Contacts of the helix formed by residues 609 - 631 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605G GLY* 2.8 18.6 + - - -
608G ALA* 1.3 82.2 - - - +
610G ARG* 1.3 65.4 + - - -
611G LEU 3.4 2.4 + - - -
612G SER 3.7 0.6 + - - -
613G ALA* 3.1 20.8 + - - +
724G ALA* 6.1 1.3 - - - -
728G TYR* 3.4 27.9 - - - -
789G PRO 5.1 0.4 - - - -
792G LEU 4.3 4.7 - - - -
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Residues in contact with ARG 610 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601G TYR* 4.3 24.8 + - - +
602G SER* 4.7 2.4 + - - +
605G GLY* 4.1 11.9 + - - -
609G GLY* 1.3 71.2 - - - -
611G LEU* 1.3 60.0 + - - +
613G ALA* 3.8 1.5 - - + +
614G ALA* 2.9 34.1 + - + +
642G GLY* 2.5 32.9 + - - -
643G GLY 5.1 0.2 - - - -
644G THR* 5.2 1.8 - - - +
778G ILE* 5.7 2.0 - - - +
789G PRO 4.3 10.0 + - - +
790G VAL* 3.4 39.5 - - - +
792G LEU 4.5 5.1 + - - -
794G VAL* 5.8 0.7 - - + -
825G THR* 5.7 9.0 + - + +
828G LEU* 3.7 27.3 - - - +
829G LEU* 4.3 9.4 - - + -
970G GLY* 3.8 25.6 + - - -
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Residues in contact with LEU 611 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609G GLY 3.4 0.6 - - - -
610G ARG* 1.3 78.9 - - - +
612G SER* 1.3 61.3 + - - +
614G ALA* 3.3 5.5 + - - +
615G TRP* 3.2 21.3 + - - +
717G MET* 4.8 16.7 - - + +
720G MET* 4.2 19.7 - - + +
721G ALA* 5.0 1.6 - - - +
724G ALA* 4.0 15.5 - - + -
792G LEU 5.4 0.6 + - - -
793G GLY 5.3 0.2 - - - -
794G VAL* 3.9 36.3 - - + +
797G ALA* 3.6 31.6 - - + -
798G PHE* 4.9 10.5 - - + -
822G PHE* 5.2 8.3 - - + -
825G THR* 5.1 15.5 - - + -
826G LEU* 5.3 4.0 - - + -
829G LEU* 5.5 1.6 - - + -
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Residues in contact with SER 612 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568G LEU* 4.4 12.3 - - - -
608G ALA 3.4 13.1 + - - -
609G GLY 3.7 1.0 + - - -
610G ARG 3.3 0.4 - - - -
611G LEU* 1.3 74.5 - - - +
613G ALA* 1.3 67.0 + - - +
615G TRP* 3.1 2.6 + - - +
616G GLN* 2.8 25.6 + - - +
619G ARG* 5.4 0.3 + - - -
721G ALA* 3.2 29.2 + - - +
724G ALA* 3.7 6.2 - - - +
725G THR* 2.8 33.4 + - - -
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Residues in contact with ALA 613 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568G LEU* 3.9 13.1 - - + +
571G LEU* 4.8 0.3 - - - +
601G TYR 4.5 3.6 - - - +
604G SER* 3.6 16.8 - - - +
605G GLY* 3.5 25.4 - - - +
609G GLY 3.1 19.2 + - - +
610G ARG* 3.3 5.4 + - + +
612G SER* 1.3 76.2 - - - +
614G ALA* 1.3 57.6 + - - +
616G GLN* 3.9 0.9 - - - +
617G LEU* 2.9 37.7 + - + +
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Residues in contact with ALA 614 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601G TYR* 5.9 5.4 - - + -
610G ARG* 2.9 20.1 + - + +
611G LEU* 3.7 4.7 - - + +
613G ALA* 1.3 76.8 - - - +
615G TRP* 1.3 57.9 + - - +
617G LEU* 3.4 9.7 + - - +
618G TYR 3.1 21.8 + - - -
821G PHE* 3.7 21.2 - - + -
825G THR* 3.9 27.1 - - + -
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Residues in contact with TRP 615 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611G LEU 3.2 5.8 + - - +
612G SER* 3.1 8.5 + - - +
614G ALA* 1.3 76.7 - - - +
616G GLN* 1.3 65.6 + - - +
618G TYR* 3.5 25.1 + + + -
619G ARG* 3.2 60.7 + - + +
714G ARG* 3.9 41.3 - - + -
717G MET* 3.5 49.6 - - + +
718G ASP* 2.8 25.7 + - - -
721G ALA* 4.4 7.4 - - + -
819G TRP* 3.6 28.5 - + - -
821G PHE* 4.0 16.3 - + - -
