Contacts of the strand formed by residues 877 - 887 (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 LEU 877 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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835A ILE* 3.6 25.1 - - + +
873A TRP* 3.9 13.7 - - + -
876A SER* 1.3 77.5 - - - +
878A ASN* 1.3 74.8 + - - +
879A ALA* 3.6 19.5 - - + -
884A VAL* 4.0 24.0 - - + -
891A TRP* 3.6 20.2 - - + -
897A SER* 2.8 37.2 + - - -
898A THR 2.9 18.6 + - - +
899A ALA* 4.0 1.3 - - + -
902A MET* 3.8 29.8 - - + -
921A LEU* 5.1 0.4 - - + -
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Residues in contact with ASN 878 (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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835A ILE 2.9 8.8 + - - -
836A ASN* 3.5 21.1 - - + +
837A VAL 2.9 26.2 + - - +
876A SER* 4.7 6.2 + - - -
877A LEU* 1.3 78.4 + - - +
879A ALA* 1.3 60.1 + - - +
880A PRO* 3.6 7.6 - - + +
896A ASN 4.1 10.6 + - - +
898A THR* 3.7 20.7 + - - +
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Residues in contact with ALA 879 (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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837A VAL* 3.6 22.0 - - + -
877A LEU* 3.6 16.8 - - + -
878A ASN* 1.3 76.3 - - - +
880A PRO* 1.3 62.1 - - - +
881A ASP 2.9 10.1 + - - -
882A ALA* 2.9 31.3 + - + +
884A VAL* 4.2 6.7 - - + -
898A THR* 2.8 15.4 + - - +
899A ALA* 3.3 0.9 - - - -
900A GLY 3.1 10.4 + - - -
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Residues in contact with PRO 880 (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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837A VAL 3.9 9.4 - - - +
878A ASN* 3.6 8.7 - - + +
879A ALA* 1.3 88.9 - - - +
881A ASP* 1.3 72.8 + - - +
898A THR* 3.5 19.1 - - - +
899A ALA 3.9 3.7 - - - +
900A GLY* 3.1 20.9 - - - +
924A ASP* 4.2 8.7 - - - +
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Residues in contact with ASP 881 (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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837A VAL 5.3 0.4 + - - -
839A ASP* 3.6 24.3 + - - +
840A LYS* 3.2 31.7 - - + +
879A ALA 3.1 0.8 - - - -
880A PRO* 1.3 98.9 - - - +
882A ALA* 1.3 59.0 + - - +
883A THR* 5.2 1.2 - - - +
900A GLY* 4.3 4.5 - - - -
901A ASN* 5.0 5.8 + - - -
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Residues in contact with ALA 882 (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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837A VAL* 3.4 28.9 - - + -
839A ASP 4.0 1.3 - - - -
841A GLY 3.3 17.0 - - - +
842A THR* 5.3 0.2 - - - -
843A VAL* 5.7 0.2 - - + -
879A ALA* 2.9 23.5 + - + +
880A PRO 3.6 0.2 - - - -
881A ASP* 1.3 78.3 - - - +
883A THR* 1.3 63.1 + - - +
884A VAL* 3.7 6.9 + - + +
899A ALA 4.2 0.2 - - - -
900A GLY 3.2 5.9 + - - -
901A ASN* 3.0 22.5 + - - +
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Residues in contact with THR 883 (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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840A LYS* 5.5 4.7 - - + +
841A GLY 3.2 7.7 + - - +
842A THR* 3.2 21.8 - - + +
843A VAL 3.1 22.9 + - - +
881A ASP 5.2 1.3 - - - +
882A ALA* 1.3 73.5 - - - +
884A VAL* 1.3 59.7 + - - +
885A SER* 4.1 2.9 + - - -
901A ASN* 3.1 37.9 - - + +
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Residues in contact with VAL 884 (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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843A VAL* 3.3 29.8 - - + +
845A LEU* 5.8 0.9 - - + -
873A TRP* 5.7 3.8 - - + -
877A LEU* 4.0 40.6 - - + -
879A ALA* 4.2 14.1 - - + -
882A ALA* 4.4 4.9 - - + +
883A THR* 1.3 75.5 - - - +
885A SER* 1.3 64.0 + - - +
886A MET* 4.4 17.2 + - + -
899A ALA* 4.4 3.4 - - + -
901A ASN 2.7 10.4 + - - +
902A MET* 3.3 17.7 - - + +
903A LYS* 2.9 22.8 + - - +
904A LEU* 5.5 0.2 - - - +
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Residues in contact with SER 885 (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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843A VAL 2.8 12.7 + - - +
844A THR* 3.3 19.3 - - - +
845A LEU* 2.9 25.9 + - - +
883A THR* 5.4 2.5 - - - -
884A VAL* 1.3 75.1 - - - +
886A MET* 1.3 65.1 + - - +
887A THR* 5.1 2.8 + - - -
903A LYS* 3.3 30.9 + - - +
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Residues in contact with MET 886 (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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845A LEU* 3.5 30.3 - - + -
873A TRP* 4.8 4.0 - - - -
884A VAL* 4.7 14.4 - - + -
885A SER* 1.3 77.7 + - - +
887A THR* 1.3 61.9 + - - +
889A THR* 3.0 34.8 - - + +
891A TRP* 3.3 45.1 - - + -
902A MET* 5.5 0.2 - - - -
903A LYS* 2.8 14.2 + - - +
904A LEU* 3.7 13.6 - - + -
905A ASN* 3.1 14.0 + - - +
907A THR* 3.0 35.0 - - + +
909A VAL* 5.0 0.4 - - + -
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Residues in contact with THR 887 (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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845A LEU 3.1 15.1 + - - +
846A GLY* 4.2 13.8 - - - -
847A GLY 5.6 0.7 - - - -
870A ARG* 4.9 0.5 - - - +
871A ASN* 4.5 1.6 - - - +
885A SER* 5.1 3.1 + - - -
886A MET* 1.3 75.4 + - - +
888A ASP* 1.3 89.9 + - + +
889A THR* 3.0 10.7 + - - -
903A LYS* 5.0 5.7 + - - -
905A ASN* 3.1 25.1 + - - +
906A ARG* 3.8 13.7 - - - +
907A THR* 3.7 0.4 - - - -
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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