Contacts of the strand formed by residues 857 - 864 (chain B) in PDB entry 5WRZ
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 ARG 857 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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848B TYR* 3.5 13.2 - - - +
851B PHE 3.8 2.7 - - - -
852B LYS 2.8 31.5 + - - -
853B GLN* 4.5 3.0 - - - +
854B LEU 3.2 23.8 + - - +
855B HIS 4.2 0.2 - - - +
856B ASN* 1.3 79.4 - - - +
858B ARG* 1.3 59.4 + - - +
923B GLU* 3.1 33.3 + - + +
924B VAL 3.4 5.6 - - - +
925B ALA* 4.1 10.8 - - + -
965B ASP 5.1 1.0 + - - -
966B GLY* 3.4 28.5 + - - +
967B VAL* 3.9 12.8 - - + +
968B ASP* 3.4 27.9 + - - +
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Residues in contact with ARG 858 (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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856B ASN* 3.9 21.0 + - - +
857B ARG* 1.3 74.8 + - - +
859B LEU* 1.3 58.5 + - - +
860B LEU* 3.6 24.2 + - + -
922B GLY 3.3 2.3 - - - +
923B GLU* 3.5 0.7 - - - -
924B VAL* 2.8 33.8 + - - +
926B LEU* 3.8 26.2 - - + +
929B MET* 3.8 24.9 - - - +
949B LYS* 4.7 5.7 - - - +
961B ASN* 5.7 1.3 + - - -
967B VAL* 3.6 5.8 - - - +
968B ASP* 3.5 27.6 + - + +
970B PRO* 4.3 17.9 - - + +
989B TYR* 3.2 28.4 + - - -
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Residues in contact with LEU 859 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813B ILE* 5.9 0.9 - - + -
814B ILE* 5.5 1.3 - - + -
817B TYR* 2.8 29.2 + - + -
858B ARG* 1.3 69.4 - - - +
860B LEU* 1.3 63.5 + - - +
921B LEU* 4.0 31.6 - - + -
922B GLY 3.4 22.7 - - - +
923B GLU* 3.9 8.1 - - + +
964B LEU* 4.1 19.3 - - + -
967B VAL* 3.5 11.1 - - + +
968B ASP 2.9 16.5 + - - +
969B VAL* 3.8 24.2 - - + -
970B PRO* 3.7 4.3 - - - +
1000B LYS* 4.5 18.4 - - + -
1001B TYR* 4.8 5.4 - - + -
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Residues in contact with LEU 860 (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 TYR* 4.0 2.0 - - - +
858B ARG* 4.1 22.2 - - + +
859B LEU* 1.3 82.6 - - - +
861B TRP* 1.3 63.5 + - - +
897B PHE* 3.7 20.8 - - + -
898B ALA 3.6 14.4 - - - +
899B ASP* 3.9 20.4 - - + -
921B LEU* 3.4 7.4 - - - -
922B GLY* 2.9 33.6 + - - +
924B VAL* 4.2 15.3 - - + -
926B LEU* 4.1 16.6 - - + -
970B PRO* 4.4 0.9 - - + -
989B TYR* 3.6 40.4 - - + -
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Residues in contact with TRP 861 (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 ILE 4.8 2.0 - - - -
817B TYR* 3.4 46.4 - + + -
818B VAL* 3.6 28.7 - - + -
860B LEU* 1.3 72.7 - - - +
862B HIS* 1.3 59.8 + - - +
897B PHE* 3.2 10.8 - - - +
898B ALA 2.9 41.6 + - - +
899B ASP 4.0 1.3 - - - -
900B MET 3.7 3.4 - - - -
901B VAL* 3.5 43.1 - - + +
904B SER* 3.1 21.4 + - - +
919B ILE* 3.4 26.9 - - + -
920B LEU 3.4 9.4 - - - -
921B LEU* 3.4 35.7 - - + -
1003B LEU* 3.8 21.3 - - + -
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Residues in contact with HIS 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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860B LEU 4.0 0.6 + - - -
861B TRP* 1.3 76.1 - - - +
863B GLY* 1.3 73.4 + - - +
864B SER* 4.2 13.1 + - - -
869B PHE* 4.7 0.9 - - - -
872B ILE* 5.0 0.4 - - - +
877B LEU* 3.8 38.9 - - + +
895B ILE* 4.8 2.7 - - + -
896B TYR* 2.6 30.3 + - + -
897B PHE* 3.9 15.0 - - + -
919B ILE* 3.7 4.7 - - - -
920B LEU* 2.9 49.2 + - + +
1101B 7U3 3.4 28.6 + + - -
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Residues in contact with GLY 863 (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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862B HIS* 1.3 77.3 + - - +
864B SER* 1.3 63.9 + - - -
904B SER* 3.4 20.7 - - - -
907B TYR* 3.5 10.9 - - - +
908B CYS* 4.2 6.5 - - - -
918B LEU 4.3 0.9 - - - -
919B ILE* 4.0 11.0 - - - -
1101B 7U3 2.9 31.9 + - - -
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Residues in contact with SER 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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862B HIS* 4.2 8.6 + - - -
863B GLY* 1.3 76.3 - - - -
865B ARG* 1.3 62.7 + - - +
866B THR* 3.6 0.9 + - - +
868B ASN* 2.8 31.2 + - - +
869B PHE* 3.2 25.6 - - - -
872B ILE* 3.8 17.0 - - - +
907B TYR 3.4 12.1 + - - -
908B CYS* 3.7 7.8 - - - +
918B LEU 3.4 12.0 + - - +
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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