Contacts of the helix formed by residues 753 - 769 (chain B) in PDB entry 4YZ9
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 TYR 753 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680B HIS* 3.5 45.9 - + + +
685B VAL* 4.3 14.8 - - + +
752B THR* 1.3 85.2 + - - +
754B THR* 1.3 86.5 + - + +
755B VAL 3.1 2.7 - - - -
756B ASP* 3.1 12.6 + - - +
757B ILE* 3.7 6.9 + - + +
820B ARG 4.9 2.9 + - - -
822B SER* 3.8 36.9 + - - -
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Residues in contact with THR 754 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741B GLU* 3.3 8.2 + - - -
752B THR* 3.2 21.6 + - - +
753B TYR* 1.3 105.3 - - + +
755B VAL* 1.3 64.6 + - - +
756B ASP 3.2 0.2 - - - -
757B ILE* 3.3 16.6 + - + +
758B PHE 3.4 4.5 + - - -
817B PRO* 3.5 30.0 - - - +
820B ARG* 3.2 31.8 + - + +
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Residues in contact with VAL 755 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685B VAL* 5.0 0.9 - - + -
687B ARG* 4.7 11.7 - - - +
738B ILE* 5.7 1.1 - - + -
739B ALA* 4.2 15.8 - - + +
741B GLU* 3.5 21.1 - - + +
742B MET* 3.4 45.8 - - + -
751B PRO* 4.3 2.5 - - + -
752B THR* 3.6 26.0 - - + +
753B TYR 3.1 0.8 - - - -
754B THR* 1.3 78.2 + - - +
756B ASP* 1.3 69.8 + - - +
758B PHE* 3.3 14.0 + - - +
759B SER* 3.3 16.0 + - - +
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Residues in contact with ASP 756 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676B LEU* 3.9 13.4 - - + +
680B HIS* 3.1 27.5 + - + +
685B VAL* 3.3 10.7 - - - +
686B HIS* 2.9 34.3 + - - +
687B ARG* 3.2 24.6 + - - -
689B LEU* 3.9 8.7 - - + +
753B TYR 3.1 7.4 + - - +
755B VAL* 1.3 77.3 - - - +
757B ILE* 1.3 60.0 + - - +
759B SER* 3.3 7.3 + - - -
760B ALA* 2.8 30.7 + - - +
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Residues in contact with ILE 757 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676B LEU* 4.1 15.7 - - + -
680B HIS* 4.3 7.4 - - + -
753B TYR* 3.9 17.5 - - + +
754B THR* 3.3 13.6 + - + +
756B ASP* 1.3 76.5 - - - +
758B PHE* 1.3 58.2 + - - +
760B ALA* 3.4 5.4 + - + +
761B GLY 2.9 23.2 + - - -
812B MET* 3.5 30.4 - - + +
820B ARG* 4.0 17.5 - - + -
821B PRO* 3.2 29.8 - - + +
822B SER* 4.0 0.4 - - - -
823B ALA* 3.6 25.6 - - - +
826B VAL* 4.9 3.1 - - + -
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Residues in contact with PHE 758 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737B TRP 4.0 4.7 - - - -
738B ILE 3.6 18.6 - - - -
739B ALA* 3.5 20.2 - - + -
740B PRO* 4.0 9.0 - - + -
754B THR 3.4 2.2 + - - -
755B VAL 3.3 10.4 + - - +
756B ASP 3.2 0.4 - - - -
757B ILE* 1.3 75.9 - - - +
759B SER* 1.3 66.4 + - - +
761B GLY 3.2 2.1 + - - -
762B CYS* 3.2 29.6 + - - -
775B PHE* 3.5 32.3 - + - -
785B ILE* 3.8 23.1 - - + -
812B MET 3.5 7.3 + - - -
813B ILE* 3.3 40.2 - - + +
815B MET* 5.8 2.5 - - - -
820B ARG* 3.5 28.9 - - - +
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Residues in contact with SER 759 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687B ARG 5.8 1.2 + - - -
688B ASP* 5.8 0.2 - - - -
689B LEU* 3.5 40.9 + - - +
737B TRP* 2.8 25.6 + - - -
738B ILE* 4.8 1.6 - - - -
755B VAL* 3.3 15.2 + - - +
756B ASP* 3.7 7.4 + - - -
758B PHE* 1.3 79.1 - - - +
760B ALA* 1.3 61.7 + - - +
762B CYS* 3.2 8.4 + - - +
763B VAL* 3.0 26.6 + - - +
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Residues in contact with ALA 760 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672B THR* 6.2 3.1 - - + -
673B THR* 5.7 1.6 - - - +
676B LEU* 4.4 11.4 - - + -
689B LEU* 4.1 13.6 - - + +
756B ASP 2.8 18.3 + - - +
757B ILE* 3.6 10.1 - - + +
759B SER* 1.3 76.8 - - - +
761B GLY* 1.3 57.2 + - - +
763B VAL* 3.0 8.2 + - - +
764B PHE* 2.8 48.2 + - + -
812B MET* 5.1 4.3 - - - -
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Residues in contact with GLY 761 (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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757B ILE 2.9 13.9 + - - -
758B PHE 3.2 4.0 + - - -
760B ALA* 1.3 76.2 - - - +
762B CYS* 1.3 62.4 + - - +
764B PHE* 3.3 2.9 + - - +
765B TYR* 3.2 22.2 + - - +
774B PRO* 4.7 0.2 - - - +
809B ILE* 4.1 6.5 - - - +
812B MET* 3.6 26.4 - - - +
813B ILE* 3.7 16.6 - - - -
