Contacts of the helix formed by residues 704 - 726 (chain D) in PDB entry 6VVT
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 PRO 704 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702D ARG 4.7 0.4 - - - +
703D PHE* 1.3 94.4 - - + +
705D MET* 1.3 64.9 + - - +
706D ILE* 4.4 3.6 - - + +
707D VAL* 2.9 31.6 + - + +
708D VAL* 3.2 7.3 + - - +
26E TYR* 5.4 9.0 - - + -
38E ASP* 2.9 38.4 - - + +
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Residues in contact with MET 705 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562D SER 4.3 8.5 - - - +
563D ASN* 3.0 34.5 - - - +
565D ILE* 4.2 18.1 - - + +
566D LEU* 4.2 18.6 - - + -
700D ALA* 5.8 4.5 - - + +
703D PHE 3.7 1.3 + - - +
704D PRO* 1.3 73.9 - - - +
706D ILE* 1.3 51.1 + - - +
708D VAL* 2.8 13.4 + - + -
709D ALA* 2.3 40.0 + - - +
983D ALA 2.9 29.8 - - - +
984D THR* 4.0 16.4 - - - +
37E ILE* 4.9 11.9 - - + -
38E ASP* 4.0 5.0 + - - +
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Residues in contact with ILE 706 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562D SER* 6.0 2.0 - - - +
563D ASN* 5.3 3.1 - - - +
704D PRO* 3.2 3.9 + - + +
705D MET* 1.3 77.1 - - - +
707D VAL* 1.3 58.3 + - - +
709D ALA* 3.7 6.4 - - - +
710D GLN* 3.0 45.1 + - + +
26E TYR* 3.7 30.1 - - + -
29E PRO* 5.1 5.4 - - + -
33E THR* 3.5 28.7 - - - +
36E PRO* 3.1 44.9 - - + -
37E ILE* 4.5 14.3 - - + +
38E ASP* 4.4 3.7 + - - +
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Residues in contact with VAL 707 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677D PRO* 3.6 24.7 - - + -
699D LEU* 5.9 1.1 - - + -
703D PHE* 3.6 32.1 - - + -
704D PRO* 2.9 29.8 + - + +
706D ILE* 1.3 77.3 - - - +
708D VAL* 1.3 54.9 + - + +
710D GLN* 3.6 4.0 + - - +
711D THR* 2.7 37.4 + - - +
25E ALA 4.0 13.0 - - - +
26E TYR* 3.6 26.9 - - + +
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Residues in contact with VAL 708 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565D ILE* 4.7 16.2 - - + -
696D ILE* 4.5 10.3 - - + -
699D LEU* 3.6 32.8 - - + +
700D ALA* 3.6 33.4 - - + +
703D PHE* 4.1 4.5 - - + +
704D PRO 3.2 12.3 + - - +
705D MET* 2.8 20.9 + - + +
707D VAL* 1.3 71.1 - - - +
709D ALA* 1.3 65.2 + - - +
711D THR* 3.2 1.1 + - - -
712D VAL* 2.9 42.3 + - + +
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Residues in contact with ALA 709 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438D LEU* 4.4 16.3 - - + +
562D SER* 4.0 33.9 - - - +
565D ILE* 5.0 4.2 - - - +
705D MET 2.3 29.6 + - - +
706D ILE* 3.7 9.2 - - + +
708D VAL* 1.3 69.5 - - - +
710D GLN* 1.3 64.0 + - + +
712D VAL* 3.4 4.6 + - - +
713D ASP* 3.1 24.5 + - - +
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Residues in contact with GLN 710 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706D ILE* 3.0 32.3 + - + +
707D VAL* 4.1 3.7 - - - +
709D ALA* 1.3 77.1 - - + +
711D THR* 1.3 57.2 + - - +
713D ASP* 3.3 7.8 + - - +
714D LYS* 3.0 39.8 + - - +
26E TYR* 2.6 35.5 + - - +
27E ASP* 3.1 24.7 - - - +
28E THR 3.6 21.0 + - - -
29E PRO* 4.7 2.8 - - - +
30E LEU* 5.6 1.4 - - - +
33E THR* 6.1 0.6 - - - +
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Residues in contact with THR 711 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675D LEU 4.4 9.3 + - - +
676D LEU* 4.2 24.0 - - + -
677D PRO* 3.8 23.7 - - + +
696D ILE* 6.2 0.9 - - + -
699D LEU* 4.6 19.7 - - + +
707D VAL* 2.7 24.5 + - - +
708D VAL* 3.7 7.2 - - - -
