Contacts of the strand formed by residues 889 - 893 (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 THR 889 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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845A LEU* 3.9 25.0 - - + +
869A TYR* 3.7 8.7 - - - -
871A ASN* 3.1 25.1 - - - +
873A TRP 4.7 1.8 - - - +
886A MET* 3.0 35.7 - - + -
887A THR 3.1 14.0 + - - -
888A ASP* 1.3 74.6 - - - +
890A GLN* 1.3 71.1 + - - +
891A TRP* 4.5 0.7 - - - -
906A ARG 3.6 1.6 + - - -
907A THR* 3.2 8.0 - - - -
908A ILE 3.0 24.9 + - - +
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Residues in contact with GLN 890 (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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867A ASN* 5.3 2.5 + - - +
869A TYR* 3.6 21.0 + - + -
871A ASN 2.9 9.5 + - - -
872A ILE* 3.5 29.2 - - + +
873A TRP 3.0 24.3 + - - +
889A THR* 1.3 74.4 - - - +
891A TRP* 1.3 57.7 + - - +
892A SER* 3.7 0.9 + - - -
908A ILE* 3.5 8.4 - - + +
1035A PHE* 3.4 39.2 + - + -
1036A MET* 3.2 37.3 + - + +
1038A ILE 3.2 25.3 + - - -
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Residues in contact with TRP 891 (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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873A TRP* 3.3 34.9 - + + +
875A GLY 2.8 22.9 + - - -
877A LEU* 3.6 40.6 - - + -
884A VAL* 6.1 0.2 - - + -
886A MET* 3.3 33.4 - - + -
889A THR* 3.8 2.9 - - + +
890A GLN* 1.3 70.7 - - - +
892A SER* 1.3 67.2 + - - +
893A MET* 3.5 22.0 + - + +
897A SER* 4.0 15.0 - - - -
902A MET* 3.7 25.8 - - + -
904A LEU* 5.5 0.2 - - + -
908A ILE 2.8 12.8 + - - +
909A VAL* 3.5 24.6 - - + -
910A GLY 2.8 31.2 + - - -
921A LEU* 4.2 11.2 - - + -
1035A PHE* 3.2 3.5 - - - -
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Residues in contact with SER 892 (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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873A TRP 2.7 15.0 + - - -
874A SER* 3.9 14.8 + - - -
875A GLY 3.0 26.7 + - - +
890A GLN 3.7 1.4 + - - -
891A TRP* 1.3 70.8 - - - +
893A MET* 1.3 59.4 + - - +
894A ASN* 3.1 18.5 + - - +
912A ASN* 3.4 15.6 + - - +
1035A PHE* 3.7 20.9 - - - -
1036A MET* 4.3 14.6 - - - +
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Residues in contact with MET 893 (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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875A GLY 3.4 7.2 - - - -
891A TRP* 3.5 17.9 + - + +
892A SER* 1.3 68.4 - - - +
894A ASN* 1.3 60.9 + - - +
895A GLY* 3.3 18.0 + - - +
897A SER* 3.6 20.4 - - - +
909A VAL* 3.3 30.3 - - + -
910A GLY 2.9 11.6 + - - +
911A PHE* 3.4 39.9 - - + -
912A ASN* 2.8 25.3 + - - +
919A THR* 4.2 5.0 + - - +
920A THR 4.4 2.0 - - - +
921A LEU* 3.8 23.6 - - + -
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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