Contacts of the helix formed by residues 713 - 736 (chain C) in PDB entry 1XFV
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 713 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712C PHE* 1.3 75.9 - - - +
714C GLN* 1.3 69.1 + - - +
715C GLU* 4.5 7.3 + - - +
716C LYS* 2.7 28.6 + - - +
717C LYS* 3.1 8.5 + - - -
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Residues in contact with GLN 714 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712C PHE 4.0 0.2 + - - -
713C SER* 1.3 69.7 - - - +
715C GLU* 1.3 68.6 + - - +
717C LYS* 2.9 52.8 + - - +
718C ARG* 3.2 19.7 + - - +
126Q ARG* 3.6 34.9 + - - +
129Q ASP* 4.0 11.9 + - - +
132Q GLY* 3.7 23.7 + - - +
134Q GLY* 4.4 9.3 - - - +
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Residues in contact with GLU 715 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713C SER* 2.9 11.6 + - - +
714C GLN* 1.3 75.0 - - - +
716C LYS* 1.3 65.4 + - - +
718C ARG* 2.7 40.3 + - - +
719C LYS* 3.2 38.8 + - - +
767C GLN* 2.5 44.0 + - - +
797C ILE* 5.9 0.6 - - - +
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Residues in contact with LYS 716 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712C PHE* 3.0 56.2 - - + +
713C SER* 2.7 22.7 + - - +
715C GLU* 1.3 73.6 - - - +
717C LYS* 1.3 70.3 + - - +
719C LYS* 2.5 28.8 + - + +
720C ILE* 2.6 35.6 + - + +
790C PHE* 5.9 1.3 - - + -
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Residues in contact with LYS 717 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709C ASN* 3.0 32.3 + - + +
710C HIS* 4.0 9.0 + - - +
712C PHE* 3.0 24.2 + - + +
713C SER 3.1 6.6 + - - +
714C GLN* 2.9 47.5 + - - +
716C LYS* 1.3 78.1 - - - +
718C ARG* 1.3 63.8 + - - +
720C ILE* 3.2 9.9 - - - +
721C SER* 2.9 25.4 + - - -
126Q ARG* 4.1 9.1 + - - +
127Q GLU* 5.7 0.4 - - - +
129Q ASP 2.9 25.6 - - - +
130Q ILE 3.7 10.3 - - - +
131Q ASP 3.7 4.0 - - - -
132Q GLY* 3.4 20.2 - - - +
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Residues in contact with ARG 718 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714C GLN* 3.4 13.0 + - - +
715C GLU* 2.7 51.8 + - - +
716C LYS 3.2 0.2 - - - -
717C LYS* 1.3 73.9 - - - +
719C LYS* 1.3 50.8 + - - +
721C SER* 3.8 0.8 - - - -
722C ILE* 2.6 47.1 + - + +
763C LEU* 3.9 20.6 - - + +
766C HIS* 4.1 22.0 + - - +
767C GLN* 2.5 58.8 - - - +
131Q ASP 3.4 17.2 + - - +
132Q GLY* 3.9 19.4 + - - -
133Q ASP 4.9 0.4 - - - +
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Residues in contact with LYS 719 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715C GLU* 3.2 32.8 + - + +
716C LYS* 2.5 21.5 + - + +
718C ARG* 1.3 69.2 - - - +
720C ILE* 1.3 56.2 + - - +
721C SER 2.5 16.8 + - - -
722C ILE* 2.7 16.6 + - + +
723C PHE* 3.0 11.6 + - - +
767C GLN* 3.4 21.3 - - - +
790C PHE* 5.5 3.6 - - + -
793C PHE* 3.9 18.2 - - + -
794C GLN* 5.0 13.9 - - - +
797C ILE* 3.3 36.7 - - + +
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Residues in contact with ILE 720 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709C ASN* 4.4 12.6 - - - +
712C PHE* 4.5 12.8 - - + -
716C LYS* 2.6 37.2 + - + +
717C LYS* 3.2 19.1 - - - +
719C LYS* 1.3 71.4 - - - +
721C SER* 1.3 64.3 + - - +
723C PHE* 4.0 3.8 - - + +
724C ARG* 2.8 51.1 + - - +
790C PHE* 3.4 36.0 - - + -
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Residues in contact with SER 721 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704C TYR* 4.0 33.4 + - - -
709C ASN* 3.7 18.4 + - - -
717C LYS 2.9 17.7 + - - -
718C ARG 3.8 2.0 - - - -
