Contacts of the helix formed by residues 609 - 631 (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 GLY 609 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605E GLY* 2.9 18.3 + - - -
608E ALA* 1.3 82.7 - - - +
610E ARG* 1.3 66.6 + - - -
611E LEU 3.5 2.2 - - - -
613E ALA* 3.3 20.8 + - - +
724E ALA* 5.6 2.7 - - - -
728E TYR* 3.5 28.9 - - - -
789E PRO 5.3 0.2 - - - -
792E LEU 4.3 3.6 - - - -
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Residues in contact with ARG 610 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601E TYR* 3.9 20.2 + - - +
602E SER* 4.4 10.9 + - - +
605E GLY* 4.2 10.8 + - - -
609E GLY* 1.3 72.6 - - - -
611E LEU* 1.3 63.8 + - - +
613E ALA* 3.4 3.5 + - - +
614E ALA* 3.0 27.6 + - + +
642E GLY 2.5 28.5 + - - -
643E GLY* 4.4 1.2 - - - -
644E THR* 4.7 2.8 - - - +
778E ILE* 5.9 0.2 - - - +
789E PRO 4.2 6.8 + - - +
790E VAL* 3.0 41.1 - - - +
791E TRP* 5.3 0.2 - - - -
792E LEU 4.5 6.0 + - - +
794E VAL* 5.1 3.4 - - + -
828E LEU* 3.6 23.9 - - - +
829E LEU* 4.5 11.2 - - + -
970E GLY* 3.1 33.1 + - - -
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Residues in contact with LEU 611 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609E GLY 3.5 0.4 - - - -
610E ARG* 1.3 78.8 - - - +
612E SER* 1.3 62.8 - - - +
614E ALA* 3.3 7.9 + - + +
615E TRP* 3.1 20.4 + - - +
717E MET* 4.0 23.1 - - + -
720E MET* 4.2 22.7 - - + +
721E ALA* 5.2 2.5 - - - +
724E ALA* 4.4 11.8 - - + +
794E VAL* 3.8 28.1 - - + +
797E ALA* 3.9 28.0 - - + -
798E PHE* 4.8 8.1 - - + -
821E PHE* 5.9 1.1 - - + -
822E PHE* 5.2 7.2 - - + -
825E THR* 5.0 12.1 - - - +
826E LEU* 5.7 2.7 - - + -
829E LEU* 6.2 3.1 - - + -
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Residues in contact with SER 612 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568E LEU* 3.5 16.0 - - - +
608E ALA 3.5 9.0 + - - -
609E GLY 3.9 1.0 + - - -
610E ARG 3.4 0.2 - - - -
611E LEU* 1.3 74.8 - - - +
613E ALA* 1.3 66.9 + - - +
615E TRP* 3.2 1.7 + - - +
616E GLN* 2.9 21.7 + - - +
619E ARG* 5.5 0.2 + - - -
721E ALA* 3.0 33.4 + - - +
724E ALA* 3.6 6.8 - - - +
725E THR* 2.8 33.4 + - - -
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Residues in contact with ALA 613 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568E LEU* 3.8 14.4 - - + +
571E LEU* 4.7 1.2 - - - +
601E TYR* 4.7 3.1 - - - +
604E SER* 3.7 16.4 - - - +
605E GLY* 3.7 24.0 - - - +
609E GLY 3.3 19.2 + - - +
610E ARG* 3.7 4.3 - - - +
612E SER* 1.3 78.3 - - - +
614E ALA* 1.3 58.1 + - - +
616E GLN* 3.9 0.9 - - - +
617E LEU* 2.9 38.1 + - + +
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Residues in contact with ALA 614 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601E TYR* 6.0 3.1 - - + -
610E ARG* 3.0 21.4 + - + +
611E LEU* 3.6 9.4 - - + +
612E SER 3.2 0.2 - - - -
613E ALA* 1.3 76.1 - - - +
615E TRP* 1.3 57.7 + - - +
617E LEU* 3.5 11.2 - - - +
618E TYR 3.2 21.0 + - - -
821E PHE* 3.6 27.4 - - + -
825E THR* 4.5 14.6 - - + -
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Residues in contact with TRP 615 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611E LEU 3.1 10.8 + - - +
612E SER* 3.2 4.9 + - - +
614E ALA* 1.3 74.8 - - - +
616E GLN* 1.3 63.4 + - - +
618E TYR* 3.4 23.4 + + + -
619E ARG* 3.1 60.3 + - + +
714E ARG* 3.9 42.0 - - + -
717E MET* 3.5 50.8 - - + +
718E ASP* 2.9 24.1 + - - -
721E ALA* 4.3 8.1 - - + -
819E TRP* 3.6 27.4 - + - -
821E PHE* 3.9 18.4 - + - -
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Residues in contact with GLN 616 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568E LEU* 3.4 36.5 - - + +
571E LEU* 3.9 22.1 + - + -
572E GLN* 3.8 40.5 - - - +
612E SER 2.9 6.8 + - - +
