Contacts of the helix formed by residues 703 - 732 (chain D) in PDB entry 3TE3
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 SER 703 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701D TRP 3.3 4.6 + - - -
702D VAL* 1.3 75.7 - - - +
704D GLY* 1.3 62.8 + - - +
705D GLU* 3.6 8.7 + - - +
706D GLU* 3.0 38.4 + - - +
707D PHE* 3.3 21.0 + - - +
699F GLY 4.4 7.4 - - - -
700F GLY 3.7 10.8 - - - -
701F TRP* 4.8 2.5 - - - -
702F VAL* 4.3 1.7 - - - +
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Residues in contact with GLY 704 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703D SER* 1.3 74.2 - - - +
705D GLU* 1.3 56.3 + - - +
707D PHE* 3.8 8.6 - - - +
708D TYR* 2.9 30.4 + - - +
699F GLY* 4.2 1.6 - - - -
700F GLY* 3.2 29.5 + - - +
701F TRP 4.1 0.4 - - - +
702F VAL* 4.5 7.6 - - - -
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Residues in contact with GLU 705 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703D SER* 3.4 6.8 + - - +
704D GLY* 1.3 73.7 - - - +
706D GLU* 1.3 69.3 + - - +
708D TYR* 3.3 8.1 + - + +
709D MET* 3.0 54.2 + - + +
699F GLY* 3.3 24.5 + - - +
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Residues in contact with GLU 706 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701D TRP 4.3 2.5 - - - +
702D VAL* 3.6 10.3 - - + +
703D SER* 3.0 37.0 + - - +
705D GLU* 1.3 80.5 - - - +
707D PHE* 1.3 65.1 + - - +
709D MET* 2.9 30.2 + - + +
710D LEU* 3.0 12.5 + - - +
704E GLY* 6.1 0.3 - - - -
707E PHE* 3.4 44.3 - - + -
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Residues in contact with PHE 707 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702D VAL* 5.8 1.3 - - + +
703D SER 3.3 14.2 + - - +
704D GLY* 3.8 6.7 - - - +
706D GLU* 1.3 78.9 - - - +
708D TYR* 1.3 61.3 + - + +
710D LEU* 3.3 8.3 + - - +
711D THR* 2.8 48.3 + - + +
707E PHE* 4.2 6.6 - - + -
702F VAL* 3.3 35.7 - - + -
706F GLU* 3.7 42.6 - - + -
707F PHE* 4.1 13.7 - + + -
710F LEU* 3.7 25.1 - - + -
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Residues in contact with TYR 708 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704D GLY 2.9 20.0 + - - +
705D GLU* 3.5 10.5 - - + +
707D PHE* 1.3 81.1 - - + +
709D MET* 1.3 71.5 + - + +
711D THR* 2.9 25.5 + - - -
712D ARG* 2.9 54.8 + - + +
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Residues in contact with MET 709 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705D GLU* 3.0 37.8 + - + +
706D GLU* 2.9 24.9 + - + +
708D TYR* 1.3 84.6 - - + +
710D LEU* 1.3 62.5 + - - +
712D ARG* 3.1 9.4 + - - +
713D ARG* 3.0 28.6 + - + +
707E PHE* 5.7 3.6 - - + -
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Residues in contact with LEU 710 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706D GLU 3.0 9.0 + - - +
707D PHE* 3.4 11.7 - - - +
709D MET* 1.3 76.8 - - - +
711D THR* 1.3 56.4 + - - +
713D ARG* 3.1 10.9 + - + +
714D VAL* 2.9 30.5 + - + +
707E PHE* 3.5 31.9 - - + -
710E LEU* 4.1 26.5 - - + -
711E THR* 3.9 32.5 - - + +
714E VAL* 4.3 25.4 - - + -
707F PHE* 5.2 1.3 - - + -
710F LEU* 4.4 11.9 - - + -
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Residues in contact with THR 711 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707D PHE* 2.8 51.2 + - + +
708D TYR* 2.9 18.8 + - - -
710D LEU* 1.3 72.5 - - - +
712D ARG* 1.3 67.8 + - - +
714D VAL* 3.8 1.1 - - - +
715D LEU* 2.9 33.7 + - - +
710F LEU* 3.7 27.4 - - + -
713F ARG* 4.9 7.5 + - - +
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Residues in contact with ARG 712 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708D TYR* 2.9 57.1 + - + +
709D MET* 3.4 10.3 - - - +
711D THR* 1.3 82.1 + - - +
713D ARG* 1.3 72.3 + - - +
715D LEU* 3.2 27.9 - - - +
716D GLN* 3.0 23.6 + - - +
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Residues in contact with ARG 713 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709D MET* 3.0 21.0 + - + +
710D LEU* 3.6 11.4 - - + +
712D ARG* 1.3 81.1 + - - +
