Contacts of the strand formed by residues 900 - 910 (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 SER 900 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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734B ILE* 4.5 9.9 - - - +
738B ASN 5.1 1.2 + - - -
739B ILE* 3.7 31.4 - - - +
805B GLN* 4.4 9.2 + - - -
807B PHE* 4.4 6.9 - - - +
892B ALA 3.4 15.0 - - - -
893B ALA* 3.9 5.4 - - - +
899B ILE* 1.3 86.7 - - - +
901B ASP* 1.3 66.8 + - - +
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Residues in contact with ASP 901 (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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739B ILE* 4.1 5.9 - - - +
740B VAL 5.3 0.8 - - - +
742B ARG* 2.8 49.9 + - - +
777B ILE* 4.1 0.3 - - - +
805B GLN* 4.2 7.1 - - - +
807B PHE* 4.3 7.5 - - + +
808B PHE* 3.0 34.4 - - - +
809B ILE* 3.2 27.3 + - - +
892B ALA 3.2 12.7 + - - +
900B SER* 1.3 79.9 - - - +
902B GLY* 1.3 71.1 + - - +
903B VAL* 4.9 0.4 - - - -
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Residues in contact with GLY 902 (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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739B ILE* 3.7 8.8 - - - +
740B VAL 4.6 1.6 + - - -
741B SER* 3.6 21.5 - - - +
742B ARG* 2.7 26.5 + - - +
890B VAL 3.3 10.5 - - - -
891B LYS* 4.0 8.7 - - - -
901B ASP* 1.3 83.4 + - - +
903B VAL* 1.3 60.8 + - - +
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Residues in contact with VAL 903 (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* 3.9 2.0 - - - -
742B ARG* 3.4 20.0 - - - +
745B PHE* 4.0 10.1 - - + -
809B ILE* 3.3 42.2 - - + +
811B LEU* 3.6 28.3 - - + +
888B VAL 3.7 1.9 - - - +
889B GLU* 3.3 4.3 - - - -
890B VAL* 2.8 35.6 + - + -
901B ASP* 4.7 0.4 - - - +
902B GLY* 1.3 75.0 - - - -
904B ARG* 1.3 63.0 + - - +
905B LYS* 3.7 25.4 - - + +
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Residues in contact with ARG 904 (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* 3.7 28.8 + - - +
742B ARG 2.9 13.8 + - - +
743B SER* 3.1 51.3 + - - +
887B GLU* 3.0 46.2 + - + +
888B VAL 3.7 2.7 - - - -
889B GLU* 3.4 23.5 + - + +
903B VAL* 1.3 72.3 - - - +
905B LYS* 1.3 62.9 + - - +
906B SER* 4.6 3.1 + - - -
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Residues in contact with LYS 905 (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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745B PHE* 3.7 37.2 - - + -
810B ASP* 4.0 13.9 + - - +
811B LEU* 3.0 34.1 + - + +
812B ARG* 5.1 4.9 - - - +
813B LEU* 4.6 18.2 - - + +
887B GLU* 3.8 1.4 - - - +
888B VAL* 3.0 30.9 + - - +
903B VAL* 3.7 23.6 - - + +
904B ARG* 1.3 77.7 - - - +
906B SER* 1.3 64.8 + - - +
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Residues in contact with SER 906 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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813B LEU* 4.5 4.0 - - - +
885B LEU* 3.6 26.9 - - - +
886B GLN 3.1 19.6 + - - -
887B GLU* 4.1 12.6 + - - +
904B ARG 4.6 3.1 + - - -
905B LYS* 1.3 79.4 + - - +
907B LEU* 1.3 60.3 + - - +
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Residues in contact with LEU 907 (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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813B LEU* 3.6 36.3 - - + -
814B PRO* 3.9 19.3 - - + +
815B TYR 4.8 0.9 - - - -
817B VAL* 3.6 40.8 - - + -
825B ILE* 5.4 1.3 - - + -
850B PHE* 3.6 30.3 - - + -
878B ILE* 5.2 6.3 - - + -
885B LEU* 3.8 4.0 - - - -
886B GLN 3.2 27.6 + - - +
888B VAL* 3.7 9.2 - - + +
906B SER* 1.3 75.0 - - - +
908B LYS* 1.3 61.2 + - - +
909B VAL* 3.6 2.4 + - + +
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Residues in contact with LYS 908 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A THR* 5.0 4.9 + - - -
119A PRO 3.2 25.7 + - - -
120A GLY* 4.7 3.4 - - - -
121A SER 5.6 0.2 - - - +
175A GLU* 3.3 17.0 + - - +
815B TYR* 3.4 45.6 + - + +
816B SER* 3.3 10.1 - - - -
817B VAL* 3.1 25.8 + - - +
884B GLY 4.3 4.0 - - - -
885B LEU* 4.2 18.2 - - + +
907B LEU* 1.3 73.8 - - - +
909B VAL* 1.3 59.3 + - - +
910B VAL* 3.9 9.9 - - + -
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Residues in contact with VAL 909 (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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817B VAL* 3.5 24.7 - - + +
819B ARG* 4.2 13.0 - - + -
850B PHE* 4.7 2.2 - - + -
880B PRO* 3.7 26.7 - - + -
882B LYS 3.6 17.9 - - - +
883B THR* 3.4 12.5 - - - -
884B GLY* 3.1 31.7 + - - +
886B GLN* 3.5 27.8 - - + -
907B LEU* 3.9 8.3 - - + +
908B LYS* 1.3 74.3 - - - +
910B VAL* 1.3 59.4 + - - +
911B PRO* 4.0 0.5 - - - +
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Residues in contact with VAL 910 (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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815B TYR* 6.2 0.9 - - + -
816B SER* 4.3 20.9 - - - -
817B VAL 3.2 6.5 + - - +
818B VAL* 3.3 7.4 - - - +
819B ARG 3.3 17.8 + - - -
883B THR* 4.7 1.1 - - - -
908B LYS* 3.8 8.9 + - + -
909B VAL* 1.3 78.3 - - - +
911B PRO* 1.3 92.1 - - + +
913B GLY* 5.6 4.3 - - - +
1327B HIS* 5.3 14.8 - - + +
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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