Contacts of the helix formed by residues 680 - 703 (chain A) in PDB entry 1TF5
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 GLU 680 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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652A TRP* 6.0 1.6 - - - -
653A LYS* 5.0 2.9 + - - -
678A GLY 4.6 4.1 - - - +
679A LYS* 1.3 79.8 - - - +
681A PRO* 1.3 72.1 - - + +
682A ASP* 4.2 8.1 - - + +
683A GLU* 2.7 49.9 + - + +
684A MET* 2.9 13.9 + - - +
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Residues in contact with PRO 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639A ILE* 4.5 13.1 - - + +
640A ALA* 6.2 0.4 - - - -
643A THR* 4.2 22.4 - - - +
645A ARG* 6.3 2.7 - - + -
653A LYS* 3.8 23.3 - - - +
680A GLU* 1.3 97.8 - - + +
682A ASP* 1.3 61.9 + - - +
684A MET* 3.5 9.4 + - + +
685A LEU* 3.2 24.8 + - - +
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Residues in contact with ASP 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680A GLU* 4.8 7.0 - - + -
681A PRO* 1.3 80.7 - - + +
683A GLU* 1.3 67.3 + - + +
685A LEU* 3.7 14.5 - - - +
686A GLU* 3.8 9.5 + - - +
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Residues in contact with GLU 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A LYS* 3.5 19.7 - - + +
680A GLU* 2.7 50.4 + - + +
682A ASP* 1.3 74.1 - - + +
684A MET* 1.3 63.8 + - - +
685A LEU 2.8 5.9 + - - -
686A GLU* 3.0 14.9 + - - +
687A LEU* 3.1 26.5 + - + +
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Residues in contact with MET 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639A ILE* 4.0 13.5 - - + -
643A THR* 4.3 24.2 - - + -
653A LYS* 5.4 4.0 - - + -
655A ASP* 4.7 6.5 - - - +
657A LEU* 6.3 1.3 - - - -
675A ASP 4.8 1.6 - - - +
676A ILE* 3.3 37.2 - - + -
677A PHE* 3.8 16.6 - - - +
678A GLY 5.1 0.9 - - - +
679A LYS* 3.8 24.7 - - + +
680A GLU 2.9 19.9 + - - +
681A PRO* 4.0 4.5 - - - +
683A GLU* 1.3 71.5 - - - +
685A LEU* 1.3 59.7 + - - +
687A LEU* 3.9 9.4 - - - +
688A ILE* 3.0 40.5 + - + +
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Residues in contact with LEU 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632A LYS* 3.8 23.1 - - + +
635A LEU* 4.0 15.7 - - + +
636A GLU* 4.4 27.8 - - + +
639A ILE* 3.4 22.4 - - + +
681A PRO 3.2 16.8 + - - +
682A ASP* 3.7 7.9 - - - +
683A GLU 2.8 1.8 + - - -
684A MET* 1.3 75.8 - - - +
686A GLU* 1.3 87.4 + - + +
688A ILE* 4.0 1.7 - - - +
689A MET* 3.1 25.8 + - + +
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Residues in contact with GLU 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632A LYS* 2.9 23.4 + - - -
682A ASP* 3.8 8.4 + - - +
683A GLU* 3.0 8.0 + - - +
685A LEU* 1.3 96.0 - - - +
687A LEU* 1.3 61.8 + - + +
689A MET* 3.3 4.5 + - - +
690A ASP* 2.6 44.0 + - - +
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Residues in contact with LEU 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674A SER 5.6 1.6 - - - +
675A ASP* 3.3 56.5 - - + +
676A ILE* 5.7 1.1 - - + -
679A LYS* 5.0 3.4 - - + -
683A GLU* 3.1 31.8 + - + +
684A MET* 3.9 7.0 - - - +
686A GLU* 1.3 80.4 - - + +
688A ILE* 1.3 64.6 + - + +
690A ASP* 3.4 14.1 + - - +
691A ARG* 3.2 31.1 + - - +
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Residues in contact with ILE 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635A LEU* 3.8 22.7 - - + -
639A ILE* 4.4 12.1 - - + -
657A LEU* 4.4 17.9 - - + -
661A ILE* 4.2 24.0 - - + -
665A TYR* 6.3 0.2 - - + -
666A LEU* 4.5 8.1 - - + -
671A LEU* 4.8 5.6 - - + -
676A ILE* 4.0 29.4 - - + -
684A MET* 3.0 26.1 + - + +
687A LEU* 1.3 76.0 - - + +
689A MET* 1.3 64.5 + - - +
691A ARG* 3.4 10.2 - - - +
692A ILE* 3.1 25.4 + - + +
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Residues in contact with MET 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628A GLU* 4.8 3.8 - - - +
631A ILE* 3.6 26.7 - - + -
632A LYS* 3.4 58.1 - - + +
635A LEU* 3.7 18.8 - - + -
685A LEU* 3.1 20.7 + - + +
686A GLU* 3.6 6.3 - - - +
687A LEU 3.2 0.2 - - - -
688A ILE* 1.3 75.3 - - - +
690A ASP* 1.3 67.2 + - - +
692A ILE* 2.9 32.8 + - + +
693A ILE* 2.8 37.0 + - + +
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Residues in contact with ASP 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686A GLU* 2.6 33.2 + - - +
687A LEU* 3.6 11.9 - - - +
688A ILE 3.4 0.2 - - - -
689A MET* 1.3 75.1 - - - +
691A ARG* 1.3 71.0 + - - +
693A ILE* 3.0 20.0 + - - +
694A THR* 3.2 15.4 + - - -
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Residues in contact with ARG 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666A LEU* 4.0 15.7 - - + +
671A LEU* 3.5 38.8 - - + +
674A SER* 4.5 10.8 - - - -
675A ASP* 3.4 24.0 + - - +
687A LEU* 3.2 29.7 + - - +
688A ILE* 3.4 7.6 - - - +