714D VAL* 1.3 56.5 + - - +
716D GLN* 2.7 39.0 + - - +
717D LEU* 2.9 32.2 + - - +
714E VAL* 3.9 18.8 - - + -
715E LEU* 6.0 2.2 - - + -
718E GLU* 2.6 33.2 + - - +
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Residues in contact with VAL 714 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710D LEU* 2.9 19.6 + - + +
711D THR 3.8 3.6 - - - +
713D ARG* 1.3 71.6 - - - +
715D LEU* 1.3 66.4 + - - +
717D LEU* 3.2 10.7 + - + +
718D GLU* 2.9 43.1 + - - +
714E VAL* 3.8 15.7 - - + -
710F LEU* 4.2 21.1 - - + -
713F ARG* 3.9 15.0 - - + +
714F VAL* 3.8 25.8 - - + -
717F LEU* 4.0 11.4 - - + -
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Residues in contact with LEU 715 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711D THR* 2.9 24.0 + - - +
712D ARG* 3.2 38.6 - - - +
714D VAL* 1.3 72.1 - - - +
716D GLN* 1.3 63.2 + - - +
718D GLU* 3.3 12.2 + - - +
719D THR* 3.1 32.0 + - - +
713F ARG* 4.1 23.1 - - - +
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Residues in contact with GLN 716 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712D ARG 3.0 13.1 + - - +
713D ARG* 2.7 49.8 + - - +
715D LEU* 1.3 73.4 - - - +
717D LEU* 1.3 66.0 + - - +
719D THR* 3.3 7.4 + - + -
720D VAL* 3.0 43.3 + - + +
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Residues in contact with LEU 717 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713D ARG 2.9 15.6 + - - +
714D VAL* 3.5 12.8 - - + +
716D GLN* 1.3 76.1 - - - +
718D GLU* 1.3 64.3 + - - +
720D VAL* 3.9 1.1 - - - +
721D LEU* 2.9 31.4 + - + +
714E VAL* 3.7 31.0 - - + +
717E LEU* 3.9 29.6 - - + -
718E GLU* 3.5 35.9 - - + +
721E LEU* 3.9 22.1 - - + +
717F LEU* 4.2 11.9 - - + -
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Residues in contact with GLU 718 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716B GLN* 5.5 1.2 + - - -
714D VAL* 2.9 21.2 + - - +
715D LEU* 3.6 14.4 - - - +
717D LEU* 1.3 76.3 - - - +
719D THR* 1.3 57.2 + - - +
721D LEU* 3.6 5.9 - - - +
722D GLU* 2.9 30.2 + - - +
713F ARG* 2.9 49.1 + - - +
717F LEU* 3.5 28.6 - - + +
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Residues in contact with THR 719 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715D LEU* 3.1 21.4 + - - +
716D GLN* 3.6 11.6 - - - -
718D GLU* 1.3 74.4 - - - +
720D VAL* 1.3 67.6 + - + +
722D GLU* 3.3 17.7 + - - +
723D GLY* 3.1 18.0 + - - -
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Residues in contact with VAL 720 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716D GLN* 3.0 37.3 + - + +
717D LEU* 4.8 0.4 - - - -
719D THR* 1.3 76.3 - - + +
721D LEU* 1.3 64.5 + - - +
723D GLY* 3.1 5.5 + - - -
724D VAL* 2.9 22.7 + - + +
721E LEU* 3.6 24.2 - - + -
725E VAL* 4.0 22.4 - - + -
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Residues in contact with LEU 721 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716B GLN* 5.2 2.9 - - - +
717D LEU* 2.9 19.9 + - + +
718D GLU* 3.6 5.2 - - - +
720D VAL* 1.3 78.1 - - - +
722D GLU* 1.3 63.4 + - - +
724D VAL* 3.0 9.6 + - + +
725D VAL* 2.9 29.8 + - - +
717E LEU* 6.4 0.9 - - + -
721E LEU* 3.9 27.5 - - + +
717F LEU* 3.9 42.6 - - + +
720F VAL* 3.9 25.6 - - + -
721F LEU* 4.5 12.6 - - + +
724F VAL* 4.7 9.2 - - + -
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Residues in contact with GLU 722 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712B ARG* 3.3 36.4 + - - +
716B GLN* 4.4 9.6 - - - +
718D GLU 2.9 18.4 + - - +
719D THR* 3.5 16.1 - - - +
720D VAL 3.3 0.2 - - - -
721D LEU* 1.3 74.4 - - - +
723D GLY* 1.3 67.1 + - - +
725D VAL 3.5 0.2 + - - -
726D SER* 3.1 20.9 + - - +
----------------------------------------------------------
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Residues in contact with GLY 723 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719D THR 3.1 6.5 + - - -
720D VAL 3.1 7.4 + - - -
722D GLU* 1.3 84.9 - - - +
724D VAL* 1.3 55.5 + - - +
726D SER* 3.1 9.3 + - - -
