Contacts of the strand formed by residues 1156 - 1163 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1010D ILE* 3.7 14.6 - - + -
1011D ALA 3.5 1.8 - - - +
1012D VAL* 4.2 10.5 - - + -
1052D CYS* 3.0 7.8 - - - +
1053D PHE* 2.7 47.5 + - + +
1056D ILE* 3.4 21.3 - - + -
1142D MET* 3.6 42.2 - - + +
1145D PHE* 3.8 31.9 - - + -
1152D THR* 4.7 5.3 + - + -
1154D LYS 3.8 12.3 + - - +
1155D LYS* 1.3 80.8 - - - +
1157D THR* 1.3 60.9 + - - +
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Residues in contact with THR1157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010D ILE* 3.3 10.2 - - - +
1011D ALA* 2.9 42.2 + - - -
1013D ASP* 5.4 1.7 + - - -
1014D GLY 5.6 2.4 + - - -
1050D GLY* 3.2 22.7 - - - +
1051D SER 3.2 14.4 - - - +
1052D CYS* 4.1 6.1 - - + +
1053D PHE* 5.1 0.9 - - - -
1155D LYS* 4.6 7.8 - - - +
1156D ILE* 1.3 79.6 + - - +
1158D ILE* 1.3 78.7 + - - +
1159D ALA* 3.3 3.7 + - - +
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Residues in contact with ILE1158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008D PHE* 3.5 53.4 - - + -
1009D ASP 3.6 3.8 - - - -
1010D ILE* 4.2 2.5 - - + -
1048D TYR* 3.8 22.7 - - + +
1049D LYS 4.0 0.3 - - - -
1050D GLY* 3.0 23.2 + - - -
1051D SER* 2.9 21.6 + - - +
1052D CYS 6.0 0.2 - - - +
1053D PHE* 3.9 24.0 - - + -
1065D GLY 5.9 0.2 - - - +
1112D PHE* 4.4 6.3 - - + -
1157D THR* 1.3 69.3 - - - +
1159D ALA* 1.3 62.2 - - - +
1160D ASP 3.1 22.4 + - - +
1161D CYS* 3.8 13.0 - - - -
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Residues in contact with ALA1159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009D ASP* 2.5 26.8 + - + +
1010D ILE 4.8 0.4 - - - -
1011D ALA* 4.1 20.2 - - + -
1014D GLY 6.0 0.2 - - - +
1016D PRO* 6.4 1.8 - - + -
1049D LYS* 3.3 17.0 + - - +
1050D GLY* 5.1 0.9 + - - -
1157D THR* 3.3 7.4 + - - -
1158D ILE* 1.3 72.8 - - - +
1160D ASP* 1.3 59.5 + - + +
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Residues in contact with ASP1160 (chain D).
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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1007D PHE* 5.1 2.0 - - + -
1009D ASP* 3.2 35.6 + - + +
1049D LYS* 2.9 33.7 + - - +
1158D ILE* 3.1 13.8 - - - +
1159D ALA* 1.3 76.6 - - + +
1161D CYS* 1.3 91.7 + - - +
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Residues in contact with CYS1161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007D PHE* 3.3 24.6 - - - +
1008D PHE* 3.9 10.3 - - + -
1039D LEU 5.1 0.2 - - - -
1040D SER* 2.9 30.3 - - - +
1041D THR* 4.3 6.8 - - - +
1048D TYR* 4.0 3.4 - - - -
1049D LYS* 3.4 41.4 - - - +
1158D ILE* 3.8 6.3 - - - -
1160D ASP* 1.3 94.0 + - - +
1162D GLY* 1.3 59.1 + - - +
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Residues in contact with GLY1162 (chain D).
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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1006D VAL* 3.3 5.7 - - - +
1007D PHE* 3.1 45.1 + - - -
1040D SER 3.1 10.7 + - - +
1041D THR* 4.0 10.5 - - - -
1161D CYS* 1.3 75.4 - - - +
1163D GLN* 1.3 60.2 + - - -
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Residues in contact with GLN1163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004D PRO* 3.5 23.8 - - - +
1005D THR 3.0 20.4 - - - +
1006D VAL* 4.0 10.3 - - + +
1037D ARG* 3.6 27.0 + - - +
1041D THR* 3.9 14.1 - - + +
1162D GLY* 1.3 73.0 - - - -
1164D LEU* 1.3 67.1 + - - +
1165D GLU* 2.9 26.7 + - - +
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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