719C LYS 2.5 5.9 + - - -
720C ILE* 1.3 74.4 - - - +
722C ILE* 1.3 65.0 + - - -
723C PHE 2.6 6.8 + - - -
724C ARG* 2.8 8.6 + - - +
725C GLY* 2.7 23.4 + - - -
763C LEU* 4.5 2.2 - - - -
130Q ILE 4.0 4.9 + - - -
131Q ASP* 4.0 8.7 - - - +
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Residues in contact with ILE 722 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718C ARG* 2.6 36.9 + - + +
719C LYS* 2.7 8.5 + - + +
721C SER* 1.3 70.9 - - - +
723C PHE* 1.3 55.9 + - - +
726C ILE* 3.2 28.5 + - + +
760C VAL* 3.5 32.1 - - + +
763C LEU* 2.9 49.1 - - + +
764C LEU* 3.3 22.2 - - + -
767C GLN* 4.7 7.0 - - - +
776C LEU* 4.5 1.8 - - + -
793C PHE* 3.8 24.2 - - + -
797C ILE* 6.5 0.2 - - + -
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Residues in contact with PHE 723 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719C LYS 3.0 11.7 + - - +
720C ILE* 4.0 4.9 - - + +
721C SER 2.6 1.4 + - - -
722C ILE* 1.3 75.7 - - - +
724C ARG* 1.3 58.8 + - - +
725C GLY 3.0 1.6 - - - -
726C ILE* 2.5 43.6 + - + +
727C GLN* 2.8 48.9 + - + +
780C LEU* 5.2 3.8 - - + -
782C PHE* 5.0 4.5 - + - -
786C GLU* 4.0 29.4 - - + -
789C ASN* 4.2 18.2 - - - -
790C PHE* 3.8 40.6 - + + -
793C PHE* 3.9 30.0 - + + -
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Residues in contact with ARG 724 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657C ILE* 5.1 0.7 - - - -
700C TYR* 4.1 10.0 - - - +
703C ASP* 3.2 47.4 + - - +
704C TYR* 4.2 18.9 + - + +
706C ASN* 5.0 10.1 - - - +
709C ASN* 4.1 22.2 - - - +
712C PHE* 6.1 1.6 - - - -
720C ILE* 2.8 44.1 + - - +
721C SER* 2.8 15.4 + - - +
723C PHE* 1.3 75.9 - - - +
725C GLY* 1.3 62.0 + - - +
727C GLN* 3.3 29.9 + - - +
728C ALA* 3.3 10.6 + - - +
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Residues in contact with GLY 725 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657C ILE* 3.5 26.7 - - - -
704C TYR* 4.2 3.7 - - - -
721C SER 2.7 16.8 + - - -
722C ILE 4.3 0.9 - - - -
724C ARG* 1.3 75.6 - - - +
726C ILE* 1.3 55.5 + - - -
728C ALA* 2.8 26.5 + - - +
729C TYR 3.0 5.0 + - - -
756C ILE* 3.6 13.3 - - - +
760C VAL* 4.8 5.8 - - - -
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Residues in contact with ILE 726 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722C ILE* 3.2 24.7 + - + +
723C PHE* 2.5 44.0 + - + +
725C GLY* 1.3 70.7 - - - +
727C GLN* 1.3 67.8 + - + +
729C TYR* 3.1 8.7 + - - +
730C ASN* 2.9 21.0 + - - +
756C ILE* 5.0 1.3 - - - -
760C VAL* 4.5 3.5 - - + +
773C PHE* 4.0 27.1 - - + -
776C LEU* 3.9 36.3 - - + -
777C TYR* 4.6 16.8 - - + -
780C LEU* 5.1 3.1 - - + -
782C PHE* 4.3 13.7 - - + -
793C PHE* 5.2 1.8 - - + -
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Residues in contact with GLN 727 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700C TYR* 3.3 41.3 - - + -
723C PHE* 2.8 52.8 + - + +
724C ARG* 3.4 31.7 - - - +
726C ILE* 1.3 76.1 - - + +
728C ALA* 1.3 63.7 - - - +
730C ASN* 3.0 23.2 - - - +
731C GLU 3.3 4.2 + - - -
782C PHE* 5.2 4.0 - - + -
786C GLU* 3.4 19.4 - - - +
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Residues in contact with ALA 728 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657C ILE* 4.3 13.5 - - + -
697C ILE* 4.8 8.3 - - + -
700C TYR* 3.3 24.6 - - + -
701C LEU* 4.3 11.4 - - + +
724C ARG 3.3 3.1 + - - +
725C GLY* 2.8 19.7 + - - +
727C GLN* 1.3 78.3 - - - +
729C TYR* 1.3 63.8 + - - +
730C ASN 3.0 0.9 + - - -
731C GLU* 3.3 2.8 + - - +
732C ILE* 2.8 29.1 + - + +
756C ILE* 4.8 4.7 - - + -
