Contacts of the strand formed by residues 1156 - 1163 (chain F) in PDB entry 1AWV
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 ILE1156 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1010F ILE* 4.1 14.1 - - + -
1011F ALA 3.7 2.0 - - - +
1012F VAL* 4.2 13.0 - - + -
1052F CYS* 2.9 8.3 - - - +
1053F PHE* 2.9 49.1 + - + +
1056F ILE* 3.7 18.4 - - + -
1142F MET* 3.9 32.8 - - + -
1145F PHE* 3.4 37.5 - - + -
1152F THR* 3.9 15.8 - - + +
1154F LYS 3.6 1.8 + - - +
1155F LYS* 1.3 80.5 - - - +
1157F THR* 1.3 59.2 + - - +
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Residues in contact with THR1157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010F ILE* 3.6 7.9 - - - +
1011F ALA* 2.9 42.5 + - - +
1013F ASP* 5.0 3.3 + - - -
1014F GLY 5.5 1.6 + - - -
1050F GLY* 3.1 32.1 - - - +
1051F SER 3.3 4.0 - - - +
1052F CYS* 4.1 0.4 - - - +
1053F PHE* 5.3 0.9 - - - -
1155F LYS* 3.0 36.6 + - - +
1156F ILE* 1.3 73.4 - - - +
1158F ILE* 1.3 71.7 + - - +
1159F ALA* 3.2 3.4 + - - +
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Residues in contact with ILE1158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008F PHE* 3.8 29.2 - - + -
1009F ASP 3.7 3.1 - - - -
1010F ILE* 4.1 6.7 - - + -
1048F TYR* 3.4 38.1 - - + +
1049F LYS 3.8 0.5 - - - -
1050F GLY* 2.9 24.6 + - - -
1051F SER* 2.8 22.3 + - - +
1052F CYS 5.8 0.4 - - - +
1053F PHE* 3.7 26.2 - - + -
1065F GLY 5.8 0.9 - - - +
1112F PHE* 4.5 4.5 - - + -
1157F THR* 1.3 70.5 - - - +
1159F ALA* 1.3 61.0 + - - +
1160F ASP 3.3 20.8 + - - +
1161F CYS* 3.7 17.5 - - + -
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Residues in contact with ALA1159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009F ASP* 2.7 19.0 + - + +
1010F ILE 4.6 0.9 - - - -
1011F ALA* 3.6 25.8 - - + -
1016F PRO* 6.4 0.4 - - + -
1049F LYS* 3.3 20.0 + - - +
1050F GLY* 4.9 1.4 + - - -
1157F THR* 3.2 7.6 + - - -
1158F ILE* 1.3 73.5 - - - +
1160F ASP* 1.3 59.4 + - + +
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Residues in contact with ASP1160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007F PHE* 5.3 2.9 - - - -
1009F ASP* 2.5 56.1 + - + +
1049F LYS* 3.2 25.8 - - - -
1158F ILE* 3.2 5.3 - - - +
1159F ALA* 1.3 78.1 - - + +
1161F CYS* 1.3 74.8 + - - +
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Residues in contact with CYS1161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007F PHE* 3.1 31.0 - - - +
1008F PHE* 3.4 15.0 - - + -
1040F SER* 3.0 31.6 - - - +
1041F THR* 4.6 2.1 - - - -
1048F TYR* 3.9 4.9 - - - -
1049F LYS* 3.4 39.5 - - - +
1158F ILE* 3.7 6.7 - - + -
1160F ASP* 1.3 88.8 + - - +
1162F GLY* 1.3 56.8 + - - +
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Residues in contact with GLY1162 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1006F VAL* 3.3 2.0 - - - -
1007F PHE* 2.7 54.9 + - - -
1040F SER* 3.3 10.3 + - - -
1041F THR* 3.7 15.3 - - - -
1161F CYS* 1.3 75.1 - - - +
1163F GLN* 1.3 58.4 + - - -
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Residues in contact with GLN1163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004F PRO* 3.8 11.3 - - - +
1005F THR 3.3 7.6 - - - +
1006F VAL* 3.9 8.5 - - + +
1007F PHE* 4.2 0.9 - - - -
1037F ARG* 3.2 41.8 + - - +
1041F THR* 3.3 18.2 - - + +
1162F GLY* 1.3 72.8 - - - -
1164F LEU* 1.3 70.1 + - - +
1165F GLU* 2.8 34.0 + - - +
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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