613E ALA 4.2 0.2 - - - +
615E TRP* 1.3 74.3 - - - +
617E LEU* 1.3 61.3 + - - +
619E ARG* 2.8 43.2 + - - +
620E ALA* 2.8 32.0 + - - +
623E GLU* 5.5 3.6 + - - -
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Residues in contact with LEU 617 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571E LEU* 4.1 18.3 - - + +
599E VAL* 3.6 41.7 - - + -
600E GLY 3.9 15.5 - - - +
601E TYR* 3.7 37.9 - - + -
604E SER* 4.9 2.5 - - - +
613E ALA* 2.9 26.4 + - + +
614E ALA* 3.5 9.2 - - - +
616E GLN* 1.3 74.5 - - - +
618E TYR* 1.3 65.9 + - - +
620E ALA* 3.2 5.1 + - - +
621E GLN* 2.9 38.0 + - + +
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Residues in contact with TYR 618 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614E ALA 3.2 10.8 + - - +
615E TRP* 3.4 29.1 + + + +
617E LEU* 1.3 78.4 - - - +
619E ARG* 1.3 59.6 + - - +
621E GLN* 3.5 12.7 + - - +
622E GLU* 3.0 50.7 + - - +
658E SER 4.2 5.6 - - - -
659E GLN 4.7 0.2 - - - -
660E PRO* 3.6 31.5 - - + +
661E PRO* 4.0 16.6 - - - +
706E PRO* 5.6 1.8 - - + +
707E VAL 4.7 2.3 + - - -
709E PRO* 3.5 34.1 - - + +
714E ARG* 4.8 0.9 - - - -
819E TRP* 4.5 4.8 + + - -
821E PHE* 3.9 37.2 - + + -
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Residues in contact with ARG 619 (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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612E SER 5.5 0.2 + - - -
615E TRP* 3.1 64.1 + - + +
616E GLN* 2.8 48.1 + - - +
618E TYR* 1.3 73.6 - - - +
620E ALA* 1.3 66.6 + - - +
622E GLU* 3.2 18.4 + - - +
623E GLU* 2.9 33.8 + - + +
714E ARG* 4.6 4.0 - - - +
718E ASP* 3.8 12.9 + - - -
721E ALA* 5.5 4.2 - - - +
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Residues in contact with ALA 620 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571E LEU* 3.7 43.3 - - + +
574E ALA* 5.1 0.7 - - + -
575E PRO* 4.3 7.4 - - - +
599E VAL* 6.1 1.6 - - + -
616E GLN* 2.8 21.3 + - - +
617E LEU* 3.7 3.4 - - + +
619E ARG* 1.3 76.3 - - - +
621E GLN* 1.3 61.9 + - + +
623E GLU* 3.4 1.6 + - - +
624E MET* 3.0 40.0 + - - +
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Residues in contact with GLN 621 (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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599E VAL* 4.8 9.0 - - + +
601E TYR* 4.5 3.3 + - - -
617E LEU* 2.9 27.2 + - + +
618E TYR* 3.7 16.2 - - - +
620E ALA* 1.3 77.0 - - + +
622E GLU* 1.3 64.6 + - - +
623E GLU 3.2 0.2 + - - -
624E MET* 3.9 6.0 - - - +
625E ALA* 3.0 26.0 + - - +
635E LEU* 5.4 0.7 - - - +
637E LEU* 3.3 33.1 - - + +
639E HIS* 3.5 8.8 - - - -
659E GLN* 2.9 23.6 + - - +
660E PRO* 3.3 32.4 - - + +
663E THR* 4.2 6.5 - - + +
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Residues in contact with GLU 622 (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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618E TYR* 3.0 39.5 + - + +
619E ARG* 3.2 17.1 - - - +
621E GLN* 1.3 76.9 - - - +
623E GLU* 1.3 64.5 + - + +
625E ALA* 3.5 6.4 + - - +
626E GLN* 3.2 21.7 + - - +
660E PRO* 4.5 12.8 - - + +
661E PRO* 5.6 3.9 - - + +
663E THR* 4.9 0.9 - - - -
709E PRO* 4.7 1.9 - - - +
714E ARG* 2.7 39.6 + - - -
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Residues in contact with GLU 623 (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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572E GLN 5.1 3.3 - - - +
575E PRO* 3.7 27.1 - - + +
616E GLN* 5.5 3.1 + - - -
619E ARG* 2.9 25.0 + - - +
620E ALA* 5.1 0.9 - - - -
622E GLU* 1.3 76.7 - - + +
624E MET* 1.3 66.8 + - - +
626E GLN* 3.1 8.9 + - + +
627E VAL* 2.9 25.7 + - + +
