Contacts of the helix formed by residues 710 - 733 (chain E) in PDB entry 6V3O
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 LYS 710 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707E VAL* 6.5 0.2 - - + -
708E SER 3.5 3.5 + - - +
709E PRO* 1.3 75.9 - - - +
711E PRO* 1.3 74.5 - - + +
712E GLU* 3.0 31.2 + - - +
713E TRP* 3.1 53.8 + - + +
714E ARG* 3.1 21.6 + - - +
814E GLU* 4.6 9.8 + - - -
818E GLU* 5.4 3.8 - - - -
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Residues in contact with PRO 711 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709E PRO 4.3 2.5 - - - +
710E LYS* 1.3 89.5 - - + +
712E GLU* 1.3 69.7 + - + +
714E ARG* 3.3 12.6 + - + +
715E LYS* 2.9 30.4 + - - +
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Residues in contact with GLU 712 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710E LYS* 3.0 36.6 + - - +
711E PRO* 1.3 95.7 - - + +
713E TRP* 1.3 65.3 + - + +
715E LYS* 3.5 11.3 + - + +
716E LEU* 3.0 32.3 + - + +
811E VAL* 4.9 11.2 - - + +
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Residues in contact with TRP 713 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707E VAL* 4.6 12.3 - - + -
708E SER 4.7 1.6 - - - -
709E PRO* 3.9 6.3 - - + -
710E LYS* 3.1 57.9 + - + +
712E GLU* 1.3 76.4 + - + +
714E ARG* 1.3 65.5 + - - +
716E LEU* 3.3 2.6 + - - +
717E MET* 2.9 29.9 + - - +
811E VAL* 3.9 21.3 + - + +
814E GLU* 4.3 10.9 + - - -
815E MET* 3.3 42.9 - - + +
818E GLU* 4.0 37.5 - - + -
819E TRP* 3.5 48.2 - + + -
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Residues in contact with ARG 714 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615E TRP* 3.9 31.9 - - + -
619E ARG* 4.6 6.3 - - - +
622E GLU* 2.7 42.2 + - - -
709E PRO* 4.0 37.2 + - + +
710E LYS 3.1 13.0 + - - +
711E PRO* 3.3 12.8 + - + +
713E TRP* 1.3 75.9 - - - +
715E LYS* 1.3 57.4 + - - +
717E MET* 3.2 3.3 + - - +
718E ASP* 2.8 38.9 + - - +
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Residues in contact with LYS 715 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711E PRO 2.9 17.4 + - - +
712E GLU* 3.8 10.3 - - + +
714E ARG* 1.3 75.9 - - - +
716E LEU* 1.3 73.7 + - - +
718E ASP* 3.2 11.6 + - + +
719E GLU* 3.0 66.6 + - + +
805E ASP* 6.3 0.4 - - - +
808E ASN* 4.7 10.5 + - - +
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Residues in contact with LEU 716 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712E GLU 3.0 19.0 + - - +
713E TRP* 3.8 4.9 - - - +
714E ARG 3.3 0.2 - - - -
715E LYS* 1.3 78.1 - - + +
717E MET* 1.3 61.0 + - - +
719E GLU* 3.4 16.0 + - + +
720E MET* 2.9 40.3 + - + +
800E PHE* 6.1 0.7 - - + -
801E ALA* 4.2 13.5 - - + -
808E ASN* 3.8 40.4 - - - +
811E VAL* 4.6 16.2 - - + -
812E LEU* 3.6 35.4 - - + -
815E MET* 4.8 5.2 - - - -
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Residues in contact with MET 717 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611E LEU* 4.0 25.1 - - + -
615E TRP* 3.5 46.8 - - + -
713E TRP 2.9 20.7 + - - +
714E ARG 3.6 0.4 - - - +
716E LEU* 1.3 74.8 - - - +
718E ASP* 1.3 58.5 + - - +
720E MET* 3.6 22.4 - - + +
721E ALA* 2.9 32.8 + - + +
815E MET* 4.9 3.1 - - + -
819E TRP* 3.8 22.7 - - + -
821E PHE* 3.9 15.9 - - + -
822E PHE* 3.9 22.2 - - + -
