Contacts of the helix formed by residues 705 - 726 (chain D) in PDB entry 5UHA
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 705 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703D ARG 3.8 2.9 - - - +
704D TYR* 1.3 99.8 - - + +
706D MET* 1.3 67.6 + - - +
707D ILE* 3.4 4.3 - - + +
708D VAL* 3.2 31.9 + - + +
709D VAL* 3.4 8.7 + - - +
28E GLY 6.2 1.6 - - - +
29E TYR* 5.5 4.7 - - + -
41E ASP* 3.3 25.1 - - + +
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Residues in contact with MET 706 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562D SER 4.9 7.3 - - - +
563D ASN* 4.7 18.4 - - - +
705D PRO* 1.3 71.2 - - - +
707D ILE* 1.3 63.5 + - - +
709D VAL* 2.9 20.7 + - - +
710D ALA* 3.2 13.1 + - - +
985D THR* 4.7 22.0 - - - +
987D LYS* 4.5 14.4 - - + +
40E ILE* 4.2 20.6 - - + -
41E ASP* 2.5 22.4 + - - +
44E LEU* 4.3 16.4 - - + -
50E LYS* 3.9 32.3 - - - +
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Residues in contact with ILE 707 (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 0.2 - - - -
705D PRO* 5.0 3.1 - - + -
706D MET* 1.3 74.3 - - - +
708D VAL* 1.3 72.4 + - + +
710D ALA* 4.2 6.8 - - + +
711D GLN* 3.2 46.4 + - + +
29E TYR* 4.4 21.5 - - + -
32E PRO* 3.6 24.5 - - + -
36E THR* 4.0 17.9 - - + +
39E PRO* 3.8 26.9 - - + -
40E ILE* 5.0 5.3 - - + +
41E ASP* 2.9 20.2 + - + +
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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
----------------------------------------------------------
677D LEU 5.1 5.6 - - - +
678D PRO* 5.6 4.5 - - + -
700D LEU* 5.2 2.2 - - + -
704D TYR* 4.1 26.7 - - + -
705D PRO* 3.2 32.9 + - + +
706D MET 3.0 0.8 - - - -
707D ILE* 1.3 79.4 - - + +
709D VAL* 1.3 54.2 + - - +
711D GLN* 3.2 6.6 + - - +
712D THR* 2.6 52.6 + - - +
28E GLY 4.2 9.9 - - - +
29E TYR* 4.0 25.8 - - + -
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Residues in contact with VAL 709 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565D ILE* 4.5 23.1 - - + -
697D ILE* 4.2 25.1 - - + +
700D LEU* 3.6 39.0 - - + +
701D ALA* 4.1 8.7 - - + +
704D TYR* 4.0 2.7 - - + +
705D PRO 3.6 12.6 - - - +
706D MET* 2.9 9.5 + - - +
708D VAL* 1.3 77.0 - - + +
710D ALA* 1.3 53.7 + - - +
712D THR* 3.0 7.0 + - - -
713D VAL* 2.7 36.8 + - + +
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Residues in contact with ALA 710 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438D LEU* 4.3 12.7 - - + +
562D SER* 3.8 39.7 - - - +
565D ILE* 4.7 2.9 - - + +
706D MET 3.2 8.8 + - - +
707D ILE* 4.4 7.2 - - + +
709D VAL* 1.3 79.6 - - - +
711D GLN* 1.3 63.0 + - + +
713D VAL* 3.3 22.8 - - - +
714D ASP* 3.3 13.5 + - - +
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Residues in contact with GLN 711 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437D LYS* 6.5 1.3 - - - -
707D ILE* 3.2 46.6 + - + +
708D VAL* 3.2 5.0 + - - +
709D VAL 3.2 0.4 - - - -
710D ALA* 1.3 77.8 - - + +
712D THR* 1.3 63.2 + - - +
714D ASP* 3.5 6.5 + - - +
715D LYS* 3.3 32.0 + - - +
29E TYR* 4.0 7.2 - - - +
30E ASP* 3.5 48.0 + - + +
31E THR 4.6 1.6 + - - -
32E PRO* 4.0 10.5 - - - +
33E LEU* 5.2 8.5 - - + +
36E THR* 4.8 3.2 + - - +
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Residues in contact with THR 712 (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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676D LEU 3.6 23.2 + - - +
677D LEU* 4.0 15.9 + - + +
678D PRO* 5.4 1.0 - - - +
697D ILE* 6.3 0.2 - - + -
700D LEU* 4.1 24.7 - - + +
