Contacts of the helix formed by residues 1163 - 1177 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1161A TYR 3.1 2.3 + - - +
1162A THR* 1.3 82.2 - - - +
1164A GLY* 1.3 59.1 + - - +
1165A LYS* 3.1 30.3 + - - +
1166A GLU* 3.3 30.3 + - - +
1167A GLN* 3.2 27.4 + - - +
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Residues in contact with GLY1164 (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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1162A THR 3.5 2.4 + - - -
1163A SER* 1.3 71.7 + - - +
1165A LYS* 1.3 58.9 + - - +
1167A GLN* 3.6 17.5 - - - +
1168A GLN* 3.1 27.9 + - - +
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Residues in contact with LYS1165 (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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1163A SER* 3.1 11.2 + - - +
1164A GLY* 1.3 75.1 - - - +
1166A GLU* 1.3 57.2 + - + +
1168A GLN* 3.3 4.6 + - - +
1169A MET* 2.7 49.2 + - + +
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Residues in contact with GLU1166 (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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1156A ASN 4.4 1.2 - - - +
1157A LEU* 3.5 48.5 - - + +
1160A GLY* 3.7 30.0 - - - +
1161A TYR 3.9 2.9 - - - +
1162A THR* 5.1 0.2 - - - -
1163A SER* 3.3 36.1 + - - +
1165A LYS* 1.3 78.8 - - + +
1167A GLN* 1.3 57.6 + - - +
1169A MET* 4.6 6.5 - - + +
1170A ALA* 2.8 33.5 + - - +
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Residues in contact with GLN1167 (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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1161A TYR 4.4 12.0 + - - +
1162A THR 4.9 2.9 + - - +
1163A SER 3.2 14.6 + - - +
1164A GLY* 3.6 18.6 + - - +
1165A LYS 3.3 0.2 - - - -
1166A GLU* 1.3 78.3 - - - +
1168A GLN* 1.3 63.3 + - - +
1170A ALA* 4.5 0.2 - - - -
1171A TYR* 3.2 19.9 + - - +
1206A GLU* 2.8 31.9 + - + +
1207A LEU* 3.2 25.1 - - + +
1211A LYS* 5.3 3.6 - - - +
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Residues in contact with GLN1168 (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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1164A GLY 3.1 19.8 + - - +
1165A LYS* 3.3 5.1 + - - +
1167A GLN* 1.3 74.1 - - - +
1169A MET* 1.3 53.8 + - - +
1171A TYR* 3.2 8.8 + - - +
1172A ASN* 2.8 62.2 + - - +
1211A LYS* 3.8 26.6 + - - +
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Residues in contact with MET1169 (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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1153A LYS* 3.4 27.4 - - - +
1157A LEU* 4.6 9.0 - - + -
1165A LYS* 2.7 31.9 + - + +
1166A GLU* 4.0 7.9 - - + +
1168A GLN* 1.3 70.3 - - - +
1170A ALA* 1.3 62.0 + - - +
1172A ASN* 3.9 9.6 + - + +
1173A THR* 3.0 34.2 + - + +
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Residues in contact with ALA1170 (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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1154A ILE* 3.8 18.6 - - + -
1157A LEU* 3.8 15.1 - - + +
1158A TYR* 4.1 23.3 - - + +
1166A GLU 2.8 20.5 + - - +
1167A GLN* 3.8 5.2 - - - +
1169A MET* 1.3 76.8 - - - +
1171A TYR* 1.3 61.8 + - - +
1173A THR* 3.1 13.3 + - - -
1174A LEU* 3.2 21.3 + - - +
1207A LEU* 4.3 3.4 - - + -
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Residues in contact with TYR1171 (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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1167A GLN 3.2 12.1 + - - +
1168A GLN* 3.2 12.9 + - - +
1170A ALA* 1.3 79.7 - - - +
1172A ASN* 1.3 76.7 + - - +
1174A LEU* 3.6 3.8 + - - +
1175A MET* 3.1 59.6 + - + +
1207A LEU* 4.4 8.9 - - + +
1210A ARG* 4.9 4.5 + - - -
1211A LYS* 3.8 66.6 - - + -
1214A LEU* 3.1 25.8 - - + +
1215A ILE* 4.4 8.1 - - + -
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Residues in contact with ASN1172 (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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1168A GLN* 2.8 56.7 + - - +
1169A MET* 3.9 9.0 + - + +
1171A TYR* 1.3 84.1 - - - +
1173A THR* 1.3 57.0 + - + +
1175A MET* 3.2 4.1 + - - +
1176A GLU* 2.8 58.1 + - - +
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Residues in contact with THR1173 (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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1150A ILE* 5.1 15.3 - - - +
1153A LYS* 3.8 27.0 - - - -
1154A ILE* 3.8 13.5 - - - +
1169A MET* 3.0 27.2 + - + +
1170A ALA* 3.1 9.4 + - - -
1172A ASN* 1.3 77.6 - - + +
1174A LEU* 1.3 61.3 + - - +
1176A GLU* 3.6 18.6 + - - +
1177A VAL* 3.6 18.0 + - - +
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Residues in contact with LEU1174 (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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1150A ILE* 4.2 7.2 - - + -
1154A ILE* 3.7 24.5 - - + -
1158A TYR* 3.9 15.5 - - - +
1170A ALA 3.2 19.8 + - - +
1171A TYR* 4.0 3.8 - - - +
1173A THR* 1.3 82.8 + - - +
1175A MET* 1.3 61.7 + - - +
1177A VAL* 3.8 15.2 - - + +
1182A LEU* 3.6 35.3 - - + +
1185A VAL* 3.8 19.7 - - + -
1199A PHE* 3.8 22.2 - - + -
1207A LEU* 4.9 0.4 - - + -
1215A ILE* 3.9 26.2 - - + -
1218A ARG* 4.1 2.9 + - - -
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Residues in contact with MET1175 (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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1171A TYR* 3.1 59.4 + - + +
1172A ASN* 3.9 3.4 - - - +
1174A LEU* 1.3 77.5 - - - +
1176A GLU* 1.3 65.4 + - + +
1177A VAL 3.3 1.5 + - - +
1182A LEU* 4.7 2.2 - - + -
1214A LEU* 3.9 13.7 - - - +
1215A ILE* 3.7 35.9 - - + -
1218A ARG* 2.9 58.2 + - + +
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Residues in contact with GLU1176 (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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1172A ASN* 2.8 45.5 + - - +
1173A THR* 4.0 13.9 - - - +
1174A LEU 3.5 0.4 - - - -
1175A MET* 1.3 73.9 - - + +
1177A VAL* 1.3 58.2 + - - +
1178A SER 4.3 0.2 + - - -
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Residues in contact with VAL1177 (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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1146A LYS* 6.0 0.4 - - + -
1150A ILE* 4.8 15.0 - - + -
1173A THR 3.6 11.1 + - - +
1174A LEU* 3.8 17.4 - - + +
1175A MET 3.4 10.6 - - - +
1176A GLU* 1.3 79.2 - - - +
1178A SER* 1.3 69.6 + - - +
1181A MET* 3.4 44.4 - - + -
1182A LEU* 4.2 8.6 - - + +
1185A VAL* 5.3 2.7 - - + -
1218A ARG* 3.5 9.7 + - - -
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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