690A ASP* 1.3 81.3 - - - +
692A ILE* 1.3 57.0 + - - +
694A THR* 3.5 4.8 + - - -
695A LYS* 2.9 31.3 + - - +
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Residues in contact with ILE 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631A ILE* 4.2 10.8 - - + -
635A LEU* 5.0 0.7 - - + -
665A TYR* 3.4 29.8 - - + -
666A LEU* 3.3 26.2 - - + -
688A ILE* 3.1 20.9 - - + +
689A MET* 2.9 39.0 + - + +
691A ARG* 1.3 77.7 - - - +
693A ILE* 1.3 52.5 + - + +
695A LYS* 3.2 5.7 - - - +
696A TYR* 2.7 33.2 + - + +
776A MET* 3.4 27.5 - - + +
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Residues in contact with ILE 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628A GLU* 3.1 33.2 - - + +
632A LYS* 6.1 1.6 - - - -
689A MET* 2.8 37.9 + - + +
690A ASP* 3.0 11.2 + - - +
692A ILE* 1.3 75.5 - - + +
694A THR* 1.3 55.0 + - - +
696A TYR* 2.7 22.1 + - + -
697A ASN* 2.6 52.6 + - - +
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Residues in contact with THR 694 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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690A ASP 3.2 8.9 + - - -
691A ARG* 4.0 6.3 - - - -
693A ILE* 1.3 77.4 - - - +
695A LYS* 1.3 54.9 + - - +
697A ASN* 3.1 15.5 + - + +
698A GLU* 2.7 38.4 + - + +
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Residues in contact with LYS 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665A TYR 3.3 22.6 + - - -
666A LEU* 3.7 13.0 - - + +
667A ASP* 2.6 41.8 + - - +
691A ARG 2.9 19.4 + - - +
692A ILE* 3.2 9.0 - - - +
694A THR* 1.3 77.8 - - - +
696A TYR* 1.3 60.4 + - - +
698A GLU* 3.6 23.5 - - - +
699A LYS* 3.5 26.1 + - - +
776A MET* 3.4 27.0 + - + +
777A LYS* 4.9 0.8 - - - +
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Residues in contact with TYR 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624A ARG* 3.0 54.4 - - + +
628A GLU* 3.1 37.0 + - + -
631A ILE* 6.1 0.2 - - + -
692A ILE* 2.7 12.2 + - + +
693A ILE* 2.7 40.5 + - + +
695A LYS* 1.3 69.2 - - - +
697A ASN* 1.3 72.7 + - - -
698A GLU 3.1 1.8 - - - -
699A LYS* 3.4 3.1 + - - +
700A GLU* 2.8 61.6 + - + +
708A MET* 5.2 1.4 - - - +
709A ARG* 4.8 0.5 + - - -
776A MET* 3.6 12.3 - - + -
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Residues in contact with ASN 697 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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693A ILE* 2.6 49.9 + - - +
694A THR* 3.1 15.0 + - + +
696A TYR* 1.3 96.2 + - - +
698A GLU* 1.3 68.7 + - - +
700A GLU* 4.0 8.7 - - - +
701A GLU* 3.1 25.3 + - - +
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Residues in contact with GLU 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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694A THR* 2.7 23.8 + - + +
695A LYS* 3.6 26.8 - - - +
697A ASN* 1.3 77.2 - - - +
699A LYS* 1.3 68.8 + - - +
700A GLU 2.9 0.3 + - - -
702A GLN* 2.9 49.4 + - - +
703A PHE* 4.4 9.2 - - + -
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Residues in contact with LYS 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695A LYS* 3.5 18.5 + - - +
696A TYR* 3.4 4.2 + - - +
698A GLU* 1.3 83.9 - - - +
700A GLU* 1.3 64.9 + - - +
703A PHE* 2.9 40.9 + - + +
708A MET* 4.4 13.1 - - + +
711A PHE* 3.4 30.0 - - - -
775A VAL 3.6 15.7 - - - +
776A MET* 5.3 8.1 - - + -
778A ALA 2.7 31.8 + - - +
779A GLU* 3.9 12.7 - - - +
780A ILE* 4.8 4.2 - - - +
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Residues in contact with GLU 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696A TYR* 2.8 45.6 + - + +
697A ASN* 3.3 12.2 - - - +
698A GLU 2.9 0.8 + - - -
699A LYS* 1.3 81.0 - - - +
701A GLU* 1.3 63.6 + - + +
703A PHE 2.9 1.9 - - - +
704A GLY 2.5 27.8 - - - +
705A LYS 5.2 3.6 - - - +
708A MET* 3.8 29.6 - - + +
709A ARG* 2.6 35.2 + - - -
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Residues in contact with GLU 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697A ASN 3.1 10.0 + - - +
700A GLU* 1.3 87.0 - - + +
702A GLN* 1.3 65.9 + - - +
704A GLY 3.7 9.5 - - - +
705A LYS* 5.2 4.7 - - - +
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Residues in contact with GLN 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698A GLU* 2.9 42.5 + - - +
701A GLU* 1.3 78.5 - - - +
703A PHE* 1.3 90.6 + - + +
704A GLY 3.7 2.3 + - - -
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Residues in contact with PHE 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698A GLU* 4.4 9.9 - - - -
699A LYS* 2.9 45.8 + - + +
700A GLU* 2.9 4.9 - - - +
702A GLN* 1.3 113.2 - - + +
704A GLY* 1.3 60.9 + - - +
707A GLN* 5.1 2.1 - - - +
708A MET* 5.3 4.5 + - - +
780A ILE* 5.8 2.9 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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