708D VAL* 2.6 41.2 + - - +
709D VAL* 3.5 8.2 - - - -
711D GLN* 1.3 69.8 - - - +
713D VAL* 1.3 65.2 + - - +
714D ASP 3.0 2.9 + - - -
715D LYS* 3.3 8.1 + - - +
716D LEU* 3.2 31.4 + - + +
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Residues in contact with VAL 713 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438D LEU* 4.0 13.0 - - + -
527D LEU* 3.7 22.3 - - + +
565D ILE* 5.5 2.0 - - + -
575D ALA* 3.1 28.3 - - + +
577D PRO* 4.3 9.7 - - + +
697D ILE* 3.9 21.8 - - + -
709D VAL* 2.7 22.8 + - + +
710D ALA* 3.3 19.5 - - - +
712D THR* 1.3 73.9 - - - +
714D ASP* 1.3 64.4 + - - +
716D LEU* 3.5 9.5 + - + +
717D LYS* 3.2 20.6 + - - +
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Residues in contact with ASP 714 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437D LYS* 3.3 30.5 - - - +
438D LEU* 3.3 23.9 + - - +
439D HIS* 5.4 0.5 + - - -
525D HIS* 3.3 9.8 + - - -
527D LEU* 5.4 0.9 - - - -
710D ALA 3.3 14.3 + - - +
711D GLN* 3.6 8.6 - - - +
712D THR 3.0 0.6 - - - -
713D VAL* 1.3 79.4 - - - +
715D LYS* 1.3 66.8 + - + +
717D LYS* 2.8 48.3 + - - +
718D ASP* 3.4 15.3 + - - +
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Residues in contact with LYS 715 (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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675D GLU 5.3 4.1 + - - -
676D LEU* 3.6 47.1 - - + +
678D PRO* 5.5 8.7 - - - -
711D GLN* 3.3 20.0 - - - +
712D THR* 3.3 7.5 + - - +
714D ASP* 1.3 77.1 - - + +
716D LEU* 1.3 62.0 + - - +
718D ASP* 3.7 7.4 + - - +
719D ALA* 3.3 20.8 + - - +
30E ASP* 3.1 28.6 + - - -
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Residues in contact with LEU 716 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577D PRO* 4.4 19.7 - - + -
581D MET* 4.8 0.3 - - - +
585D LEU* 4.2 12.1 - - + +
673D PHE* 3.5 33.2 - - + -
676D LEU* 3.7 23.8 - - + -
677D LEU* 4.6 7.4 - - + -
693D GLN* 5.6 3.8 - - + +
696D ILE* 5.8 4.0 - - + -
697D ILE* 4.5 22.4 - - + -
700D LEU* 6.2 0.2 - - + -
712D THR* 3.2 23.2 + - + +
713D VAL* 3.6 14.8 - - - +
714D ASP 3.1 0.6 - - - -
715D LYS* 1.3 77.4 - - - +
717D LYS* 1.3 63.7 + - - +
719D ALA* 3.0 4.3 + - - +
720D GLY* 2.9 21.0 + - - -
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Residues in contact with LYS 717 (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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434D PRO 3.2 12.6 + - - +
435D GLN 4.5 1.0 + - - -
436D LEU 2.6 29.7 + - - -
437D LYS* 5.4 1.2 - - - +
525D HIS* 3.4 20.2 + - + +
526D PRO* 4.0 15.7 - - + -
527D LEU* 4.7 7.0 - - + -
577D PRO* 5.4 1.3 - - - +
581D MET* 3.5 34.4 - - - +
713D VAL 3.2 10.5 + - - +
714D ASP* 2.8 30.8 + - - +
716D LEU* 1.3 79.3 - - - +
718D ASP* 1.3 85.2 + - - +
720D GLY 3.4 0.5 + - - -
721D PHE* 3.2 30.5 + - + -
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Residues in contact with ASP 718 (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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177B LYS* 4.6 13.2 + - - -
434D PRO 3.5 12.0 - - - +
435D GLN* 5.4 1.1 - - - +
437D LYS* 6.0 2.3 + - - +
714D ASP* 3.4 11.4 + - - +
715D LYS* 4.1 8.5 - - - +
717D LYS* 1.3 99.7 + - - +
719D ALA* 1.3 63.5 + - - +
721D PHE* 3.3 8.3 + - - +
722D TYR* 3.1 24.1 + - - +
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Residues in contact with ALA 719 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585D LEU* 3.8 14.8 - - + -
676D LEU* 3.8 19.5 - - + -
715D LYS 3.3 12.8 + - - +
716D LEU 3.0 11.5 + - - +