727D GLN* 2.9 37.7 + - - +
----------------------------------------------------------
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Residues in contact with VAL 724 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720D VAL* 2.9 24.8 + - + +
721D LEU* 3.0 13.2 + - + +
723D GLY* 1.3 72.0 - - - +
725D VAL* 1.3 65.2 + - - +
727D GLN* 3.0 18.5 + - - +
728D ILE* 2.9 21.8 + - + +
721E LEU* 4.4 7.0 - - + -
724E VAL* 4.1 11.9 - - + -
725E VAL* 4.1 28.9 - - + -
728E ILE* 4.5 10.8 - - + -
724F VAL* 3.5 32.3 - - + -
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Residues in contact with VAL 725 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712B ARG* 3.8 8.3 - - - +
715B LEU* 3.9 20.1 - - + +
716B GLN* 3.8 24.9 - - - +
719B THR* 4.1 15.7 - - - +
721D LEU* 2.9 22.9 + - + +
722D GLU* 4.2 1.3 - - - +
724D VAL* 1.3 72.9 - - - +
726D SER* 1.3 67.1 + - - +
728D ILE* 3.6 13.4 - - + +
729D ASP* 2.9 24.6 + - - +
720F VAL* 4.3 15.0 - - + -
724F VAL* 4.0 19.7 - - + -
727F GLN* 5.8 0.2 - - - +
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Residues in contact with SER 726 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708B TYR* 5.8 2.0 - - - -
712B ARG* 4.2 19.1 - - - -
715B LEU* 4.4 8.1 - - - -
722D GLU* 3.1 14.2 + - - +
723D GLY* 3.1 16.8 + - - -
725D VAL* 1.3 84.2 - - - +
727D GLN* 1.3 57.7 + - - +
729D ASP* 3.4 1.6 + - - +
730D ALA* 2.9 29.6 + - - +
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Residues in contact with GLN 727 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723D GLY* 2.9 22.1 + - - +
724D VAL* 3.0 14.2 + - - +
726D SER* 1.3 78.9 + - - +
728D ILE* 1.3 57.4 + - - +
730D ALA* 3.2 9.1 + - - +
731D VAL* 3.0 27.4 + - - +
728E ILE* 3.8 31.0 - - + +
729E ASP* 4.6 7.0 + - - +
----------------------------------------------------------
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Residues in contact with ILE 728 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724D VAL* 2.9 15.8 + - + +
725D VAL* 3.6 12.8 - - - +
727D GLN* 1.3 69.2 - - - +
729D ASP* 1.3 68.8 + - - +
731D VAL* 3.1 11.2 + - + +
732D GLY* 3.0 19.1 + - - -
728E ILE* 3.3 35.2 - - + -
724F VAL* 3.6 35.4 - - + +
727F GLN* 3.5 42.2 - - + +
728F ILE* 4.6 14.4 - - + +
731F VAL* 5.2 6.0 - - + +
----------------------------------------------------------
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Residues in contact with ASP 729 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713A ARG* 4.8 10.6 + - - -
715B LEU* 3.5 38.6 - - + +
718B GLU* 4.9 0.7 - - - +
725D VAL 2.9 19.0 + - - +
726D SER 3.8 3.3 - - - +
728D ILE* 1.3 80.1 - - + +
730D ALA* 1.3 65.6 + - - +
732D GLY* 3.1 19.4 + - - +
727F GLN* 5.1 4.5 - - - +
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Residues in contact with ALA 730 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726D SER 2.9 14.2 + - - +
727D GLN* 3.2 11.6 + - - +
729D ASP* 1.3 80.7 + - - +
731D VAL* 1.3 66.3 + - - +
732D GLY 4.1 2.3 - - - +
733D SER* 4.7 2.1 + - - -
----------------------------------------------------------
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Residues in contact with VAL 731 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727D GLN 3.0 16.7 + - - +
728D ILE* 3.1 13.7 + - + +
730D ALA* 1.3 79.4 - - - +
732D GLY* 1.3 67.1 + - - +
733D SER* 2.9 14.2 + - - -
728E ILE* 5.2 7.2 - - + -
731E VAL* 4.8 25.4 - - + -
731F VAL* 3.6 36.6 - - + -
----------------------------------------------------------
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Residues in contact with GLY 732 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728D ILE 3.0 16.7 + - - -
729D ASP* 3.1 13.7 + - - +
730D ALA 4.1 1.6 - - - +
731D VAL* 1.3 76.5 - - - +
733D SER* 1.3 61.6 + - - -
731F VAL* 4.9 8.7 - - - -
----------------------------------------------------------
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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