Contacts of the helix formed by residues 814 - 826 (chain B) in PDB entry 2XWU
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 814 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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772B THR* 5.9 0.4 - - - +
776B LEU* 4.2 9.9 - - + +
812B ARG 3.8 3.1 + - - +
813B LEU* 1.3 73.6 - - - +
815B VAL* 1.3 61.1 + - - +
816B LYS* 3.3 11.8 + - - +
817B ALA* 3.0 34.7 + - + +
818B VAL* 3.2 26.9 + - - +
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Residues in contact with VAL 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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808B PHE* 3.6 39.0 - - + +
810B CYS 5.7 0.2 - - - +
813B LEU* 3.4 22.9 + - + +
814B ASP* 1.3 71.9 + - - +
816B LYS* 1.3 62.4 + - - +
818B VAL* 3.7 7.8 - - + +
819B PHE* 3.1 23.6 + - + +
844B LEU* 6.0 3.1 - - + -
853B SER* 4.0 20.9 - - - +
854B VAL* 4.9 4.9 - - + +
857B VAL* 3.3 27.6 - - + -
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Residues in contact with LYS 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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814B ASP* 3.3 9.2 + - - +
815B VAL* 1.3 80.5 - - - +
817B ALA* 1.3 56.4 + - - +
819B PHE* 3.6 3.3 + - - +
820B GLN* 3.1 31.2 + - - +
857B VAL* 4.3 14.0 - - + +
860B GLU* 3.9 16.6 + - - +
861B ASP* 3.0 43.8 + - - +
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Residues in contact with ALA 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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776B LEU* 3.4 24.6 - - + +
780B GLN* 5.5 8.1 - - - +
814B ASP* 3.0 32.1 + - - +
816B LYS* 1.3 73.8 - - - +
818B VAL* 1.3 60.8 + - - +
820B GLN* 3.2 9.2 + - - +
821B CYS* 2.9 28.8 + - - +
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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
----------------------------------------------------------
772B THR* 4.1 26.0 - - + -
776B LEU* 4.1 12.6 - - + -
793B PHE* 4.8 1.1 - - + -
797B LEU* 3.5 38.8 - - + +
808B PHE* 4.8 7.2 - - + -
813B LEU* 4.7 6.5 - - + -
814B ASP 3.2 18.2 - - - +
815B VAL* 3.7 9.6 - - - +
817B ALA* 1.3 74.9 - - - +
819B PHE* 1.3 65.0 + - - +
821B CYS* 3.1 4.9 + - - +
822B ALA* 3.0 22.3 + - - +
840B PHE* 4.0 15.0 - - + -
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Residues in contact with PHE 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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815B VAL* 3.1 9.8 + - + +
816B LYS 3.8 3.6 - - - +
818B VAL* 1.3 80.7 - - - +
820B GLN* 1.3 59.7 + - - +
822B ALA* 3.5 6.2 + - - +
823B VAL* 2.8 51.8 + - + +
840B PHE* 4.6 4.9 - + + -
841B PHE* 3.7 17.0 - + - -
844B LEU* 3.7 26.9 - - + -
857B VAL* 3.5 35.2 - - + -
858B VAL* 4.7 9.9 - - + -
861B ASP* 3.5 36.1 - - + -
862B GLY* 4.1 9.2 - - - -
864B MET* 5.1 2.7 - - + -
865B LEU* 3.7 26.9 - - + -
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Residues in contact with GLN 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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779B PHE* 6.2 0.4 - - + -
816B LYS* 3.1 19.2 + - - +
817B ALA* 3.3 13.9 - - - +
818B VAL 3.1 0.2 - - - -
819B PHE* 1.3 75.6 - - - +
821B CYS* 1.3 64.3 + - - +
823B VAL* 3.5 5.7 + - - +
824B LEU* 3.1 42.7 + - + +
861B ASP* 5.7 4.6 - - - -
864B MET* 3.8 29.6 - - - +
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Residues in contact with CYS 821 (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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776B LEU* 4.1 11.0 - - + -
779B PHE* 3.8 48.4 - - + -
790B VAL* 5.2 4.9 - - - -
793B PHE* 4.2 26.5 - - + -
794B MET* 4.9 5.8 - - - -
817B ALA 2.9 14.4 + - - +
818B VAL* 3.4 9.2 - - - +
820B GLN* 1.3 75.4 - - - +
822B ALA* 1.3 59.0 + - - +
824B LEU* 3.4 1.9 + - - +
825B ALA* 3.0 29.3 + - - +
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Residues in contact with ALA 822 (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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794B MET* 3.2 35.2 - - + -
818B VAL 3.0 10.6 + - - +
819B PHE 3.8 1.8 - - - +
820B GLN 3.3 0.2 - - - -
821B CYS* 1.3 76.0 - - - +
823B VAL* 1.3 63.4 - - - +
825B ALA 3.4 6.1 + - - -
826B LEU* 3.4 6.8 + - - +
837B SER* 2.5 19.6 + - - -
840B PHE* 3.4 16.6 - - + -
841B PHE* 3.3 20.4 - - + -
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Residues in contact with VAL 823 (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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819B PHE* 2.8 50.3 + - + +
820B GLN* 3.9 7.2 - - - +
821B CYS 3.3 0.2 - - - -
822B ALA* 1.3 76.3 - - - +
824B LEU* 1.3 64.9 + - + +
826B LEU* 3.5 18.0 + - - +
827B LYS* 4.3 2.9 + - - +
841B PHE* 3.6 16.2 - - + -
864B MET* 3.9 37.7 - - + +
865B LEU* 4.2 8.5 - - + +
868B ALA* 3.9 16.3 - - + +
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Residues in contact with LEU 824 (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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779B PHE* 4.2 23.8 - - + -
783B PRO* 5.6 6.1 - - + -
784B ARG* 5.4 0.2 + - - -
820B GLN* 3.1 39.8 + - + +
821B CYS 3.9 3.8 - - - +
823B VAL* 1.3 78.3 - - + +
825B ALA* 1.3 64.4 + - - +
827B LYS* 3.1 19.4 + - + +
828B PHE* 3.2 16.8 - - + -
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Residues in contact with ALA 825 (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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790B VAL* 3.9 26.0 - - + -
794B MET* 4.8 2.5 - - - -
821B CYS 3.0 17.9 + - - +
822B ALA* 3.6 7.9 - - - +
823B VAL 3.3 0.2 - - - -
824B LEU* 1.3 77.9 - - - +
826B LEU* 1.3 61.6 + - - +
827B LYS 3.0 0.4 - - - -
828B PHE* 3.0 34.2 + - + +
833B THR* 4.4 3.0 - - + +
834B VAL* 3.8 9.4 - - - +
837B SER* 3.8 15.7 - - - +
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Residues in contact with LEU 826 (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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822B ALA 3.4 9.9 - - - +
823B VAL* 3.6 11.4 - - - +
824B LEU 3.2 1.0 - - - -
825B ALA* 1.3 76.4 - - - +
827B LYS* 1.3 58.9 + - + +
828B PHE 3.3 1.5 + - - +
834B VAL* 3.6 22.3 - - + +
837B SER* 3.4 24.2 - - - +
838B CYS* 3.7 31.4 - - - +
841B PHE* 3.5 21.5 - - + -
865B LEU* 3.9 16.2 - - + -
868B ALA* 4.6 11.9 - - + +
869B VAL* 4.6 4.5 - - + -
872B ALA* 5.6 1.0 - - - +
877B ALA* 5.4 3.1 - - - +
885B PHE* 4.0 27.8 - - + -
888B ILE* 4.2 4.0 - - + -
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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