Contacts of the strand formed by residues 956 - 961 (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 ASN 956 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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928A ALA* 2.9 42.3 + - - +
930A GLN 3.3 7.4 + - - -
931A SER* 2.9 38.2 + - - +
933A PHE* 5.0 2.0 - - + -
954A HIS 3.8 1.6 + - - -
955A ASP* 1.3 75.8 - - - +
957A SER* 1.3 60.9 + - - +
986A ASN 5.2 0.4 + - - +
987A LEU* 3.2 34.7 + - - +
988A PHE* 3.3 21.6 - - + -
989A ARG* 3.1 26.9 + - - +
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Residues in contact with SER 957 (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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931A SER 3.1 6.0 + - - -
932A ALA* 3.3 8.1 - - - +
933A PHE* 3.0 26.9 + - - -
955A ASP 4.2 0.7 + - - -
956A ASN* 1.3 73.6 - - - +
958A ILE* 1.3 64.1 + - - +
959A TRP* 4.0 10.1 - - - -
989A ARG* 3.3 23.4 + - - -
991A SER* 4.3 6.5 - - - -
1046A GLU* 2.2 34.6 + - - -
1047A VAL* 4.5 7.4 - - - +
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Residues in contact with ILE 958 (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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933A PHE* 3.6 9.9 - - + +
935A MET* 3.7 22.2 - - + -
957A SER* 1.3 74.5 - - - +
959A TRP* 1.3 71.0 + - - +
960A VAL* 4.5 1.3 - - + -
976A LEU* 4.1 20.9 - - + -
977A VAL* 4.3 13.9 - - + -
988A PHE* 3.0 48.2 - - + -
989A ARG 2.7 19.9 + - - +
990A ALA* 3.7 1.0 - - - -
991A SER* 2.7 25.7 + - - -
1002A PRO* 3.6 8.5 - - - +
1004A LEU* 4.0 20.6 - - + -
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Residues in contact with TRP 959 (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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908A ILE* 4.7 1.8 - - + +
932A ALA* 3.8 28.8 - - + +
933A PHE 2.9 13.3 + - - +
934A VAL* 3.9 13.9 - - + -
935A MET* 3.1 24.5 + - - +
957A SER* 4.3 3.6 - - - -
958A ILE* 1.3 75.3 - - - +
960A VAL* 1.3 68.3 + - - +
991A SER* 3.2 19.7 + - - -
993A ARG* 3.6 27.6 - - + -
994A VAL 3.6 19.3 - - - -
995A VAL* 3.0 37.9 - - + -
1032A ALA* 5.5 0.2 - - + -
1038A ILE* 3.7 30.7 - - + -
1042A ASN* 3.4 29.6 - - - -
1043A PHE* 4.5 5.9 - - - -
1046A GLU* 3.4 28.6 - - + +
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Residues in contact with VAL 960 (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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935A MET* 3.2 7.4 - - + +
937A THR* 4.8 8.7 - - - +
958A ILE* 4.5 2.5 - - + -
959A TRP* 1.3 81.5 - - - +
961A ASN* 1.3 66.6 + - - +
962A PHE* 3.5 55.1 + - + -
976A LEU* 3.5 30.7 - - + -
994A VAL* 5.8 0.3 - - - +
995A VAL* 3.9 16.3 + - - +
996A GLY 4.6 1.0 + - - -
1000A VAL 5.0 1.7 - - - +
1002A PRO* 3.7 28.2 - - + +
1017A LEU* 4.3 7.9 - - + -
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Residues in contact with ASN 961 (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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934A VAL* 4.8 4.5 - - + +
935A MET 2.7 13.3 + - - +
936A ARG* 3.3 16.6 - - + +
937A THR 2.7 31.7 + - - -
959A TRP 4.2 0.4 - - - -
960A VAL* 1.3 70.7 - - - +
962A PHE* 1.3 66.4 + - - +
963A LEU* 3.2 19.2 + - - +
995A VAL* 4.4 14.0 - - + +
996A GLY* 3.0 36.5 - - - +
997A PHE* 4.3 1.4 - - - +
1033A ALA 4.5 7.3 - - - +
1034A THR* 5.0 6.1 + - - -
1035A PHE 5.1 1.2 + - - -
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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