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Residues in contact with MET 624 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565E PHE* 4.9 1.6 - - + -
571E LEU* 6.1 1.1 - - - -
574E ALA* 4.1 19.1 - - - +
575E PRO* 4.0 25.1 - - + +
578E VAL* 4.1 16.1 - - + +
597E VAL* 3.6 45.3 - - + -
599E VAL* 5.6 5.8 - - - -
620E ALA* 3.0 27.7 + - - +
621E GLN* 3.9 5.6 - - - +
623E GLU* 1.3 75.2 - - - +
625E ALA* 1.3 58.0 + - - +
627E VAL* 3.2 8.3 + - - +
628E ALA* 2.8 30.1 + - - +
635E LEU* 3.7 20.6 - - + +
637E LEU* 4.4 7.9 - - + -
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Residues in contact with ALA 625 (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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621E GLN 3.0 16.6 + - - +
622E GLU* 3.5 6.3 - - - +
624E MET* 1.3 77.6 - - - +
626E GLN* 1.3 55.9 + - - +
628E ALA* 3.3 3.6 + - - +
629E LYS* 2.9 30.7 + - - +
635E LEU* 4.0 11.6 - - + +
661E PRO 5.0 1.8 - - - +
662E ASP* 3.8 24.7 - - + +
663E THR* 4.0 13.9 - - + -
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Residues in contact with GLN 626 (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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622E GLU* 3.2 10.9 + - - +
623E GLU* 3.1 11.9 + - - +
625E ALA* 1.3 78.1 - - - +
627E VAL* 1.3 64.6 + - + +
629E LYS* 3.4 20.7 + - - +
630E ARG* 3.0 41.2 + - - +
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Residues in contact with VAL 627 (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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575E PRO* 4.0 21.8 - - + +
578E VAL* 4.1 12.1 - - + -
579E GLU* 3.7 46.9 - - + +
582E PHE* 4.2 5.8 - - + -
623E GLU* 2.9 17.8 + - + +
624E MET* 3.2 9.4 + - - +
626E GLN* 1.3 76.1 - - + +
628E ALA* 1.3 66.1 + - - +
630E ARG* 3.2 20.7 + - - +
631E TYR* 3.3 21.7 + - + -
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Residues in contact with ALA 628 (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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582E PHE* 3.9 20.9 - - + -
624E MET 2.8 17.4 + - - +
625E ALA* 3.7 4.7 - - - +
626E GLN 3.3 0.2 - - - -
627E VAL* 1.3 77.3 - - - +
629E LYS* 1.3 62.2 + - - +
631E TYR* 3.2 2.8 + - - -
632E GLY 2.9 5.0 + - - -
633E VAL* 2.9 41.6 + - - +
635E LEU* 3.8 22.9 - - + -
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Residues in contact with LYS 629 (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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625E ALA 2.9 17.3 + - - +
626E GLN* 3.8 20.4 + - - +
628E ALA* 1.3 75.6 - - - +
630E ARG* 1.3 64.3 + - + +
632E GLY* 3.2 12.5 + - - -
633E VAL 5.0 1.6 - - - -
662E ASP* 4.8 17.3 + - + +
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Residues in contact with ARG 630 (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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579E GLU* 3.3 34.1 + - - -
626E GLN* 3.0 31.5 + - + +
627E VAL* 3.7 14.2 - - - +
628E ALA 3.2 0.4 - - - -
629E LYS* 1.3 78.7 - - + +
631E TYR* 1.3 76.3 + - + +
632E GLY 3.3 0.6 + - - -
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Residues in contact with TYR 631 (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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579E GLU* 3.3 40.9 + - + +
582E PHE* 3.6 52.0 - + + -
583E SER* 3.2 22.0 + - - -
588E MET* 3.7 21.5 - - + +
627E VAL* 3.4 16.2 - - + +
628E ALA 3.2 2.9 + - - +
630E ARG* 1.3 93.6 + - + +
632E GLY* 1.3 63.5 + - - +
633E VAL* 3.5 3.5 - - + +
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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) + - + + + + + -
------------------------------------------------------------
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