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Residues in contact with TYR 729 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725C GLY 3.0 6.2 + - - +
726C ILE* 3.3 12.3 - - + +
728C ALA* 1.3 75.6 - - - +
730C ASN* 1.3 69.9 + - - +
732C ILE* 3.3 9.7 + - - +
733C GLU* 3.0 43.5 + - + -
753C LYS* 3.3 37.5 + - + -
756C ILE* 3.8 26.5 - - + +
757C THR* 3.4 15.7 - - - -
773C PHE* 3.2 39.3 - + + -
777C TYR* 3.6 25.2 - + + -
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Residues in contact with ASN 730 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696C LYS* 5.2 2.1 + - - -
700C TYR* 6.1 0.4 - - - -
726C ILE 2.9 11.7 + - - +
727C GLN* 3.0 15.7 - - - +
728C ALA 3.0 0.6 + - - -
729C TYR* 1.3 83.2 - - - +
731C GLU* 1.3 75.2 + - - +
732C ILE 2.7 0.7 + - - -
733C GLU* 2.6 27.9 + - - +
734C ASN* 3.0 15.6 + - - +
777C TYR* 3.7 18.2 + - + +
782C PHE* 3.0 51.0 - - + +
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Residues in contact with GLU 731 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693C SER* 2.4 30.4 + - - -
696C LYS* 2.8 54.3 + - + +
697C ILE* 3.9 20.0 - - + -
700C TYR* 4.2 9.9 - - + -
727C GLN 3.3 2.8 + - - +
728C ALA 3.3 5.1 + - - +
730C ASN* 1.3 85.7 + - - +
732C ILE* 1.3 66.7 + - - +
734C ASN* 3.3 24.2 + - - +
735C VAL* 3.1 16.6 + - - +
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Residues in contact with ILE 732 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697C ILE* 3.0 51.6 - - + -
728C ALA* 2.8 27.1 + - + +
729C TYR* 3.3 9.9 - - - +
730C ASN 2.7 3.8 + - - -
731C GLU* 1.3 76.2 - - - +
733C GLU* 1.3 66.4 + - - +
734C ASN 2.8 0.5 + - - -
735C VAL* 2.9 11.7 + - - +
736C LEU* 3.0 13.1 + - + -
749C PHE* 3.6 41.0 - - + +
752C LEU* 4.4 20.4 - - + -
753C LYS* 4.3 14.1 - - + +
756C ILE* 5.4 7.6 - - + -
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Residues in contact with GLU 733 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729C TYR* 3.0 31.3 + - + +
730C ASN 2.6 18.2 + - - +
732C ILE* 1.3 74.5 - - - +
734C ASN* 1.3 65.0 + - - +
736C LEU* 3.4 9.0 + - - +
737C LYS* 3.2 32.3 + - + +
753C LYS* 3.2 33.1 + - - +
777C TYR* 4.1 18.2 - - + +
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Residues in contact with ASN 734 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693C SER* 5.0 1.0 + - - -
730C ASN* 3.0 16.8 + - - +
731C GLU* 3.1 38.7 + - - +
732C ILE 2.8 2.8 + - - -
733C GLU* 1.3 72.0 - - - +
735C VAL* 1.3 55.1 + - + +
737C LYS* 2.6 40.9 + - - +
738C SER* 4.1 0.8 - - - -
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Residues in contact with VAL 735 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678C VAL* 5.6 2.2 - - + -
690C LYS* 4.3 18.8 - - + +
693C SER* 3.1 29.4 - - - +
694C VAL* 5.1 4.0 - - + +
697C ILE* 4.6 11.4 - - + -
731C GLU 3.1 16.8 - - - +
732C ILE* 2.9 6.6 + - - +
734C ASN* 1.3 71.7 - - - +
736C LEU* 1.3 53.1 + - - +
737C LYS 2.6 0.7 + - - -
738C SER* 2.6 41.5 + - - -
741C ILE* 3.1 30.2 - - + +
749C PHE* 4.9 18.8 - - + -
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Residues in contact with LEU 736 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732C ILE* 3.0 10.1 + - + +
733C GLU* 3.6 12.8 - - - +
735C VAL* 1.3 76.2 - - - +
737C LYS* 1.3 69.6 + - + +
738C SER 3.4 2.1 + - - -
741C ILE* 4.7 7.4 - - + -
746C LYS* 3.6 42.2 - - + +
749C PHE* 4.3 15.6 - - + -
750C GLN* 2.9 37.9 - - + +
753C LYS* 4.0 26.5 - - + +
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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