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Residues in contact with GLN 616 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568G LEU* 3.7 27.7 - - + +
571G LEU* 3.8 26.6 + - + -
572G GLN* 3.3 43.5 + - + +
612G SER 2.8 16.6 + - - +
613G ALA 4.1 0.7 - - - +
615G TRP* 1.3 77.3 - - - +
617G LEU* 1.3 57.3 + - - +
619G ARG* 2.9 40.5 + - - +
620G ALA* 3.0 29.8 + - - +
623G GLU* 5.5 2.6 + - - -
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Residues in contact with LEU 617 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571G LEU* 4.0 17.7 - - + -
599G VAL* 3.5 41.7 - - + -
600G GLY 3.7 16.8 - - - +
601G TYR* 3.7 37.2 - - + -
604G SER* 4.6 2.9 - - - +
613G ALA* 2.9 27.3 + - + +
614G ALA* 3.5 6.5 - - - +
615G TRP 3.2 0.2 - - - -
616G GLN* 1.3 74.1 - - - +
618G TYR* 1.3 66.3 + - - +
620G ALA* 3.3 3.1 + - + +
621G GLN* 3.1 40.9 + - + +
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Residues in contact with TYR 618 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614G ALA 3.1 14.2 + - - +
615G TRP* 3.7 29.8 - + + +
616G GLN 3.5 0.2 - - - -
617G LEU* 1.3 75.5 - - - +
619G ARG* 1.3 64.9 + - - +
621G GLN* 4.6 3.6 + - - -
622G GLU* 3.1 46.6 + - - +
658G SER 4.1 10.8 - - - -
660G PRO* 3.7 37.5 - - + +
661G PRO* 3.8 17.3 - - - +
706G PRO* 5.5 2.0 - - + +
707G VAL 4.9 1.7 + - - -
709G PRO* 3.6 34.1 - - + +
714G ARG* 4.6 1.1 - - - -
819G TRP* 4.5 5.7 + + - -
821G PHE* 3.9 32.5 - + + -
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Residues in contact with ARG 619 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612G SER 5.4 0.4 + - - -
615G TRP* 3.2 64.4 + - + +
616G GLN* 2.9 44.3 + - - +
618G TYR* 1.3 79.5 - - + +
620G ALA* 1.3 63.3 + - - +
622G GLU* 3.2 16.0 + - - +
623G GLU* 3.0 42.2 + - + +
714G ARG* 4.7 4.5 - - - +
718G ASP* 3.6 15.4 + - - +
721G ALA* 5.3 5.1 - - - +
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Residues in contact with ALA 620 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571G LEU* 3.7 40.6 - - + +
574G ALA* 5.0 6.1 - - + -
575G PRO* 4.7 7.4 - - + -
599G VAL* 6.0 1.6 - - + -
616G GLN* 3.0 21.6 + - - +
617G LEU* 3.9 3.4 - - + +
619G ARG* 1.3 76.8 - - - +
621G GLN* 1.3 63.5 + - + +
623G GLU* 3.4 1.9 + - - +
624G MET* 3.0 35.7 + - - +
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Residues in contact with GLN 621 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599G VAL* 4.7 7.1 - - + +
601G TYR* 4.0 13.7 + - - -
617G LEU* 3.1 36.1 + - + +
618G TYR* 3.8 3.9 + - - +
620G ALA* 1.3 76.6 - - + +
622G GLU* 1.3 64.4 + - - +
624G MET* 4.0 5.9 - - - +
625G ALA* 3.1 25.8 + - - +
635G LEU* 5.3 1.2 - - - +
637G LEU* 4.5 24.3 - - + +
639G HIS* 4.0 9.9 + - - -
659G GLN* 2.7 29.5 + - - +
660G PRO* 3.4 20.2 - - + +
663G THR* 3.8 14.7 + - + +
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Residues in contact with GLU 622 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618G TYR* 3.1 32.4 + - - +
619G ARG* 3.2 17.0 + - - +
621G GLN* 1.3 78.6 - - - +
623G GLU* 1.3 66.0 + - + +
625G ALA* 3.5 4.2 + - - +
626G GLN* 3.3 41.5 + - - +
660G PRO* 4.4 11.6 - - + +
661G PRO* 5.4 6.4 - - + +
663G THR* 4.4 8.5 - - - +
709G PRO* 4.8 1.4 - - - +
714G ARG* 2.6 42.1 + - - -
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Residues in contact with GLU 623 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572G GLN 5.7 0.5 - - - +
575G PRO* 3.8 26.0 - - + +
616G GLN* 5.5 2.3 + - - -
