Contacts of the helix formed by residues 763 - 782 (chain B) in PDB entry 4Q0W
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 763 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761B LYS 4.0 0.8 + - - -
762B ARG* 1.3 75.9 - - - +
764B SER* 1.3 61.9 + - - +
765B ASP* 3.0 21.5 + - - +
766B GLU* 2.9 50.5 + - - +
767B VAL* 2.9 28.6 + - - +
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Residues in contact with SER 764 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763B ASP* 1.3 73.7 - - - +
765B ASP* 1.3 62.1 + - - +
767B VAL* 3.4 7.9 + - - +
768B THR* 2.9 34.4 + - - -
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Residues in contact with ASP 765 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763B ASP* 3.0 11.4 + - - +
764B SER* 1.3 78.1 - - - +
766B GLU* 1.3 59.1 + - + +
768B THR* 3.2 8.5 + - - -
769B MET* 2.9 36.4 + - + +
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Residues in contact with GLU 766 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761B LYS 3.9 4.7 - - - +
762B ARG* 3.3 25.0 - - + +
763B ASP* 2.9 46.1 + - - +
765B ASP* 1.3 77.4 - - + +
767B VAL* 1.3 62.9 + - - +
769B MET* 3.3 11.6 + - + +
770B ASP* 3.1 28.1 + - - +
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Residues in contact with VAL 767 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762B ARG* 3.6 47.1 - - + +
763B ASP 2.9 21.2 + - - +
764B SER* 3.8 7.2 - - - +
766B GLU* 1.3 74.6 - - - +
768B THR* 1.3 63.8 + - - +
770B ASP* 3.2 3.6 + - - +
771B MET* 3.0 40.8 + - + +
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Residues in contact with THR 768 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE* 3.9 18.4 - - + +
36B TYR* 4.3 18.3 + - - +
764B SER* 2.9 21.6 + - - -
765B ASP* 3.4 8.3 - - - +
767B VAL* 1.3 77.7 - - - +
769B MET* 1.3 63.3 + - + +
771B MET* 3.2 10.0 + - - +
772B ILE* 3.0 43.0 + - + +
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Residues in contact with MET 769 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765B ASP* 2.9 28.5 + - + +
766B GLU* 3.3 12.5 + - + +
768B THR* 1.3 74.7 - - - +
770B ASP* 1.3 61.3 + - - +
772B ILE* 3.6 10.3 + - - +
773B LYS* 3.0 27.4 + - - +
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Residues in contact with ASP 770 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762B ARG* 2.3 51.5 + - - +
766B GLU* 3.1 12.1 + - - +
767B VAL 3.6 4.5 - - - +
768B THR 3.2 0.4 - - - -
769B MET* 1.3 76.8 - - - +
771B MET* 1.3 59.9 + - + +
773B LYS* 3.3 22.6 + - - +
774B GLU* 2.9 41.4 + - - +
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Residues in contact with MET 771 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE* 3.9 24.0 - - + -
39B LEU* 3.5 33.4 - - + -
54B HIS* 3.4 55.6 - - + +
767B VAL* 3.0 39.1 + - + +
768B THR* 3.2 8.9 + - - +
770B ASP* 1.3 73.0 - - + +
772B ILE* 1.3 65.6 + - - +
774B GLU* 3.2 4.1 + - - +
775B VAL* 2.9 27.5 + - - +
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Residues in contact with ILE 772 (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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35B ILE* 4.5 19.3 - - + -
76B PHE* 4.7 16.8 - - + -
768B THR* 3.0 35.7 + - + +
769B MET* 3.8 11.4 - - - +
771B MET* 1.3 76.8 - - - +
773B LYS* 1.3 56.1 + - - +
775B VAL* 3.3 6.3 + - - +
776B GLN* 2.9 56.5 + - + +
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Residues in contact with LYS 773 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769B MET 3.0 17.6 + - - +
770B ASP* 3.3 28.2 + - - +
772B ILE* 1.3 76.9 - - - +
774B GLU* 1.3 63.0 + - - +
776B GLN* 3.4 10.2 + - - +
777B GLU* 2.9 28.4 + - + +
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Residues in contact with GLU 774 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASN* 4.3 3.8 - - - +
54B HIS* 2.6 39.4 + - - +
55B ILE* 4.5 8.7 - - + -
770B ASP* 2.9 26.3 + - - +
771B MET* 3.2 5.8 + - - +
773B LYS* 1.3 81.0 - - - +
775B VAL* 1.3 61.6 + - - +