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Residues in contact with ASP 718 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615E TRP* 2.9 26.3 + - - +
619E ARG* 3.8 16.4 + - - -
714E ARG* 2.8 22.6 + - - +
715E LYS* 3.2 11.9 + - - +
717E MET* 1.3 78.5 - - - +
719E GLU* 1.3 63.9 + - + +
721E ALA* 3.4 10.0 + - - +
722E VAL* 3.4 19.0 + - - +
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Residues in contact with GLU 719 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715E LYS* 3.0 54.0 + - + +
716E LEU* 4.0 15.3 - - + +
718E ASP* 1.3 76.9 - - + +
720E MET* 1.3 63.9 + - + +
722E VAL* 3.4 9.2 + - - +
723E VAL* 3.2 26.0 + - - +
800E PHE* 3.8 27.6 - - + -
804E LYS* 5.7 2.6 - - - +
808E ASN* 5.1 2.3 + - - -
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Residues in contact with MET 720 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611E LEU* 4.2 9.6 - - + -
716E LEU* 2.9 26.6 + - + +
717E MET* 3.6 33.2 - - + +
719E GLU* 1.3 76.1 - - + +
721E ALA* 1.3 58.7 + - - +
723E VAL* 3.2 6.1 + - - -
724E ALA* 2.8 31.3 + - - +
797E ALA* 3.7 29.7 - - + +
798E PHE* 4.0 28.0 - - + -
800E PHE* 5.1 2.2 - - + -
801E ALA* 4.2 12.8 - - + -
812E LEU* 3.8 28.7 - - + -
815E MET* 4.7 0.4 - - + -
822E PHE* 4.4 8.5 - - + -
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Residues in contact with ALA 721 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611E LEU* 5.2 3.1 - - + +
612E SER* 3.0 42.8 + - - +
615E TRP* 4.3 15.3 - - + -
619E ARG* 5.5 3.8 - - - +
717E MET* 2.9 17.9 + - + +
718E ASP* 3.7 5.8 - - - +
719E GLU 3.2 0.4 - - - -
720E MET* 1.3 77.1 - - - +
722E VAL* 1.3 61.4 + - + +
724E ALA* 4.5 1.1 - - - -
725E THR* 3.1 14.2 + - - -
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Residues in contact with VAL 722 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718E ASP 3.5 15.7 - - - +
719E GLU* 3.4 9.2 + - - +
720E MET 3.3 0.6 - - - -
721E ALA* 1.3 77.5 - - + +
723E VAL* 1.3 66.4 + - + +
725E THR* 4.0 2.7 - - - -
726E GLU* 3.0 30.3 + - + +
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Residues in contact with VAL 723 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719E GLU 3.2 16.6 - - - +
720E MET* 3.2 6.4 + - - +
722E VAL* 1.3 78.6 - - + +
724E ALA* 1.3 58.1 + - - +
726E GLU* 3.4 14.8 + - - +
727E GLU* 2.9 27.5 + - - +
796E ALA* 3.8 32.5 - - + +
797E ALA* 4.3 4.7 - - - -
800E PHE* 3.6 40.8 - - + -
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Residues in contact with ALA 724 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608E ALA 4.7 1.3 - - - +
609E GLY* 5.9 2.0 - - - -
611E LEU* 4.4 15.7 - - + +
612E SER* 3.6 14.4 - - - +
720E MET 2.8 17.0 + - - +
722E VAL 3.3 0.2 - - - -
723E VAL* 1.3 76.8 - - - +
725E THR* 1.3 57.3 + - - +
727E GLU* 3.1 2.9 + - - +
728E TYR* 2.8 30.8 + - - +
793E GLY* 3.3 32.9 - - - +
797E ALA* 4.0 6.2 - - + +
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Residues in contact with THR 725 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608E ALA* 2.9 32.8 + - + +
612E SER* 2.8 27.6 + - - -
721E ALA 3.1 9.9 + - - -
722E VAL* 4.1 2.7 - - - -
724E ALA* 1.3 74.1 - - - +
726E GLU* 1.3 66.6 + - - +
728E TYR* 3.8 1.5 - - - +
729E ARG* 2.9 52.9 + - - +
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Residues in contact with GLU 726 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722E VAL* 3.0 25.9 + - + +
