Contacts of the strand formed by residues 1005 - 1012 (chain A) in PDB entry 1AWS
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1003A ASN 3.7 6.9 + - - -
1004A PRO* 1.3 77.3 + - - +
1006A VAL* 1.3 67.4 + - - +
1021A SER* 4.3 11.2 - - - +
1022A PHE 3.1 15.7 + - - +
1023A GLU* 4.6 1.7 - - - +
1133A LYS* 3.9 30.3 + - + +
1163A GLN* 3.6 5.0 - - - +
1164A LEU* 3.1 35.1 + - + -
1165A GLU* 3.2 29.0 + - + +
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Residues in contact with VAL1006 (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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1005A THR* 1.3 79.7 - - - +
1007A PHE* 1.3 61.5 + - - +
1008A PHE* 5.5 0.7 - - + -
1021A SER* 3.1 6.3 - - - -
1022A PHE* 2.7 46.0 + - + -
1024A LEU* 3.7 41.5 - - + -
1036A PHE* 3.9 12.1 - - + -
1037A ARG* 4.0 16.8 - - + +
1040A SER* 3.8 23.1 - - - +
1162A GLY 3.2 13.2 - - - +
1163A GLN* 4.5 4.5 - - + -
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Residues in contact with PHE1007 (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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1006A VAL* 1.3 78.6 - - - +
1008A PHE* 1.3 78.5 + - - +
1009A ASP* 3.7 13.0 - - - -
1019A ARG* 3.5 45.8 - - + +
1020A VAL 3.1 11.7 - - - +
1021A SER* 4.0 11.0 - - - -
1022A PHE* 4.6 0.9 - - - -
1040A SER* 5.1 0.2 - - - -
1160A ASP* 4.4 7.6 - - - -
1161A CYS* 3.2 27.0 - - - +
1162A GLY* 3.1 48.5 + - - -
1163A GLN 4.8 0.2 - - - -
1164A LEU* 3.6 35.9 - - + -
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Residues in contact with PHE1008 (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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1006A VAL* 5.5 0.2 - - + -
1007A PHE* 1.3 89.9 - - - +
1009A ASP* 1.3 62.8 + - - +
1010A ILE* 3.6 17.4 + - + +
1019A ARG* 3.3 3.5 - - - -
1020A VAL* 2.8 37.0 + - + +
1022A PHE* 3.6 29.6 - + + -
1036A PHE* 3.5 24.0 - + - -
1040A SER* 3.9 17.7 - - - -
1048A TYR* 3.9 16.6 - + - -
1053A PHE* 4.1 13.5 - + - -
1112A PHE* 3.5 26.9 - + - -
1114A ILE* 5.1 0.7 - - + -
1158A ILE* 3.8 21.8 - - + -
1160A ASP 3.7 3.6 - - - -
1161A CYS* 3.9 12.8 - - + -
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Residues in contact with ASP1009 (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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1007A PHE* 3.7 8.2 - - - -
1008A PHE* 1.3 71.1 - - - +
1010A ILE* 1.3 58.0 + - - +
1018A GLY 3.1 15.1 - - - +
1019A ARG* 3.5 39.2 + - - +
1158A ILE* 4.4 0.4 - - - +
1159A ALA* 2.7 42.1 + - + +
1160A ASP* 2.8 30.8 + - + +
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Residues in contact with ILE1010 (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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1008A PHE* 3.7 30.7 - - + +
1009A ASP* 1.3 73.3 - - - +
1011A ALA* 1.3 58.0 + - - +
1016A PRO* 4.2 0.4 - - - +
1017A LEU* 2.8 38.7 + - + +
1018A GLY 2.9 17.8 + - - +
1020A VAL* 4.4 13.9 - - + -
1053A PHE* 3.7 24.2 - - + -
1138A ILE* 4.5 8.3 - - + -
1142A MSE 4.0 18.2 - - + -
1156A ILE* 3.6 25.4 - - + -
1157A THR 3.2 15.7 - - - +
1158A ILE* 4.2 3.8 - - - -
1159A ALA* 5.0 0.4 - - - -
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Residues in contact with ALA1011 (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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1009A ASP 3.9 0.2 + - - -
1010A ILE* 1.3 75.4 - - - +
1012A VAL* 1.3 64.2 + - - +
1013A ASP 3.9 0.9 - - - -
1014A GLY* 3.9 22.7 - - - +
1015A GLU 3.5 14.1 - - - +
1016A PRO* 4.0 4.5 - - + -
1017A LEU* 4.0 1.1 - - - +
1155A LYS 3.6 0.9 - - - +
1156A ILE* 3.5 5.9 - - - -
1157A THR* 3.1 36.1 + - - +
1159A ALA* 4.2 18.6 - - + -
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Residues in contact with VAL1012 (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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1011A ALA* 1.3 72.6 - - - +
1013A ASP* 1.3 84.9 + - - +
1015A GLU* 3.1 29.0 + - - +
1017A LEU* 3.4 34.5 - - + -
1145A PHE* 3.5 37.9 - - + -
1154A LYS* 3.8 19.1 - - + +
1155A LYS 3.6 3.1 - - - -
1156A ILE* 3.8 7.6 - - + -
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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