718D ASP* 1.3 80.7 - - - +
720D GLY* 1.3 62.5 + - - +
721D PHE 3.2 0.7 + - - -
722D TYR* 3.3 2.7 + - - +
723D TRP* 3.3 33.9 + - + -
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Residues in contact with GLY 720 (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 33.7 - - - -
584D GLY* 3.3 4.1 - - - -
585D LEU* 3.5 13.6 - - - +
716D LEU 2.9 11.6 + - - -
717D LYS 3.4 1.5 + - - -
719D ALA* 1.3 75.8 - - - +
721D PHE* 1.3 52.1 + - - +
723D TRP 3.3 0.2 + - - -
724D ALA* 2.6 37.2 + - - +
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Residues in contact with PHE 721 (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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727C GLU* 3.8 17.6 + - - +
728C GLY* 3.6 25.1 + - - -
731C TYR* 4.3 13.5 - + + -
434D PRO* 3.7 27.8 - - + -
526D PRO* 4.0 13.9 - - + -
580D ASP* 3.9 26.2 - - + -
581D MET* 3.5 34.3 - - + -
717D LYS* 3.2 30.9 + - + +
718D ASP* 3.7 8.1 - - - +
719D ALA 3.2 0.8 - - - -
720D GLY* 1.3 76.5 - - - +
722D TYR* 1.3 65.6 + - - +
723D TRP 3.2 0.5 + - - -
724D ALA* 3.7 2.9 - - - +
725D THR* 3.2 24.1 + - - -
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Residues in contact with TYR 722 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727C GLU* 4.0 15.0 - - - +
1015C SER* 6.0 0.9 - - - -
718D ASP 3.1 16.7 + - - +
719D ALA* 3.3 5.4 + - - +
721D PHE* 1.3 77.2 - - - +
723D TRP* 1.3 94.6 + + + +
725D THR* 3.6 3.6 - - - -
726D ARG* 3.2 68.9 + - - -
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Residues in contact with TRP 723 (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* 3.5 22.4 - - - +
585D LEU* 5.6 0.4 - - + -
587D TYR* 4.2 28.1 - + + -
588D LEU* 3.2 32.8 - - + +
629D VAL* 4.2 29.4 - - + -
672D MET* 4.6 26.4 - - + +
719D ALA* 3.3 29.0 + - + +
721D PHE 3.1 0.4 - - - -
722D TYR* 1.3 103.4 - + + +
724D ALA* 1.3 65.8 + - - +
725D THR 3.1 1.1 - - - -
726D ARG* 3.4 18.9 + - + +
727D SER* 3.1 25.1 + - - -
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Residues in contact with ALA 724 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725C PRO* 4.0 22.9 - - + +
727C GLU 6.1 0.2 - - - +
728C GLY 6.2 0.9 - - - +
580D ASP* 3.2 35.7 - - + +
583D THR* 4.8 2.7 - - + -
584D GLY* 3.5 6.7 - - - +
720D GLY 2.6 22.9 + - - +
721D PHE* 3.7 7.4 - - + +
723D TRP* 1.3 73.2 - - - +
725D THR* 1.3 61.0 + - - +
727D SER* 2.3 27.4 + - - -
728D GLY 4.5 0.5 + - - -
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Residues in contact with THR 725 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724C MET* 3.7 23.0 - - + +
725C PRO* 3.7 12.6 - - - +
726C TRP* 3.6 7.1 + - + +
727C GLU* 2.6 37.3 + - - +
1019C PHE* 3.6 28.0 - - + -
1020C PRO* 5.2 0.9 - - - +
721D PHE 3.2 4.3 + - - -
722D TYR 3.6 2.9 - - - -
723D TRP 3.1 0.6 - - - -
724D ALA* 1.3 80.3 - - - +
726D ARG* 1.3 82.4 + - - +
727D SER 3.5 2.1 + - - -
728D GLY* 4.2 5.9 + - - -
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Residues in contact with ARG 726 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727C GLU* 2.7 34.1 + - - -
1012C ASP* 3.1 27.8 + - - +
1015C SER* 4.0 10.1 + - - -
1019C PHE* 4.5 8.0 - - + -
1020C PRO* 3.8 37.7 - - + +
1021C TYR* 4.5 0.2 - - - -
587D TYR* 3.5 22.7 + - - -
722D TYR* 3.2 64.3 + - - +
723D TRP* 3.4 20.0 + - + -
724D ALA 3.3 0.4 - - - -
725D THR* 1.3 90.7 - - + +
727D SER* 1.3 57.9 + - - +
728D GLY 3.4 2.0 - - - +
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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