777B GLU* 3.3 7.7 + - - +
778B LEU* 2.9 23.6 + - - +
963B PHE* 3.5 13.1 - - + -
967B GLN* 3.8 29.3 + - - +
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Residues in contact with VAL 775 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE* 4.8 2.5 - - + -
54B HIS* 4.0 21.8 - - + +
55B ILE* 4.8 4.0 - - + +
58B PHE* 3.2 66.4 - - + -
76B PHE* 3.8 17.3 - - + -
771B MET 2.9 18.7 + - - +
772B ILE* 3.7 4.3 - - - +
774B GLU* 1.3 76.7 - - - +
776B GLN* 1.3 60.2 + - - +
778B LEU* 3.2 9.3 + - + +
779B LEU* 2.9 28.6 + - + +
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Residues in contact with GLN 776 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B PHE* 3.3 43.9 - - + +
772B ILE* 2.9 41.0 + - - +
773B LYS* 3.8 7.3 - - - +
775B VAL* 1.3 75.8 - - - +
777B GLU* 1.3 64.5 + - - +
779B LEU* 3.3 8.1 + - - +
780B SER* 3.1 21.1 + - - -
786B TYR* 3.5 46.2 + - + +
788B THR* 4.3 9.9 + - - -
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Residues in contact with GLU 777 (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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773B LYS* 2.9 16.2 + - + +
774B GLU* 3.3 11.0 + - - +
776B GLN* 1.3 77.2 - - - +
778B LEU* 1.3 63.8 + - - +
780B SER* 2.9 23.6 + - - -
781B ARG* 2.6 60.0 + - - +
963B PHE* 3.6 16.4 - - + -
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Residues in contact with LEU 778 (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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55B ILE* 4.0 19.7 - - + +
58B PHE* 4.2 7.9 - - + -
59B PHE* 4.0 35.9 - - + +
62B ILE* 4.0 12.1 - - + -
774B GLU 2.9 13.5 + - - +
775B VAL* 3.2 10.3 + - - +
777B GLU* 1.3 75.9 - - - +
779B LEU* 1.3 64.2 + - - +
781B ARG* 3.1 6.6 + - - +
782B PHE* 3.1 33.9 + - + -
960B LEU* 3.8 22.4 - - + -
963B PHE* 3.9 25.9 - - + -
964B MET* 4.5 2.9 - - - -
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Residues in contact with LEU 779 (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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58B PHE* 5.0 0.2 - - + -
62B ILE* 3.6 26.2 - - + -
74B PHE* 3.6 55.0 - - + -
76B PHE* 3.8 24.7 - - + -
775B VAL* 2.9 20.9 + - + +
776B GLN* 3.6 10.8 - - - +
778B LEU* 1.3 76.5 - - - +
780B SER* 1.3 61.1 + - - +
782B PHE* 3.1 12.1 + - - +
784B ILE* 2.9 45.9 + - + +
786B TYR* 4.1 10.5 - - + -
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Residues in contact with SER 780 (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 GLN 3.1 13.7 + - - -
777B GLU* 2.9 30.7 + - - -
779B LEU* 1.3 76.5 - - - +
781B ARG* 1.3 57.3 + - - +
783B GLY* 2.9 18.7 + - - +
784B ILE 4.1 6.9 + - - +
786B TYR* 4.7 9.8 - - - -
956B ASP* 5.7 0.3 - - - +
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Residues in contact with ARG 781 (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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777B GLU* 2.6 47.9 + - - +
778B LEU 3.1 6.9 + - - +
780B SER* 1.3 78.6 - - - +
782B PHE* 1.3 53.9 + - - +
783B GLY 3.2 1.0 + - - -
956B ASP* 2.7 40.0 + - - +
959B MET* 2.8 76.3 + - + +
960B LEU* 3.7 18.1 - - + +
962B SER* 3.7 7.1 + - - -
963B PHE* 3.6 32.1 - - - +
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Residues in contact with PHE 782 (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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59B PHE* 3.7 20.4 - + - -
62B ILE* 3.6 28.9 - - + -
63B CYS* 4.1 5.6 - - - -
66B LEU* 3.4 29.3 - - + +
778B LEU* 3.1 39.1 + - + -
779B LEU 3.1 11.4 + - - +
781B ARG* 1.3 77.8 - - - +
783B GLY* 1.3 59.2 + - - +
784B ILE* 3.5 16.7 + - + +
953B GLY 4.3 1.6 - - - +
954B VAL 3.7 0.9 - - - -
955B PRO* 3.4 31.6 - - + +
960B LEU* 3.7 15.7 - - + -
979B LEU* 3.6 33.0 - - + -
982B LEU* 4.3 7.0 - - + -
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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
------------------------------------------------------------
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