 3.8 24.5 - - + -
904B LYS* 6.1 0.4 - - - +
1159B HIS 2.9 17.2 + - - +
1160B ASP* 3.7 9.9 - - - +
1162B ILE* 1.3 76.0 - - - +
1164B GLU* 1.3 66.3 + - - +
1166B CYS* 2.9 8.2 + - + +
1167B LEU* 2.9 46.1 + - + +
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Residues in contact with GLU1164 (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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1080B TYR* 5.4 0.3 - - - +
1081B ALA* 3.6 18.9 + - + +
1082B THR* 2.7 40.1 + - - +
1085B LEU* 3.7 14.1 - - + +
1160B ASP 3.0 15.6 + - - +
1161B ALA 3.2 6.9 + - - +
1163B LEU* 1.3 77.4 - - - +
1165B ALA* 1.3 63.4 + - - +
1167B LEU* 3.0 22.9 + - + +
1168B CYS* 3.0 33.5 + - - -
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Residues in contact with ALA1165 (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* 3.8 17.0 - - + +
1123B LEU* 3.3 35.4 - - + -
1161B ALA 3.0 12.1 + - - +
1162B ILE 3.4 4.9 - - - +
1164B GLU* 1.3 79.2 - - - +
1166B CYS* 1.3 62.2 + - - +
1167B LEU 3.4 0.2 + - - -
1168B CYS* 3.7 16.1 + - - +
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Residues in contact with CYS1166 (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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893B VAL* 3.6 46.4 - - + +
896B LEU* 4.3 7.2 - - + -
1123B LEU* 5.5 1.3 - - - -
1126B ALA* 4.4 10.5 - - - -
1162B ILE* 2.9 31.3 + - - +
1163B LEU* 2.9 12.7 + - + +
1165B ALA* 1.3 79.8 - - - +
1167B LEU* 1.3 64.4 + - - +
1168B CYS 4.8 0.9 - - - +
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Residues in contact with LEU1167 (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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897B LEU* 5.5 12.6 - - + -
1163B LEU* 2.9 43.6 + - + +
1164B GLU* 3.0 14.1 + - + +
1166B CYS* 1.3 81.0 - - - +
1168B CYS* 1.3 67.8 + - - +
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Residues in contact with CYS1168 (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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1164B GLU* 3.0 41.8 + - - +
1165B ALA* 3.7 12.2 + - - +
1166B CYS 3.6 1.7 - - - +
1167B LEU* 1.3 86.6 - - - +
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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