619G ARG* 3.0 31.7 + - - +
620G ALA* 5.0 0.5 - - - -
622G GLU* 1.3 80.2 - - + +
624G MET* 1.3 61.1 + - - +
626G GLN* 3.0 19.3 + - - +
627G VAL* 2.9 30.9 + - + +
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Residues in contact with MET 624 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565G PHE* 4.9 0.7 - - - -
571G LEU* 6.4 0.4 - - - -
574G ALA* 4.0 21.1 - - - +
575G PRO* 3.9 25.5 - - + +
578G VAL* 4.2 18.2 - - + +
597G VAL* 3.5 44.9 - - + -
599G VAL* 5.8 3.8 - - - -
620G ALA* 3.0 26.8 + - - +
621G GLN* 4.0 3.8 - - - +
623G GLU* 1.3 75.0 - - - +
625G ALA* 1.3 58.0 + - - +
627G VAL* 3.2 9.0 + - - +
628G ALA* 2.8 29.6 + - - +
635G LEU* 3.8 22.7 - - + +
637G LEU* 4.7 7.9 - - + -
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Residues in contact with ALA 625 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621G GLN 3.1 18.8 + - - +
622G GLU 3.6 4.9 - - - +
624G MET* 1.3 77.0 - - - +
626G GLN* 1.3 57.5 + - + +
628G ALA* 3.2 3.6 + - - +
629G LYS* 2.9 30.4 + - - +
635G LEU* 3.9 13.8 - - + +
637G LEU* 6.1 0.4 - - + -
661G PRO 5.4 0.7 - - - +
662G ASP* 3.7 24.5 - - + +
663G THR* 4.0 11.7 - - + -
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Residues in contact with GLN 626 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622G GLU* 3.3 35.8 + - - +
623G GLU* 3.0 21.4 + - - +
625G ALA* 1.3 78.0 - - + +
627G VAL* 1.3 62.5 + - + +
629G LYS* 3.5 8.4 + - + +
630G ARG* 3.2 31.0 + - - +
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Residues in contact with VAL 627 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575G PRO* 4.0 22.0 - - + +
578G VAL* 4.2 4.9 - - + -
579G GLU* 3.6 41.1 - - + +
582G PHE* 4.1 11.2 - - + -
623G GLU* 2.9 16.7 + - + +
624G MET* 3.6 9.4 - - - +
626G GLN* 1.3 78.6 - - + +
628G ALA* 1.3 62.9 + - - +
630G ARG* 3.3 22.9 + - - +
631G TYR* 3.3 28.8 + - + -
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Residues in contact with ALA 628 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582G PHE* 3.9 20.6 - - + -
624G MET 2.8 16.5 + - - +
625G ALA* 3.2 5.1 + - - +
627G VAL* 1.3 77.9 - - - +
629G LYS* 1.3 61.7 + - - +
631G TYR 3.3 1.6 + - - -
632G GLY 3.0 5.0 + - - -
633G VAL* 2.9 43.0 + - + +
635G LEU* 3.8 22.9 - - + -
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Residues in contact with LYS 629 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625G ALA 2.9 17.1 + - - +
626G GLN* 3.9 9.6 - - + +
627G VAL 3.3 0.2 - - - -
628G ALA* 1.3 75.0 - - - +
630G ARG* 1.3 64.6 + - + +
632G GLY* 3.2 12.3 + - - +
633G VAL 5.0 2.0 - - - -
662G ASP* 6.0 6.1 - - + +
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Residues in contact with ARG 630 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579G GLU* 2.6 39.7 + - - -
626G GLN* 3.2 16.6 + - - +
627G VAL* 3.7 23.6 - - - +
628G ALA 3.2 0.2 - - - -
629G LYS* 1.3 82.1 - - + +
631G TYR* 1.3 75.1 + - + +
632G GLY 3.3 0.7 + - - -
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Residues in contact with TYR 631 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579G GLU* 3.3 37.8 + - + +
582G PHE* 3.7 48.2 - + + -
583G SER* 2.9 25.7 + - - -
588G MET* 3.7 21.5 - - + +
627G VAL* 3.3 26.7 + - + +
628G ALA 4.2 1.1 - - - +
630G ARG* 1.3 91.1 + - + +
632G GLY* 1.3 63.9 + - - +
633G VAL* 3.4 3.6 - - + -
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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