Contacts of the strand formed by residues 1005 - 1012 (chain B) 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 THR1005 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1003B ASN 3.5 8.7 + - - -
1004B PRO* 1.3 72.3 - - - +
1006B VAL* 1.3 65.4 + - - +
1021B SER* 4.5 7.0 - - - -
1022B PHE 3.2 9.2 - - - +
1133B LYS* 2.6 38.9 + - + +
1163B GLN* 2.9 8.0 - - - +
1164B LEU* 2.8 39.4 + - + -
1165B GLU* 2.5 37.7 + - + +
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Residues in contact with VAL1006 (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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1004B PRO 4.2 0.2 - - - -
1005B THR* 1.3 79.3 - - - +
1007B PHE* 1.3 59.8 + - - +
1008B PHE* 5.6 0.2 - - + -
1021B SER* 3.2 6.5 - - - -
1022B PHE* 2.6 46.3 + - + +
1024B LEU* 3.5 31.9 - - + -
1036B PHE* 3.7 31.6 - - + +
1037B ARG* 4.3 12.1 - - + +
1040B SER* 4.4 13.5 - - - +
1041B THR* 5.3 0.7 - - + -
1162B GLY 3.2 12.3 - - - +
1163B GLN* 4.0 17.7 - - + -
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Residues in contact with PHE1007 (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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1006B VAL* 1.3 80.6 - - - +
1008B PHE* 1.3 80.1 + - - +
1009B ASP* 3.0 28.3 - - - -
1019B ARG* 3.8 29.6 - - - -
1020B VAL 3.1 13.2 - - - +
1021B SER* 3.8 10.3 - - - +
1022B PHE* 4.0 2.5 - - - -
1160B ASP* 5.3 1.8 - - + -
1161B CYS* 3.4 23.1 - - - +
1162B GLY* 3.0 43.5 + - - -
1164B LEU* 3.4 41.7 - - + -
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Residues in contact with PHE1008 (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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1006B VAL* 5.6 0.2 - - + -
1007B PHE* 1.3 90.1 - - - +
1009B ASP* 1.3 60.0 + - - +
1010B ILE* 3.8 10.3 - - + -
1019B ARG* 3.4 2.6 - - - +
1020B VAL* 2.7 47.6 + - + +
1022B PHE* 3.3 28.7 - + - -
1036B PHE* 3.6 20.6 - + - -
1040B SER* 3.6 20.4 - - - -
1048B TYR* 4.1 13.0 - + - -
1053B PHE* 4.5 9.4 - + - -
1112B PHE* 3.6 22.7 - + - -
1158B ILE* 3.6 42.0 - - + -
1160B ASP 3.6 3.6 - - - -
1161B CYS* 3.9 7.0 - - + -
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Residues in contact with ASP1009 (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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1007B PHE* 3.0 29.7 - - - -
1008B PHE* 1.3 70.1 - - - +
1010B ILE* 1.3 59.5 + - - +
1016B PRO* 6.6 0.2 - - + -
1018B GLY 4.0 3.6 - - - +
1019B ARG* 3.4 31.6 + - - +
1158B ILE* 3.6 1.4 - - - +
1159B ALA* 2.8 42.0 + - + +
1160B ASP* 3.3 27.4 + - + +
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Residues in contact with ILE1010 (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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1008B PHE* 3.8 21.5 - - + -
1009B ASP* 1.3 73.8 - - - +
1011B ALA* 1.3 66.4 + - - +
1016B PRO* 3.5 5.1 - - - +
1017B LEU* 2.8 36.6 + - + -
1018B GLY 2.9 20.1 + - - +
1020B VAL* 3.9 19.1 - - + -
1053B PHE* 4.1 24.2 - - + -
1138B ILE* 4.5 7.0 - - + -
1139B VAL* 6.3 0.2 - - + -
1142B MET* 3.8 21.8 - - + -
1156B ILE* 3.7 25.6 - - + -
1157B THR 3.6 10.1 - - - +
1158B ILE* 4.4 2.7 - - + -
1159B ALA* 5.0 0.4 - - - -
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Residues in contact with ALA1011 (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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1009B ASP 3.8 0.2 + - - -
1010B ILE* 1.3 75.8 - - - +
1012B VAL* 1.3 62.5 + - - +
1013B ASP 3.7 0.7 - - - -
1014B GLY* 3.4 24.5 - - - +
1015B GLU 3.0 17.7 - - - +
1016B PRO* 4.1 2.7 - - + -
1155B LYS 3.4 3.5 - - - +
1156B ILE* 3.4 3.8 - - - -
1157B THR* 3.0 42.1 + - - +
1159B ALA* 4.3 15.3 - - + -
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Residues in contact with VAL1012 (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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1010B ILE* 5.1 1.1 - - + -
1011B ALA* 1.3 73.0 - - - +
1013B ASP* 1.3 67.7 + - - +
1015B GLU* 2.7 39.5 + - - +
1017B LEU* 3.6 43.7 - - + +
1145B PHE* 4.0 18.4 - - + -
1154B LYS* 3.6 36.5 + - + +
1155B LYS 3.7 2.7 - - - -
1156B ILE* 4.1 11.7 - - + -
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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