Contacts of the helix formed by residues 810 - 820 (chain B) in PDB entry 6WCZ
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 ASP 810 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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808B THR 3.7 1.6 + - - -
809B GLU* 1.3 98.5 - - - +
811B MET* 1.3 68.0 + - - +
812B LEU* 3.8 20.4 + - - +
813B MET* 3.2 14.9 + - + +
814B VAL 3.7 0.9 + - - -
835B TRP* 4.6 12.1 - - - -
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Residues in contact with MET 811 (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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762B GLN* 3.3 48.2 - - + +
765B GLN* 3.2 34.5 - - + +
766B LEU* 5.3 5.3 - - - +
805B TRP* 4.8 7.2 - - - +
807B THR* 3.8 13.9 - - + +
809B GLU 3.6 14.6 - - - +
810B ASP* 1.3 75.6 + - - +
812B LEU* 1.3 58.6 + - - +
813B MET 3.2 0.4 - - - -
814B VAL* 3.1 39.9 + - + +
815B TRP* 3.0 30.8 + - - +
835B TRP* 6.1 2.0 - - + -
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Residues in contact with LEU 812 (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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810B ASP* 3.2 13.7 + - - +
811B MET* 1.3 77.2 - - - +
813B MET* 1.3 78.3 + - + +
815B TRP* 3.7 5.3 + - + +
816B ASN* 3.0 29.8 + - - +
832B VAL* 3.8 25.1 - - + +
833B THR* 3.3 31.6 - - - +
834B LYS* 5.7 1.3 - - - +
835B TRP* 3.6 49.2 - - + +
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Residues in contact with MET 813 (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 GLU* 3.3 33.0 - - + +
810B ASP* 3.2 7.7 + - + +
812B LEU* 1.3 102.5 - - + +
814B VAL* 1.3 58.3 + - - +
816B ASN* 3.3 15.0 + - - +
817B ARG* 2.9 49.0 + - - +
832B VAL 5.7 0.9 - - - +
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Residues in contact with VAL 814 (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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766B LEU* 4.0 11.6 - - + +
804B GLU* 3.2 36.6 - - - +
805B TRP* 5.1 0.7 - - - -
807B THR* 3.8 17.7 - - + -
809B GLU* 4.0 15.9 - - + -
810B ASP 4.3 0.2 - - - +
811B MET* 3.1 40.3 + - + +
813B MET* 1.3 74.5 - - - +
815B TRP* 1.3 65.7 + - - +
817B ARG* 3.3 17.0 + - - +
818B VAL* 3.0 24.8 + - - +
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Residues in contact with TRP 815 (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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720B LEU* 6.2 2.7 - - + -
726B ILE* 4.6 10.3 - - + -
765B GLN 5.4 3.1 - - - +
766B LEU* 3.7 30.2 - - + +
769B PHE* 3.4 43.5 - + - -
811B MET 3.0 15.2 + - - +
812B LEU* 3.9 6.7 - - + +
814B VAL* 1.3 77.2 - - - +
816B ASN* 1.3 61.8 + - - +
819B TRP* 2.8 91.7 + + + +
832B VAL* 3.6 33.4 - - + +
835B TRP* 5.7 2.9 - - + -
838B ILE* 3.4 29.3 - - + +
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Residues in contact with ASN 816 (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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812B LEU* 3.0 20.3 + - - +
813B MET* 3.7 17.8 - - + +
814B VAL 3.2 0.2 - - - -
815B TRP* 1.3 81.4 - - - +
817B ARG* 1.3 59.1 + - + +
820B ILE* 3.0 45.0 + - - +
821B GLU* 3.2 12.6 + - - +
831B PRO* 3.4 26.9 - - - +
832B VAL* 3.5 25.1 + - + +
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Residues in contact with ARG 817 (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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804B GLU* 5.3 2.7 - - - +
807B THR* 6.1 0.4 - - - +
809B GLU* 4.6 19.2 + - - +
813B MET* 2.9 37.3 + - - +
814B VAL* 3.5 14.4 - - - +
815B TRP 3.2 0.2 - - - -
816B ASN* 1.3 75.5 - - + +
818B VAL* 1.3 65.6 + - + +
821B GLU* 2.9 40.7 + - - +
822B GLU* 2.8 26.5 + - - +
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Residues in contact with VAL 818 (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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514B GLN* 4.3 23.6 - - + +
515B ARG* 3.0 26.4 + - - +
766B LEU* 4.9 4.9 - - + -
802B LYS* 4.8 11.9 - - + +
804B GLU* 3.3 41.7 - - + +
814B VAL 3.0 9.1 + - - +
817B ARG* 1.3 79.6 - - + +
819B TRP* 1.3 82.0 + - + +
822B GLU* 4.4 4.5 - - - +
823B ASN* 2.9 14.2 + - - +
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Residues in contact with TRP 819 (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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514B GLN* 3.5 37.8 - - + +
515B ARG* 5.8 0.7 - - - -
518B TYR* 5.6 4.0 - + - -
726B ILE* 3.6 40.0 - - + +
727B VAL 3.2 28.7 - - - -
728B VAL* 4.3 6.1 - - + -
729B PRO* 4.0 16.8 - - + -
766B LEU* 3.4 28.1 - - + +
767B LEU* 5.2 7.0 - - + -
815B TRP* 2.8 58.5 + + + +
818B VAL* 1.3 101.5 - - + +
820B ILE* 1.3 65.6 + - - +
823B ASN* 3.0 15.2 - - - +
826B MET* 5.6 1.9 - - - +
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Residues in contact with ILE 820 (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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724B ARG* 6.1 5.6 - - - +
815B TRP* 5.4 1.1 - - - +
816B ASN* 3.0 31.1 + - - +
819B TRP* 1.3 83.0 - - - +
821B GLU* 1.3 72.6 + - + +
823B ASN* 3.2 17.1 - - - +
826B MET* 4.7 10.4 - - + +
828B ASP 5.7 0.9 - - - +
829B LYS* 3.3 50.2 - - + +
830B THR 3.3 21.8 - - - +
831B PRO* 3.7 1.6 - - + -
832B VAL* 3.4 28.9 - - + +
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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