Contacts of the strand formed by residues 886 - 894 (chain B) in PDB entry 2XWB
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 GLN 886 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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847B ASN* 4.2 4.3 + - - +
849B ALA* 3.3 26.6 - - + +
850B PHE* 3.6 23.6 - - + -
882B LYS* 3.4 31.2 - - - +
883B THR 3.4 17.8 + - - -
884B GLY* 3.3 9.3 + - - +
885B LEU* 1.3 80.0 + - - +
887B GLU* 1.3 62.9 + - - +
906B SER* 3.2 8.3 - - - -
907B LEU* 3.0 37.6 + - + +
909B VAL* 4.1 10.5 - - + -
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Residues in contact with GLU 887 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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847B ASN* 2.8 32.3 + - - +
850B PHE* 3.4 4.7 - - - -
886B GLN* 1.3 80.2 + - - +
888B VAL* 1.3 66.3 + - - +
889B GLU* 3.7 11.1 + - + +
904B ARG* 3.2 42.9 + - + +
905B LYS 3.8 5.8 - - - +
906B SER* 4.6 5.8 + - - +
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Residues in contact with VAL 888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811B LEU* 3.7 22.4 - - + +
813B LEU* 3.9 16.6 - - + -
825B ILE* 4.0 19.1 - - + -
844B LEU* 4.4 13.2 - - + -
850B PHE* 3.7 16.4 - - + -
878B ILE* 4.6 7.9 - - + -
887B GLU* 1.3 79.5 - - - +
889B GLU* 1.3 64.0 + - - +
890B VAL* 4.9 0.2 - - + -
903B VAL 3.7 0.9 - - - +
904B ARG* 3.4 2.8 - - - +
905B LYS 2.9 32.6 + - - +
907B LEU* 3.7 25.1 - - + -
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Residues in contact with GLU 889 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741B SER* 2.9 32.1 + - - +
811B LEU* 4.9 0.2 - - - -
844B LEU* 3.4 6.5 - - - +
845B LEU* 3.1 58.7 + - + +
887B GLU* 3.7 9.6 - - + +
888B VAL* 1.3 79.6 - - - +
890B VAL* 1.3 63.0 + - - +
891B LYS* 3.4 8.8 + - - -
903B VAL 3.2 14.4 - - - +
904B ARG* 3.6 30.7 + - + -
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Residues in contact with VAL 890 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809B ILE* 3.6 24.9 - - + +
811B LEU* 3.6 39.3 - - + -
825B ILE* 5.6 0.7 - - + -
827B ALA* 4.7 2.7 - - + -
842B VAL* 4.8 8.1 - - + -
843B GLU 3.4 10.8 - - - +
844B LEU* 3.5 28.5 - - + -
876B TYR* 4.2 18.4 - - + -
888B VAL* 4.9 0.9 - - + -
889B GLU* 1.3 73.2 - - - +
891B LYS* 1.3 62.3 + - - +
902B GLY* 3.4 1.9 - - - -
903B VAL* 3.0 30.4 + - + +
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Residues in contact with LYS 891 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736B GLU* 3.5 39.0 + - - +
737B GLU* 4.2 9.1 + - - +
739B ILE* 2.9 42.0 + - + -
741B SER* 3.2 24.2 - - - +
809B ILE* 4.1 1.1 - - - -
842B VAL* 3.3 2.4 - - - +
843B GLU* 2.7 39.7 + - + +
845B LEU* 3.8 27.8 - - + +
889B GLU* 3.4 13.6 + - - +
890B VAL* 1.3 75.9 - - - +
892B ALA* 1.3 61.6 + - - +
901B ASP 3.6 5.4 - - - +
902B GLY* 4.4 0.2 - - - -
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Residues in contact with ALA 892 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736B GLU* 4.5 1.3 + - - -
739B ILE* 4.2 4.1 - - - +
807B PHE* 4.3 6.4 - - + -
809B ILE* 3.7 17.3 - - + -
829B LEU* 4.3 4.9 - - + -
840B VAL* 3.8 14.4 - - + -
841B ARG 3.4 6.5 - - - -
842B VAL* 3.7 20.0 - - + -
891B LYS* 1.3 79.3 - - - +
893B ALA* 1.3 60.3 + - - +
900B SER* 3.3 4.5 - - - -
901B ASP 2.9 32.4 + - - +
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Residues in contact with ALA 893 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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733B ILE* 4.1 13.1 - - + +
734B ILE* 4.0 28.5 - - + +
736B GLU* 4.2 1.7 + - - +
739B ILE* 4.2 7.2 - - + -
840B VAL* 3.6 2.4 - - - -
841B ARG* 2.9 31.9 + - - +
892B ALA* 1.3 77.0 - - - +
894B VAL* 1.3 65.4 + - - +
895B TYR* 4.0 0.7 + - - -
899B ILE 3.7 7.0 - - - +
900B SER* 3.8 15.3 - - - +
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Residues in contact with VAL 894 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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733B ILE* 3.6 14.5 - - - +
734B ILE 4.8 0.3 + - - -
807B PHE* 4.1 21.3 - - + -
838B LEU* 4.3 21.8 - - + -
839B LYS 3.5 8.7 - - - +
840B VAL* 3.6 26.2 - - + -
893B ALA* 1.3 75.6 - - - +
895B TYR* 1.3 62.8 + - - +
897B HIS* 3.4 32.2 - - + +
899B ILE* 3.2 35.2 + - + +
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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