710D GLN* 1.3 78.3 - - - +
712D VAL* 1.3 62.2 + - + +
714D LYS* 3.4 3.9 + - - +
715D LEU* 3.1 40.9 + - + +
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Residues in contact with VAL 712 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438D LEU* 5.5 2.0 - - + -
527D LEU* 3.2 17.7 - - + +
565D ILE* 5.1 4.0 - - + -
575D ALA* 2.9 38.8 - - + +
577D PRO* 4.3 9.9 - - + -
581D MET* 4.7 0.7 - - - +
696D ILE* 4.5 20.6 - - + -
699D LEU* 5.9 0.2 - - + -
708D VAL* 2.9 31.7 + - + +
709D ALA* 3.9 4.9 - - - +
711D THR* 1.3 75.3 - - + +
713D ASP* 1.3 66.5 + - - +
715D LEU* 3.3 8.0 + - - +
716D LYS* 3.0 21.0 + - - +
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Residues in contact with ASP 713 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437D LYS* 3.7 8.4 - - - +
438D LEU* 2.9 35.0 + - - +
525D HIS* 3.1 10.9 + - - -
527D LEU* 4.5 2.4 - - - +
709D ALA 3.1 11.8 + - - +
710D GLN* 3.3 11.3 + - - +
712D VAL* 1.3 78.3 - - - +
714D LYS* 1.3 63.1 + - + +
716D LYS* 2.7 46.6 + - - +
717D ASP* 3.2 20.5 + - - +
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Residues in contact with LYS 714 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674D GLU 5.0 4.2 + - - -
675D LEU* 3.6 47.2 + - + +
676D LEU 5.6 0.6 + - - -
710D GLN* 3.0 28.2 + - - +
711D THR* 3.8 4.7 - - - +
713D ASP* 1.3 74.9 - - + +
715D LEU* 1.3 63.5 + - - +
717D ASP* 3.3 13.3 + - - +
718D ALA* 3.1 22.9 + - - +
27E ASP* 2.9 30.7 + - - -
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Residues in contact with LEU 715 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577D PRO* 3.9 23.8 - - + -
581D MET* 4.5 2.7 - - - +
585D LEU* 4.0 13.0 - - + +
672D PHE* 3.7 35.7 - - + -
675D LEU* 3.9 25.6 - - + -
676D LEU* 4.6 5.8 - - + -
692D GLN* 4.9 5.2 - - + +
695D ILE* 6.4 1.6 - - + -
696D ILE* 4.5 17.7 - - + -
699D LEU* 6.3 0.9 - - + -
711D THR* 3.1 25.3 + - + +
712D VAL* 3.6 10.8 - - - +
713D ASP 3.2 0.2 - - - -
714D LYS* 1.3 75.0 - - - +
716D LYS* 1.3 52.9 + - - +
718D ALA* 4.0 0.2 - - - +
719D GLY* 2.7 33.4 + - - -
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Residues in contact with LYS 716 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434D PRO 3.2 20.1 + - - +
435D GLN 4.5 1.4 - - - -
436D LEU 2.6 31.9 + - - +
525D HIS* 3.2 9.9 + - + -
526D PRO* 3.6 19.3 - - + -
527D LEU* 4.6 1.8 - - + -
581D MET* 3.2 27.9 - - + +
712D VAL 3.0 11.5 + - - +
713D ASP* 2.7 25.5 + - - +
715D LEU* 1.3 75.9 - - - +
717D ASP* 1.3 84.1 + - - +
719D GLY 3.8 0.2 - - - -
720D PHE* 2.9 49.9 + - + -
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Residues in contact with ASP 717 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LYS* 5.2 9.5 + - - -
434D PRO 4.4 3.3 - - - +
435D GLN* 5.8 0.5 - - - -
713D ASP* 3.2 13.3 + - - +
714D LYS* 3.3 12.6 + - - +
716D LYS* 1.3 99.1 + - - +
718D ALA* 1.3 57.5 + - - +
720D PHE* 3.8 4.6 - - - +
721D TYR* 2.8 33.7 + - - +
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Residues in contact with ALA 718 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585D LEU* 3.7 13.2 - - + -
588D LEU* 5.2 2.5 - - + -
675D LEU* 3.4 34.5 - - + -
714D LYS 3.1 5.9 + - - +
715D LEU 4.0 0.7 - - - +
717D ASP* 1.3 78.3 - - - +
719D GLY* 1.3 64.2 + - - +
721D TYR* 4.4 2.9 - - - -
722D TRP* 2.9 43.0 + - + +
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Residues in contact with GLY 719 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581D MET* 3.5 30.5 - - - -
