Contacts of the strand formed by residues 823 - 831 (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 VAL 823 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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814B PRO* 5.7 3.1 - - + -
817B VAL* 4.1 30.3 - - + -
818B VAL 6.0 0.7 - - - +
821B GLU* 4.1 21.5 - - + +
822B GLN* 1.3 81.1 - - - +
824B GLU* 1.3 61.2 + - - +
825B ILE* 4.9 7.6 - - + -
876B TYR 3.9 0.3 - - - +
877B VAL* 3.7 4.2 - - - +
878B ILE* 3.2 43.4 + - + +
880B PRO* 5.0 2.9 - - + -
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Residues in contact with GLU 824 (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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814B PRO* 5.5 5.0 - - - +
823B VAL* 1.3 77.2 - - - +
825B ILE* 1.3 71.4 + - - +
826B ARG* 3.0 35.8 + - - +
875B PRO* 3.1 26.6 - - + +
876B TYR 3.7 14.1 - - - +
877B VAL* 4.6 11.9 - - + +
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Residues in contact with ILE 825 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811B LEU* 4.5 6.3 - - + -
812B ARG 4.3 8.3 - - - +
813B LEU* 4.4 15.7 - - + -
814B PRO* 4.4 20.2 - - + -
823B VAL* 4.9 7.2 - - + -
824B GLU* 1.3 78.2 - - - +
826B ARG* 1.3 64.6 + - - +
844B LEU* 5.2 2.5 - - + -
875B PRO* 3.8 3.6 - - - +
876B TYR* 3.0 50.4 + - + +
878B ILE* 3.7 37.5 - - + -
888B VAL* 3.8 24.2 - - + -
890B VAL* 5.7 0.2 - - + -
907B LEU* 5.4 2.7 - - + -
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Residues in contact with ARG 826 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A SER 3.6 15.7 + - - -
313A GLY* 4.5 8.6 + - - +
314A SER* 3.5 34.9 + - - +
810B ASP 4.8 0.2 - - - -
811B LEU* 3.6 8.8 - - - +
812B ARG* 3.2 39.3 + - + +
824B GLU* 3.0 42.9 + - - +
825B ILE* 1.3 77.5 - - - +
827B ALA* 1.3 61.4 + - - +
828B VAL* 4.0 2.5 - - + -
873B SER* 3.0 24.7 + - - +
874B VAL 4.1 0.2 - - - -
875B PRO* 4.7 9.9 - - - +
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Residues in contact with ALA 827 (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* 4.7 7.0 - - + -
810B ASP 4.3 4.3 - - - -
811B LEU* 4.1 15.9 - - + +
826B ARG* 1.3 75.9 - - - +
828B VAL* 1.3 60.7 + - - +
829B LEU* 3.1 21.2 + - + +
842B VAL* 5.6 1.3 - - + -
874B VAL* 3.1 37.4 + - + +
876B TYR* 4.0 20.9 - - + -
890B VAL* 4.9 4.0 - - + -
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Residues in contact with VAL 828 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A LEU* 6.1 0.7 - - + -
312A SER* 4.5 7.2 - - - +
314A SER* 3.5 33.4 - - - +
809B ILE* 3.5 2.1 - - - -
810B ASP* 2.8 43.8 + - + +
812B ARG* 5.2 4.0 - - - -
826B ARG* 4.9 1.3 - - + -
827B ALA* 1.3 74.3 - - - +
829B LEU* 1.3 62.5 + - - +
830B TYR* 3.4 38.7 - - + +
871B SER* 3.8 21.5 - - - +
872B LEU 3.5 10.1 - - - +
873B SER* 4.2 7.9 - - - +
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Residues in contact with LEU 829 (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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807B PHE* 4.4 4.3 - - + -
808B PHE 3.6 5.8 - - - +
809B ILE* 3.9 26.0 - - + -
827B ALA* 3.1 25.1 - - + +
828B VAL* 1.3 73.8 - - - +
830B TYR* 1.3 61.2 + - - +
840B VAL* 3.5 35.7 - - + -
842B VAL* 4.1 16.2 - - + -
864B VAL* 5.0 3.6 - - + -
866B ILE* 3.3 24.4 - - + +
871B SER* 3.5 1.6 - - - -
872B LEU 2.8 32.0 + - - +
874B VAL* 4.0 13.2 - - + -
892B ALA* 4.1 10.3 - - + -
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Residues in contact with TYR 830 (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* 4.2 4.7 + - - -
237A PHE* 3.5 27.9 - + - -
239A TYR* 3.3 15.0 - + - -
310A LEU* 4.5 8.3 - - - +
807B PHE* 3.2 25.1 - - - -
808B PHE* 3.2 46.0 + + + -
810B ASP* 3.4 35.6 + - + -
812B ARG* 6.0 0.3 - - - -
828B VAL* 3.4 28.5 - - + +
829B LEU* 1.3 70.7 - - - +
831B ASN* 1.3 60.5 + - - +
832B TYR* 3.4 32.3 - + + -
870B SER 4.0 2.7 - - - -
871B SER* 3.5 23.1 - - - +
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Residues in contact with ASN 831 (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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806B ASP 4.0 2.8 - - - +
807B PHE* 4.8 0.7 - - - -
829B LEU 3.9 0.2 + - - -
830B TYR* 1.3 75.3 - - - +
832B TYR* 1.3 60.7 + - - +
833B ARG* 3.2 20.7 + - - +
836B GLN 3.2 19.6 + - - -
838B LEU* 3.3 30.0 - - + +
866B ILE* 3.2 44.8 + - + -
867B PRO 3.5 8.2 + - - +
868B PRO* 4.0 1.9 - - - +
869B LYS 3.0 21.0 + - - -
870B SER 2.9 20.0 + - - +
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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