Contacts of the strand formed by residues 838 - 844 (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 LEU 838 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807B PHE* 3.8 33.4 - - + -
831B ASN* 3.3 34.3 - - + +
833B ARG* 5.0 9.9 - - + +
836B GLN* 3.7 14.8 - - + +
837B GLU* 1.3 73.7 - - - +
839B LYS* 1.3 58.9 + - - +
840B VAL* 3.3 13.4 + - + +
865B THR* 3.4 5.6 - - - -
866B ILE* 3.0 31.1 + - + +
894B VAL* 3.7 23.8 - - + -
895B TYR 6.1 0.2 - - - +
897B HIS* 3.5 29.8 - - + +
899B ILE* 5.8 2.0 - - + -
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Residues in contact with LYS 839 (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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837B GLU 3.9 2.6 + - - -
838B LEU* 1.3 67.8 - - - +
840B VAL* 1.3 59.3 + - - +
863B THR* 3.9 25.6 + - + +
864B VAL 4.1 2.7 - - - +
865B THR* 4.3 18.6 + - + +
894B VAL* 3.2 4.6 - - - +
895B TYR* 2.8 68.6 + - + +
896B HIS* 5.3 6.7 - - + -
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Residues in contact with VAL 840 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807B PHE* 3.8 16.8 - - + -
829B LEU* 3.5 28.5 - - + -
838B LEU* 3.5 17.5 - - + +
839B LYS* 1.3 74.0 - - - +
841B ARG* 1.3 64.5 + - - +
842B VAL* 4.0 1.1 - - + +
863B THR* 3.3 8.0 - - - +
864B VAL* 2.9 38.6 + - + +
866B ILE* 3.7 26.0 - - + -
892B ALA* 3.9 10.8 - - + -
893B ALA 3.7 5.8 - - - +
894B VAL* 3.7 14.4 - - + -
895B TYR* 4.5 1.6 - - - -
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Residues in contact with ARG 841 (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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731B GLU* 5.5 1.1 - - - -
733B ILE* 3.6 19.2 - - - +
734B ILE 4.5 11.6 + - - -
735B ALA* 4.8 1.2 - - - +
736B GLU* 4.2 22.8 - - - +
739B ILE* 5.2 4.0 - - - +
840B VAL* 1.3 73.4 - - - +
842B VAL* 1.3 60.2 + - - +
843B GLU* 3.3 28.5 + - - +
859B ARG* 5.5 0.8 - - - +
861B GLN* 3.6 23.1 + - + +
862B GLN 3.6 11.0 - - - +
863B THR* 4.9 2.9 - - - +
891B LYS* 4.8 2.4 + - - +
892B ALA* 3.1 19.2 - - - +
893B ALA* 2.8 24.5 + - - +
895B TYR* 3.5 30.1 - - + +
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Residues in contact with VAL 842 (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* 4.9 3.6 - - + -
827B ALA* 5.6 0.7 - - + -
829B LEU* 4.1 22.0 - - + -
840B VAL 4.0 0.6 - - - -
841B ARG* 1.3 73.2 - - - +
843B GLU* 1.3 68.4 + - - +
861B GLN* 3.2 3.4 - - - +
862B GLN* 2.9 50.1 + - + +
864B VAL* 4.8 7.9 - - + -
874B VAL* 4.2 18.2 - - + -
876B TYR* 3.2 28.5 - - + +
890B VAL* 5.0 4.9 - - + -
891B LYS 3.4 10.8 - - - +
892B ALA* 3.8 12.1 - - + -
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Residues in contact with GLU 843 (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* 4.1 5.6 - - - +
841B ARG* 3.3 27.4 + - - +
842B VAL* 1.3 76.0 - - - +
844B LEU* 1.3 70.8 + - - +
845B LEU* 3.8 16.5 + - + +
859B ARG* 2.8 52.8 + - + +
860B HIS 3.7 13.9 - - - +
861B GLN* 3.7 14.9 - - + +
876B TYR* 4.2 3.8 - - - -
890B VAL* 3.5 4.2 - - - +
891B LYS* 2.8 38.9 + - + +
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Residues in contact with LEU 844 (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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825B ILE* 5.2 1.6 - - + -
843B GLU* 1.3 78.5 - - - +
845B LEU* 1.3 73.0 + - - +
852B SER* 4.1 22.2 - - - +
854B ALA* 3.2 20.5 - - + +
860B HIS* 3.3 13.5 + - - +
876B TYR* 3.5 47.0 + - + -
877B VAL 5.4 0.4 - - - +
878B ILE* 4.1 16.4 - - + -
888B VAL* 4.2 14.8 - - + -
889B GLU 3.2 22.0 - - - +
890B VAL* 3.5 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