584D GLY* 3.2 4.0 - - - -
585D LEU* 3.4 10.9 - - - +
715D LEU 2.7 21.7 + - - -
718D ALA* 1.3 74.2 - - - +
720D PHE* 1.3 56.4 + - - +
723D ALA* 2.8 31.9 + - - +
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Residues in contact with PHE 720 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718C GLU* 4.2 5.1 - - - +
719C GLY* 3.4 38.3 + - - +
722C TYR* 3.7 29.8 - + - -
434D PRO* 4.2 11.9 - - + -
526D PRO* 3.8 21.8 - - + -
580D ASP* 3.9 15.7 - - + -
581D MET* 3.7 24.6 - - + +
716D LYS* 2.9 45.7 + - + +
717D ASP* 3.8 4.0 - - - +
719D GLY* 1.3 71.8 - - - +
721D TYR* 1.3 67.4 + - - +
723D ALA* 3.1 9.5 + - + +
724D THR* 3.0 22.1 + - - +
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Residues in contact with TYR 721 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718C GLU* 5.2 11.4 - - - +
717D ASP 2.8 23.5 + - - +
718D ALA* 3.7 5.6 - - - +
720D PHE* 1.3 71.7 - - - +
722D TRP* 1.3 90.8 + + - +
724D THR* 2.9 28.5 + - - -
725D ARG* 3.1 53.3 + - + +
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Residues in contact with TRP 722 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584D GLY* 3.4 23.3 - - - +
587D TYR* 4.3 21.5 - + + -
588D LEU* 3.5 32.2 - - + +
622D MET* 4.7 7.2 - - + -
629D VAL* 3.9 33.4 - - + -
671D MET* 3.5 28.5 - - + +
718D ALA* 2.9 38.3 + - + +
721D TYR* 1.3 91.8 - + - +
723D ALA* 1.3 59.5 + - - +
724D THR 3.1 1.8 - - - -
725D ARG* 3.4 24.8 - - + +
726D SER* 2.7 30.3 + - - -
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Residues in contact with ALA 723 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716C PRO* 3.3 24.9 - - + +
580D ASP* 3.6 33.2 - - + +
583D THR* 4.4 3.1 - - - +
584D GLY* 3.5 8.0 - - - +
719D GLY 2.8 20.7 + - - +
720D PHE* 3.1 8.3 + - + +
722D TRP* 1.3 77.7 - - - +
724D THR* 1.3 61.2 + - + +
726D SER* 3.2 17.7 + - - -
727D GLY 4.5 0.9 + - - -
728D VAL* 4.9 1.2 + - - +
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Residues in contact with THR 724 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715C MET* 4.8 9.5 - - - +
716C PRO* 3.1 21.6 - - + +
717C TRP* 4.6 1.6 - - - -
718C GLU* 2.9 43.7 - - + +
1010C PHE* 4.5 16.5 - - - +
1011C PRO* 5.3 0.9 - - - +
720D PHE 3.0 15.9 - - - +
721D TYR 2.9 9.8 + - - +
723D ALA* 1.3 74.1 - - + +
725D ARG* 1.3 88.2 + - - +
726D SER 3.0 8.0 + - - -
727D GLY* 3.7 8.0 + - - -
728D VAL 5.3 0.2 + - - -
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Residues in contact with ARG 725 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718C GLU* 3.7 21.1 + - - +
1003C ASP* 3.9 19.6 + - - +
1006C SER* 4.7 6.9 + - - -
1010C PHE* 4.1 18.2 - - - -
1011C PRO* 3.3 39.6 - - + +
1012C TYR* 3.5 7.4 - - - -
587D TYR* 3.9 7.5 + - + -
721D TYR* 3.1 66.5 + - + +
722D TRP* 3.4 25.0 + - + +
724D THR* 1.3 97.2 + - - +
726D SER* 1.3 61.6 + - - +
727D GLY 3.2 1.8 + - - -
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Residues in contact with SER 726 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012C TYR* 3.9 7.0 - - - -
583D THR* 4.6 5.6 + - - -
587D TYR* 3.8 40.7 - - - +
722D TRP 2.7 17.1 + - - -
723D ALA* 3.2 17.7 - - - -
724D THR 3.0 1.4 - - - -
725D ARG* 1.3 78.5 - - - +
727D GLY* 1.3 60.4 + - - +
728D VAL* 3.0 24.5 - - - +
800D THR* 5.1 3.3 - - - +
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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