Contacts of the helix formed by residues 1163 - 1177 (chain B) in PDB entry 5J67
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 SER1163 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1161B TYR 3.1 2.5 + - - +
1162B THR* 1.3 81.4 - - - +
1164B GLY* 1.3 58.3 + - - +
1165B LYS* 3.1 30.1 + - - +
1166B GLU* 3.3 29.9 + - - +
1167B GLN* 3.2 28.6 + - - +
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Residues in contact with GLY1164 (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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1162B THR 3.5 3.0 + - - -
1163B SER* 1.3 70.4 + - - +
1165B LYS* 1.3 59.4 + - - +
1167B GLN* 3.6 18.0 - - - +
1168B GLN* 3.1 28.2 + - - +
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Residues in contact with LYS1165 (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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1163B SER* 3.1 11.2 + - - +
1164B GLY* 1.3 75.1 - - - +
1166B GLU* 1.3 56.9 + - + +
1168B GLN* 3.3 4.2 + - - +
1169B MET* 2.7 49.5 + - + +
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Residues in contact with GLU1166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1156B ASN 4.4 1.2 - - - +
1157B LEU* 3.5 48.1 - - + +
1160B GLY* 3.7 30.6 - - - +
1161B TYR 3.9 2.9 - - - +
1163B SER* 3.3 35.6 + - - +
1165B LYS* 1.3 79.7 - - + +
1167B GLN* 1.3 56.7 + - - +
1169B MET* 4.6 5.1 - - + +
1170B ALA* 2.8 34.2 + - - +
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Residues in contact with GLN1167 (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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1161B TYR 4.4 12.3 + - - +
1162B THR 4.8 3.8 + - - +
1163B SER 3.2 13.5 + - - +
1164B GLY* 3.6 17.9 + - - +
1165B LYS 3.3 0.2 - - - -
1166B GLU* 1.3 79.4 - - - +
1168B GLN* 1.3 61.8 + - - +
1170B ALA* 4.5 0.7 - - - -
1171B TYR* 3.2 20.4 + - - +
1206B GLU* 2.8 32.1 + - + +
1207B LEU* 3.2 24.5 - - + +
1211B LYS* 5.3 3.6 - - - +
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Residues in contact with GLN1168 (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 GLY 3.1 19.6 + - - +
1165B LYS* 3.8 4.9 - - - +
1167B GLN* 1.3 75.3 - - - +
1169B MET* 1.3 54.1 + - - +
1171B TYR* 3.2 9.4 + - - +
1172B ASN* 2.8 62.0 + - - +
1211B LYS* 3.8 25.9 + - - +
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Residues in contact with MET1169 (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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1153B LYS* 3.4 28.2 - - - +
1157B LEU* 4.6 9.0 - - + -
1165B LYS* 2.7 33.6 + - + +
1166B GLU* 4.0 6.7 - - + +
1168B GLN* 1.3 69.7 - - - +
1170B ALA* 1.3 59.6 + - - +
1172B ASN* 4.0 9.4 - - + -
1173B THR* 3.0 35.9 + - + +
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Residues in contact with ALA1170 (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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1154B ILE* 3.6 19.2 - - + +
1157B LEU* 3.8 15.6 - - + +
1158B TYR* 4.1 22.2 - - + -
1166B GLU 2.8 20.1 + - - +
1167B GLN* 3.8 5.2 - - - +
1169B MET* 1.3 76.3 - - - +
1171B TYR* 1.3 62.6 + - - +
1173B THR* 3.1 13.3 + - - -
1174B LEU* 3.2 20.8 + - - +
1207B LEU* 4.3 4.3 - - + -
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Residues in contact with TYR1171 (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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1167B GLN 3.2 12.4 + - - +
1168B GLN* 3.5 12.3 - - - +
1170B ALA* 1.3 80.2 - - - +
1172B ASN* 1.3 76.5 + - - +
1174B LEU* 3.6 3.3 + - - +
1175B MET* 3.1 65.9 + - + +
1207B LEU* 4.4 9.7 - - + +
1211B LYS* 3.7 66.9 - - + -
1214B LEU* 3.1 24.8 - - + +
1215B ILE* 4.4 8.1 - - + -
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Residues in contact with ASN1172 (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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1168B GLN* 2.8 56.2 + - - +
1169B MET* 3.9 9.2 + - + +
1170B ALA 3.3 0.4 - - - -
1171B TYR* 1.3 81.7 - - - +
1173B THR* 1.3 56.9 + - + +
1175B MET* 3.3 3.8 + - - +
1176B GLU* 2.7 58.3 + - - +
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Residues in contact with THR1173 (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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1150B ILE* 5.1 14.2 - - - +
1153B LYS* 3.8 27.6 - - - +
1154B ILE* 3.7 14.0 - - - +
1169B MET* 3.0 28.4 + - + +
1170B ALA* 3.1 8.8 + - - -
1172B ASN* 1.3 75.7 - - + +
1174B LEU* 1.3 60.8 + - - +
1176B GLU* 3.6 18.4 + - - +
1177B VAL* 3.6 17.5 + - - +
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Residues in contact with LEU1174 (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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1150B ILE* 4.2 6.7 - - + -
1154B ILE* 3.7 25.4 - - + -
1158B TYR* 3.9 16.6 - - - +
1170B ALA 3.2 20.0 + - - +
1171B TYR* 4.0 3.6 - - - +
1173B THR* 1.3 82.9 + - - +
1175B MET* 1.3 60.7 + - - +
1177B VAL* 3.8 15.9 - - + +
1182B LEU* 3.6 36.4 - - + +
1185B VAL* 3.8 19.7 - - + -
1199B PHE* 3.8 22.2 - - + -
1207B LEU* 4.9 0.4 - - + -
1215B ILE* 3.9 26.5 - - + -
1218B ARG* 4.1 3.5 + - - -
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Residues in contact with MET1175 (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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1171B TYR* 3.1 59.3 + - + +
1172B ASN* 3.9 3.4 - - - +
1174B LEU* 1.3 77.5 - - - +
1176B GLU* 1.3 66.1 + - - +
1177B VAL 3.3 1.7 + - - +
1182B LEU* 4.7 2.2 - - + -
1214B LEU* 3.9 14.1 - - - +
1215B ILE* 3.7 37.0 - - + -
1218B ARG* 2.9 58.4 + - + +
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Residues in contact with GLU1176 (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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1172B ASN* 2.7 45.3 + - - +
1173B THR* 4.0 14.4 - - - +
1174B LEU 3.5 0.4 - - - -
1175B MET* 1.3 73.5 - - + +
1177B VAL* 1.3 56.8 + - + +
1178B SER 4.3 0.3 + - - -
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Residues in contact with VAL1177 (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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1146B LYS* 6.0 1.1 - - + -
1150B ILE* 4.8 15.3 - - + -
1173B THR 3.6 11.1 + - - +
1174B LEU* 3.8 17.6 - - + +
1175B MET 3.5 10.6 - - - +
1176B GLU* 1.3 79.3 - - + +
1178B SER* 1.3 69.7 + - - +
1181B MET* 3.4 44.0 - - + -
1182B LEU* 4.1 9.1 - - + +
1185B VAL* 5.3 2.7 - - + -
1218B ARG* 3.5 9.2 + - - -
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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