Contacts of the strand formed by residues 807 - 817 (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 VAL 807 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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775A SER 4.6 0.9 - - - +
776A GLN* 3.5 37.7 - - - +
777A SER* 3.7 6.7 - - - +
794A ASN* 3.6 40.4 - - + +
805A LEU* 3.7 10.3 - - + +
806A PRO* 1.3 77.9 - - - +
808A TYR* 1.3 63.4 + - - +
809A ASP* 3.4 21.8 - - - +
828A TYR 2.9 9.8 + - - +
829A SER* 3.6 2.4 - - - -
830A MET* 3.0 28.9 + - - +
862A LEU* 4.8 2.6 - - - +
866A PHE* 4.4 0.5 - - - -
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Residues in contact with TYR 808 (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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777A SER* 3.1 23.6 + - - +
778A PHE 2.9 25.5 + - - -
779A VAL* 4.3 16.6 - - + -
807A VAL* 1.3 73.7 - - - +
809A ASP* 1.3 64.0 + - - +
810A TYR* 3.7 33.4 - + + -
830A MET* 3.8 16.6 - - + -
862A LEU* 3.6 43.1 - - + +
865A LEU* 5.5 2.6 - - - +
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Residues in contact with ASP 809 (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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774A ALA* 4.3 2.3 - - - +
776A GLN 4.3 5.4 - - - +
778A PHE* 3.2 20.9 + - - +
793A LEU* 3.3 33.2 - - + +
807A VAL* 3.4 20.1 - - - +
808A TYR* 1.3 77.6 - - - +
810A TYR* 1.3 60.3 + - - +
814A TRP* 3.9 6.5 - - + -
829A SER* 2.7 28.6 + - - +
830A MET 2.8 11.7 + - - +
831A LEU* 3.3 16.5 - - + +
832A SER 3.0 24.1 + - - -
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Residues in contact with TYR 810 (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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778A PHE* 2.8 19.2 + - - +
779A VAL* 4.2 24.5 - - + -
780A SER 2.7 36.4 + - - +
808A TYR* 3.7 31.9 - + + -
809A ASP* 1.3 82.9 - - - +
811A ALA* 1.3 58.2 + - - +
814A TRP* 3.9 2.0 - - - -
830A MET* 3.4 29.7 - - + +
831A LEU 4.6 0.7 - - - -
832A SER* 3.4 26.9 - - - -
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Residues in contact with ALA 811 (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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780A SER* 3.4 11.2 - - - -
782A GLY 3.7 7.2 - - - +
784A VAL* 3.7 14.4 - - + -
810A TYR* 1.3 77.1 - - - +
812A GLY* 1.3 64.1 + - - +
813A SER 3.5 16.4 - - - +
814A TRP* 3.3 26.9 - - + +
832A SER* 3.2 18.7 + - - +
833A GLY* 3.3 6.9 - - - -
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Residues in contact with GLY 812 (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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781A ASP* 4.0 14.0 - - - -
782A GLY 2.8 20.0 + - - +
811A ALA* 1.3 72.8 - - - +
813A SER* 1.3 62.3 + - - +
833A GLY* 3.6 2.3 - - - -
834A ASN* 3.3 22.0 + - - -
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Residues in contact with SER 813 (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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782A GLY 3.7 2.6 + - - -
783A PRO* 3.7 8.9 - - - +
784A VAL 3.0 22.7 + - - -
811A ALA* 3.5 8.8 - - - +
812A GLY* 1.3 78.5 - - - +
814A TRP* 1.3 63.8 + - - +
815A ASN* 2.8 35.3 + - - -
834A ASN* 3.3 15.9 - - - +
836A ASN* 4.0 8.1 - - - -
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Residues in contact with TRP 814 (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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778A PHE* 4.0 22.4 - + - -
784A VAL* 3.5 30.7 - - + -
786A ILE* 4.9 2.0 - - + -
791A LEU* 3.7 26.5 - - + -
793A LEU* 4.1 18.4 - - + -
809A ASP* 3.8 11.9 - - + -
811A ALA* 3.3 24.6 - - + +
813A SER* 1.3 75.8 - - - +
815A ASN* 1.3 59.7 + - - +
816A LEU* 4.0 7.6 - - + +
823A LEU* 4.3 20.6 - - + -
831A LEU* 3.6 25.8 - - + +
832A SER 2.9 21.5 + - - -
833A GLY 3.9 9.6 - - - -
834A ASN 2.6 18.5 + - - +
835A ILE* 3.4 17.0 - - + -
836A ASN 2.8 26.2 + - - +
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Residues in contact with ASN 815 (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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783A PRO* 3.6 10.1 - - - +
784A VAL 2.8 10.7 + - - -
785A ASN* 2.8 29.8 + - + +
786A ILE* 2.8 26.2 + - - +
813A SER* 2.8 29.9 + - - -
814A TRP* 1.3 72.3 - - - +
816A LEU* 1.3 63.7 + - - +
817A LYS* 4.9 8.7 - - + +
836A ASN* 3.0 34.1 + - + +
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Residues in contact with LEU 816 (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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786A ILE* 3.0 27.4 - - + +
814A TRP* 4.0 11.2 - - + +
815A ASN* 1.3 79.6 - - - +
817A LYS* 1.3 66.4 + - - +
821A ALA* 3.6 22.0 - - + +
822A ARG 4.1 4.9 - - - -
823A LEU* 3.8 33.4 - - + +
835A ILE* 4.4 10.3 - - + -
836A ASN 2.8 14.4 + - - +
837A VAL* 3.5 19.2 - - + -
838A GLN* 2.8 25.7 + - - +
842A THR 4.0 14.1 - - - +
843A VAL* 4.0 7.4 - - + -
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Residues in contact with LYS 817 (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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786A ILE 3.0 8.9 + - - +
787A SER* 3.5 16.5 + - - +
788A ASP* 2.9 26.2 + - - -
815A ASN* 4.9 8.7 - - + +
816A LEU* 1.3 79.5 - - - +
818A GLY* 1.3 64.2 + - - +
821A ALA* 3.6 1.0 - - - +
838A GLN* 3.3 43.2 + - + +
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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