Contacts of the strand formed by residues 932 - 936 (chain A) in PDB entry 1WXR
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 ALA 932 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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907A THR 3.0 7.6 + - - +
908A ILE* 3.4 9.7 - - + -
909A VAL* 2.9 28.0 + - - +
931A SER* 1.3 75.2 - - - +
933A PHE* 1.3 68.3 + - - +
957A SER* 3.3 15.9 - - - +
959A TRP* 3.8 23.1 - - + +
1043A PHE* 3.7 22.2 - - + -
1047A VAL* 5.3 1.1 - - + -
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Residues in contact with PHE 933 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902A MET* 5.8 0.2 - - - -
904A LEU* 3.5 26.5 - - + -
909A VAL* 3.4 36.6 - - + +
911A PHE* 4.3 9.4 - + + -
921A LEU* 4.8 6.5 - - + -
926A LEU* 4.3 11.2 - - + -
928A ALA* 5.0 5.8 - - + -
931A SER* 5.1 0.9 - - - -
932A ALA* 1.3 80.0 - - - +
934A VAL* 1.3 62.9 + - - +
935A MET* 3.6 20.5 + - - +
945A LEU* 3.6 32.3 - - + -
956A ASN* 5.0 3.6 - - + -
957A SER 3.0 12.0 + - - +
958A ILE* 3.6 6.1 - - + -
959A TRP* 2.9 29.4 + - - +
988A PHE* 3.7 30.7 - + - -
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Residues in contact with VAL 934 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908A ILE* 3.7 30.5 - - + -
909A VAL 2.9 9.7 + - - +
910A GLY* 4.0 0.2 - - - -
911A PHE* 3.2 30.2 + - - +
933A PHE* 1.3 72.4 - - - +
935A MET* 1.3 64.1 + - - +
936A ARG* 5.1 2.1 - - + +
959A TRP* 3.9 9.9 - - + -
961A ASN* 4.8 5.6 - - + -
995A VAL* 3.7 37.9 - - + -
1035A PHE* 3.8 25.7 - - + +
1038A ILE* 3.8 13.2 - - + -
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Residues in contact with MET 935 (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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911A PHE* 3.7 11.4 - - + -
933A PHE* 3.7 27.1 - - - +
934A VAL* 1.3 75.3 - - - +
936A ARG* 1.3 56.0 + - - +
943A ASP* 3.5 31.9 - - + +
944A LYS* 3.7 9.6 - - - +
945A LEU* 3.8 7.9 - - + +
958A ILE* 3.7 17.0 - - + -
959A TRP 3.1 13.4 + - - +
960A VAL* 3.2 7.5 - - + -
961A ASN* 2.7 31.0 + - - +
976A LEU* 2.7 48.5 - - + +
977A VAL* 4.6 4.3 - - + -
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Residues in contact with ARG 936 (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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911A PHE 3.4 19.9 + - - +
912A ASN* 3.9 8.2 + - - +
913A GLY 3.4 27.9 + - - +
918A PHE 3.8 7.4 - - - +
919A THR* 2.9 39.4 - - - +
934A VAL* 5.1 2.7 - - + +
935A MET* 1.3 76.1 - - - +
937A THR* 1.3 69.0 + - - +
942A ALA* 3.2 3.5 - - - +
943A ASP* 2.6 53.8 + - - +
960A VAL* 5.2 1.3 - - - -
961A ASN* 3.3 24.7 - - + +
963A LEU* 3.8 27.0 - - + +
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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
------------------------------------------------------------
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