723E VAL* 3.5 14.0 - - - +
725E THR* 1.3 77.3 - - - +
727E GLU* 1.3 56.6 + - - +
729E ARG* 3.9 3.6 - - - +
730E SER* 2.9 29.3 + - - -
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Residues in contact with GLU 727 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723E VAL 2.9 18.0 + - - +
724E ALA 3.7 3.1 - - - +
726E GLU* 1.3 74.3 - - - +
728E TYR* 1.3 68.2 + - - +
730E SER* 3.3 19.1 + - - -
731E VAL* 3.5 14.0 + - - +
792E LEU* 4.7 3.5 - - + +
793E GLY* 3.8 21.8 - - - +
796E ALA* 3.8 27.5 + - + +
863E LYS* 2.6 44.0 + - - +
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Residues in contact with TYR 728 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605E GLY 3.6 11.7 - - - -
606E LYS* 2.9 30.6 + - - -
607E ASP 3.9 7.4 - - - -
608E ALA* 3.9 6.5 - - - -
609E GLY* 3.5 32.8 - - - +
724E ALA 2.8 20.5 + - - +
725E THR* 3.8 4.3 - - - +
727E GLU* 1.3 72.5 - - - +
729E ARG* 1.3 63.8 + - + +
731E VAL* 3.3 4.5 + - - +
732E VAL* 3.0 53.7 + - + +
733E VAL* 5.7 1.3 - - + -
769E ILE* 5.0 0.2 - - - +
777E TRP* 3.4 30.8 + + - -
789E PRO* 4.9 10.8 - - + -
792E LEU* 3.7 38.8 - - + +
793E GLY* 4.5 0.2 - - - -
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Residues in contact with ARG 729 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568E LEU* 6.0 1.4 - - - +
607E ASP* 3.6 38.0 + - - +
608E ALA* 3.9 13.7 - - - +
725E THR* 2.9 36.8 + - + +
726E GLU* 4.1 3.6 - - - +
728E TYR* 1.3 82.0 - - + +
730E SER* 1.3 65.6 + - - +
732E VAL 4.4 0.7 - - - +
733E VAL* 3.1 34.7 + - + +
734E LYS* 2.9 32.5 + - + +
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Residues in contact with SER 730 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726E GLU* 2.9 21.0 + - - -
727E GLU* 3.5 19.5 + - - -
728E TYR 3.2 0.4 - - - -
729E ARG* 1.3 77.0 - - - +
731E VAL* 1.3 63.2 + - - +
734E LYS* 3.8 14.8 - - - +
735E GLU* 3.6 21.8 + - - +
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Residues in contact with VAL 731 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727E GLU* 3.9 10.8 - - - +
728E TYR 3.3 5.9 + - - +
729E ARG 3.1 0.4 - - - -
730E SER* 1.3 87.6 - - - +
732E VAL* 1.3 62.5 + - - +
733E VAL 3.6 0.2 - - - -
735E GLU* 4.0 11.3 - - - +
738E PHE* 3.3 38.1 - - + +
788E LEU* 5.1 0.7 - - + -
792E LEU* 4.1 20.4 - - + -
856E PHE* 4.2 9.2 - - + -
860E LEU* 3.7 26.0 - - + -
863E LYS* 4.2 25.1 - - - -
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Residues in contact with VAL 732 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606E LYS 5.3 0.9 - - - +
728E TYR* 3.0 53.1 + - + +
731E VAL* 1.3 79.1 - - - +
733E VAL* 1.3 71.4 + - + +
735E GLU 5.0 0.5 - - - +
738E PHE* 3.6 30.6 - - + +
739E VAL* 5.3 2.3 - - - +
769E ILE* 4.1 35.3 - - + +
777E TRP* 4.1 12.1 - - + -
788E LEU* 4.6 0.4 - - + -
792E LEU* 3.9 12.3 - - + -
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Residues in contact with VAL 733 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607E ASP 5.9 1.3 - - - +
728E TYR* 5.7 1.6 - - + -
729E ARG* 3.1 41.0 + - + +
732E VAL* 1.3 95.9 - - + +
734E LYS* 1.3 77.9 + - + +
735E GLU 3.5 6.3 + - - +
736E ALA* 5.6 0.7 - - - -
769E ILE* 5.9 1.3 - - + -
770E THR* 5.4 12.8 - - + -
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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