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Residues in contact with CYS 762 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736B GLY 4.9 2.7 - - - -
737B TRP* 3.5 23.3 - - + -
758B PHE* 3.2 29.1 + - - -
759B SER* 3.5 9.4 - - - +
760B ALA 3.2 0.2 - - - -
761B GLY* 1.3 76.8 - - - +
763B VAL* 1.3 57.1 + - - +
765B TYR* 3.3 3.8 + - - +
766B TYR* 2.9 28.1 + - - +
773B HIS* 3.7 24.7 - - + +
774B PRO* 4.1 13.8 - - - +
775B PHE* 4.0 21.5 - - - -
813B ILE* 4.1 4.7 - - - -
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Residues in contact with VAL 763 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649B LEU* 3.7 29.2 - - + -
669B LEU* 4.2 12.1 - - + -
672B THR* 5.3 3.6 - - + -
689B LEU* 4.9 2.0 - - + -
690B LYS* 4.2 16.4 - - - +
691B PRO* 4.2 5.6 - - + -
694B ILE* 3.9 21.8 - - + -
737B TRP* 4.1 14.1 - - + -
759B SER 3.0 14.3 + - - +
760B ALA* 3.0 12.2 + - - +
762B CYS* 1.3 72.7 - - - +
764B PHE* 1.3 67.5 + - + +
766B TYR* 3.1 7.3 + - + +
767B VAL* 3.0 23.6 + - + +
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Residues in contact with PHE 764 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669B LEU* 3.7 34.7 - - + +
672B THR* 5.8 4.0 - - + -
673B THR* 3.1 28.0 - - - -
760B ALA* 2.8 40.3 + - + +
761B GLY 3.4 9.9 - - - +
763B VAL* 1.3 76.0 - - + +
765B TYR* 1.3 61.5 + - - +
767B VAL 3.5 0.2 + - - -
768B ILE* 3.2 29.7 + - + +
808B LEU* 3.9 15.3 - - + -
809B ILE* 4.1 12.3 - - + -
812B MET* 3.7 21.3 - - + -
826B VAL* 3.9 8.5 - - + -
831B PHE* 3.7 15.7 - + - -
832B PHE* 3.6 26.9 - + - -
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Residues in contact with TYR 765 (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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761B GLY 3.2 7.2 + - - +
762B CYS 3.8 1.3 - - - +
764B PHE* 1.3 76.5 - - - +
766B TYR* 1.3 55.2 + - - +
768B ILE* 4.6 2.9 - - + +
769B SER* 2.4 48.7 + - - -
772B SER* 3.2 37.5 - - - -
773B HIS 3.7 11.0 - - - -
774B PRO* 3.5 32.8 - - + -
791B SER 3.8 3.4 + - - -
792B LEU* 3.4 43.1 - - + -
793B ASP 3.7 0.9 + - - -
794B CYS* 3.2 43.6 + - + +
795B LEU* 4.2 11.7 - - + -
809B ILE* 4.0 20.6 - - + +
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Residues in contact with TYR 766 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649B LEU* 5.1 1.6 - - + -
650B GLN* 3.6 30.8 + - + +
653B VAL* 3.5 32.5 - - + +
654B GLU* 3.9 12.8 + - - +
691B PRO* 3.6 31.6 - - + -
737B TRP* 4.1 20.2 - + + -
762B CYS 2.9 17.8 + - - +
763B VAL* 3.1 9.2 + - - +
765B TYR* 1.3 77.5 - - - +
767B VAL* 1.3 64.6 + - + +
770B GLU* 3.2 2.6 + - - -
771B GLY* 3.1 55.5 + - - -
772B SER 3.3 11.8 + - - +
773B HIS* 5.2 3.4 - - + -
781B ARG* 5.8 3.4 - - - -
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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
----------------------------------------------------------
649B LEU* 4.0 26.2 - - + -
652B TYR* 4.7 12.6 - - + -
653B VAL* 4.0 17.4 - - + +
665B PRO* 3.6 39.0 - - + +
668B LEU* 4.9 2.0 - - + -
669B LEU* 3.9 19.7 - - + -
763B VAL* 3.0 16.3 + - + +
764B PHE 4.0 2.9 - - - +
766B TYR* 1.3 77.5 - - + +
768B ILE* 1.3 67.2 + - + +
770B GLU* 3.2 16.6 + - - +
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Residues in contact with ILE 768 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665B PRO* 5.7 5.2 - - + -
666B ILE* 5.8 3.1 - - + -
669B LEU* 4.4 6.1 - - + -
764B PHE* 3.2 19.1 + - + +
765B TYR* 4.3 4.3 - - + +
767B VAL* 1.3 78.3 - - + +
769B SER* 1.3 61.0 + - - +
770B GLU* 3.5 10.0 + - - +
795B LEU* 4.2 21.3 - - + -
802B ASP* 5.8 2.7 - - - +
805B ALA* 4.0 15.9 - - + -
809B ILE* 4.3 11.9 - - + -
831B PHE* 3.5 38.6 - - + -
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Residues in contact with SER 769 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765B TYR* 2.4 42.6 + - - -
766B TYR 3.6 0.5 + - - -
768B ILE* 1.3 76.1 - - - +
770B GLU* 1.3 70.6 + - - +
772B SER* 2.6 42.5 + - - -
794B CYS* 4.0 17.9 - - - -
795B LEU* 6.5 0.2 - - - -
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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
------------------------------------------------------------
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