Contacts of the strand formed by residues 861 - 868 (chain B) in PDB entry 2B7A
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 GLY 861 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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857B LYS* 3.5 2.3 - - - +
858B GLY* 2.7 36.4 + - - +
859B ASN 3.5 0.4 - - - -
860B PHE* 1.3 83.2 - - - +
862B SER* 1.3 58.0 + - - -
882B LYS* 5.7 4.6 - - - +
883B LYS 3.3 13.9 + - - -
885B GLN* 3.4 19.7 - - - -
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Residues in contact with SER 862 (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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854B GLN* 4.3 18.0 - - - +
856B GLY 3.4 13.7 - - - -
857B LYS* 4.0 5.2 - - - +
861B GLY* 1.3 75.3 - - - -
863B VAL* 1.3 66.5 + - - +
864B GLU* 4.4 6.1 + - - +
881B VAL 3.7 0.9 - - - +
882B LYS* 3.4 4.0 - - - +
883B LYS* 3.0 45.4 + - - +
885B GLN* 3.0 23.6 + - - +
2002B IZA 6.3 0.2 - - - -
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Residues in contact with VAL 863 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854B GLN* 3.6 4.4 - - - +
855B LEU* 2.8 37.5 + - + -
856B GLY 2.8 19.0 + - - +
862B SER* 1.3 77.7 - - - +
864B GLU* 1.3 58.7 + - - +
880B ALA* 4.0 20.4 - - + -
881B VAL 3.3 9.2 - - - +
882B LYS* 3.9 20.6 - - + -
929B MET* 4.6 1.8 - - + -
994B ASP* 5.5 0.2 - - - +
2002B IZA 3.7 60.8 - - + +
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Residues in contact with GLU 864 (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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851B PHE* 3.7 37.2 - - + +
853B GLN 3.5 3.8 - - - -
854B GLN* 4.8 5.8 - - + +
855B LEU* 3.9 4.5 - - - +
862B SER* 4.4 8.9 + - - +
863B VAL* 1.3 79.2 - - - +
865B MET* 1.3 61.5 + - - +
866B CYS* 3.7 12.4 + - - -
880B ALA* 3.4 4.3 - - - -
881B VAL* 2.7 50.1 + - + +
883B LYS* 2.7 41.0 + - + +
926B LYS* 5.3 5.4 + - - +
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Residues in contact with MET 865 (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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851B PHE* 4.1 0.5 - - - -
852B LEU* 2.9 44.4 + - + +
853B GLN* 2.7 43.1 + - + +
855B LEU* 3.7 19.0 - - + +
864B GLU* 1.3 70.3 - - - +
866B CYS* 1.3 64.1 + - - +
878B VAL* 3.7 33.7 - - + -
879B VAL 3.7 3.6 - - - -
931B TYR* 3.7 36.1 - - + +
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Residues in contact with CYS 866 (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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849B LEU* 4.0 22.2 - - + -
850B LYS 3.3 8.1 - - - +
851B PHE* 3.9 17.9 - - - -
852B LEU* 4.3 5.4 - - - -
864B GLU* 4.2 22.4 - - - -
865B MET* 1.3 80.3 - - - +
867B ARG* 1.3 57.4 + - - +
868B TYR 3.9 0.2 - - - -
878B VAL* 3.4 1.8 - - - -
879B VAL* 2.7 43.2 + - - +
881B VAL* 3.8 28.7 - - + -
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Residues in contact with ARG 867 (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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848B HIS 3.3 3.6 - - - +
849B LEU* 4.6 0.7 - - - -
850B LYS* 2.8 44.1 + - + +
852B LEU* 4.0 29.2 - - + +
866B CYS* 1.3 73.2 - - - +
868B TYR* 1.3 59.2 + - - +
869B ASP* 3.3 18.9 + - + -
874B ASN* 3.3 52.0 + - - +
876B GLY 3.4 25.2 + - - +
877B GLU 3.5 4.0 - - - +
878B VAL* 3.9 19.9 - - + +
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Residues in contact with TYR 868 (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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843B GLN 4.0 5.2 + - - -
844B PHE* 3.6 38.5 - + + -
845B GLU* 3.0 56.5 + - - +
848B HIS* 3.7 21.5 + - + -
849B LEU* 3.7 19.7 - - + +
866B CYS 3.9 2.0 + - - -
867B ARG* 1.3 68.5 - - - +
869B ASP* 1.3 58.0 + - - +
870B PRO* 3.3 23.8 - - + +
876B GLY* 3.1 20.1 - - - -
877B GLU* 2.9 18.9 + - + +
879B VAL* 4.8 3.1 - - + -
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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