Contacts of the strand formed by residues 807 - 812 (chain B) in PDB entry 2WIN
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 PHE 807 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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805B GLN* 3.0 21.9 + - - +
806B ASP* 1.3 82.5 - - + +
808B PHE* 1.3 80.2 + - - +
809B ILE* 5.0 0.9 - - + -
829B LEU* 4.4 5.6 - - + -
830B TYR 3.2 24.2 - - - -
831B ASN* 4.8 0.7 - - + -
833B ARG* 5.3 0.7 - - - +
838B LEU* 3.8 26.0 - - + -
840B VAL* 3.8 40.4 - - + -
866B ILE* 4.4 8.5 - - + -
892B ALA* 4.0 26.5 - - + -
893B ALA* 5.0 0.7 - - - -
894B VAL* 4.3 11.0 - - + -
899B ILE* 4.2 29.4 - - + +
900B SER* 4.4 9.0 - - - -
901B ASP* 4.3 7.0 - - + +
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Residues in contact with PHE 808 (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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239A TYR* 3.8 27.1 - + - -
777B ILE* 3.4 38.4 - - + -
804B MET* 4.5 5.2 - - + -
805B GLN* 3.2 31.2 - - + +
807B PHE* 1.3 82.8 - - - +
809B ILE* 1.3 75.6 + - - +
810B ASP* 4.7 5.4 - - + -
829B LEU* 3.6 4.0 - - - -
830B TYR* 3.2 67.5 + + + +
832B TYR* 4.0 10.1 - + - -
901B ASP* 3.0 22.2 - - - +
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Residues in contact with ILE 809 (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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742B ARG* 3.2 19.2 + - - -
807B PHE* 5.0 3.1 - - + -
808B PHE* 1.3 87.9 - - - +
810B ASP* 1.3 62.7 + - - +
811B LEU* 3.8 11.6 + - - +
827B ALA* 4.7 4.9 - - + -
828B VAL 3.5 8.1 - - - +
829B LEU* 3.9 23.1 - - + -
842B VAL* 4.9 2.2 - - + -
890B VAL* 4.1 24.5 - - + +
891B LYS 4.1 4.3 - - - -
892B ALA* 3.5 29.4 - - + +
901B ASP* 3.2 28.6 + - + +
903B VAL* 3.3 19.5 - - + +
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Residues in contact with ASP 810 (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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209A SER* 3.6 18.1 + - - -
239A TYR* 6.1 0.5 - - - -
808B PHE* 4.5 5.4 - - + -
809B ILE* 1.3 72.5 - - - +
811B LEU* 1.3 61.5 + - - +
812B ARG* 3.1 43.5 + - - +
828B VAL* 2.8 24.6 + - + +
830B TYR* 3.4 32.0 + - + -
905B LYS* 4.0 12.7 + - - +
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Residues in contact with LEU 811 (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 5.1 + - - +
810B ASP* 1.3 70.2 - - - +
812B ARG* 1.3 58.8 + - - +
813B LEU* 3.4 24.6 + - + -
825B ILE* 4.5 11.2 - - + -
826B ARG 3.6 18.2 - - - +
827B ALA* 4.1 10.5 - - + +
876B TYR* 5.8 0.2 - - + -
888B VAL* 3.8 30.7 - - + +
890B VAL* 3.9 33.4 - - + -
903B VAL* 3.6 30.6 - - + +
905B LYS* 3.0 37.4 + - + +
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Residues in contact with ARG 812 (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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206A VAL* 4.5 12.7 + - - +
207A LEU 3.0 28.9 + - - -
208A PRO* 3.6 4.8 + - - +
209A SER* 3.9 12.1 - - - -
310A LEU* 6.3 0.2 - - - -
314A SER* 4.2 26.2 + - - +
315A ASP* 3.6 35.4 + - - +
810B ASP* 3.1 41.4 + - - +
811B LEU* 1.3 70.7 - - - +
813B LEU* 1.3 68.3 + - - +
814B PRO* 4.2 4.2 - - - +
825B ILE* 4.3 1.4 - - - +
826B ARG* 3.2 35.4 + - + +
828B VAL* 5.2 3.6 - - + -
830B TYR* 6.0 0.4 - - - -
905B LYS* 5.1 4.7 - - - +
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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
------------------------------------------------------------
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