Contacts of the helix formed by residues 681 - 703 (chain A) in PDB entry 3NC0
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 ASP 681 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677A ASP 4.0 1.7 + - - +
678A ILE* 2.8 28.7 + - + +
679A LEU 3.5 0.2 - - - -
680A LYS* 1.3 76.9 - - - +
682A PRO* 1.3 79.8 - - - +
683A GLU* 3.1 4.5 + - - +
684A THR* 3.2 25.4 + - + +
685A VAL* 2.9 24.2 + - - +
181B GLN* 3.9 12.3 + - - +
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Residues in contact with PRO 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A LYS 3.5 8.4 - - - +
681A ASP* 1.3 91.8 - - - +
683A GLU* 1.3 57.1 + - - +
685A VAL* 3.5 2.5 + - + +
686A LYS* 3.0 26.7 + - - +
744A LEU* 3.9 27.8 - - + -
747A SER* 4.6 3.3 + - - -
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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
----------------------------------------------------------
681A ASP* 3.2 5.6 + - - +
682A PRO* 1.3 77.5 - - - +
684A THR* 1.3 65.3 + - - +
686A LYS* 3.1 25.8 + - - +
687A GLN* 3.1 44.3 + - - +
150B ASN* 4.1 14.0 - - - +
176B TYR* 3.2 25.7 + - - +
181B GLN* 3.1 35.0 - - + +
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Residues in contact with THR 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A ILE* 3.8 20.5 - - + +
678A ILE* 3.0 35.7 + - + +
679A LEU* 4.5 0.3 - - - -
681A ASP* 3.1 24.5 + - + +
683A GLU* 1.3 75.1 - - - +
685A VAL* 1.3 62.2 + - - +
687A GLN* 3.4 9.7 + - - +
688A LEU* 3.0 37.0 + - - +
181B GLN* 3.1 26.5 - - - +
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Residues in contact with VAL 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A LEU* 3.7 28.0 - - - +
680A LYS 4.3 2.0 - - - -
681A ASP 2.9 26.2 + - - +
682A PRO* 3.8 5.6 - - + +
684A THR* 1.3 79.6 + - - +
686A LYS* 1.3 64.0 + - - +
687A GLN 3.1 0.4 - - - -
688A LEU* 3.4 10.8 + - + +
689A GLY* 3.1 18.4 + - - -
724A LEU* 4.9 3.1 - - + -
744A LEU* 4.6 6.3 - - + -
747A SER* 3.2 36.2 + - - +
748A MET* 4.1 13.2 - - + +
751A VAL* 3.8 13.5 - - + +
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Residues in contact with LYS 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627A PRO* 6.1 5.4 - - - -
682A PRO 3.0 14.3 + - - +
683A GLU* 3.1 28.6 + - - +
685A VAL* 1.3 78.4 - - - +
687A GLN* 1.3 60.5 + - + +
689A GLY* 3.5 2.0 + - - -
690A SER* 3.3 20.7 + - - -
747A SER* 4.1 8.2 + - - +
149B VAL* 3.0 31.9 + - - +
150B ASN* 4.3 15.8 + - - +
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Residues in contact with GLN 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A VAL* 3.4 21.7 - - + +
668A ILE* 3.8 15.4 - - + +
683A GLU* 3.1 38.5 + - - +
684A THR* 3.6 9.8 - - - +
685A VAL 3.1 0.2 - - - -
686A LYS* 1.3 74.5 - - + +
688A LEU* 1.3 58.3 + - - +
689A GLY 3.0 1.3 - - - -
690A SER* 2.9 7.7 + - - +
691A ILE* 2.7 39.6 + - + +
176B TYR* 3.7 5.9 + - - -
178B GLU* 3.3 51.4 + - - +
181B GLN* 4.5 4.6 + - - +
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Residues in contact with LEU 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A TRP* 4.1 28.7 - - + -
668A ILE* 3.8 30.9 - - + +
669A ILE* 5.3 4.7 - - + -
679A LEU* 4.1 25.4 - - + -
684A THR* 3.0 29.9 + - - +
685A VAL* 3.4 18.6 + - + +
687A GLN* 1.3 74.7 - - - +
689A GLY* 1.3 62.4 + - - +
691A ILE* 4.0 5.9 - - + +
692A LEU* 3.1 31.4 + - + +
720A VAL* 4.6 14.8 - - + -
724A LEU* 5.5 1.8 - - + -
751A VAL* 3.9 17.0 - - + -
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Residues in contact with GLY 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A VAL 3.1 13.3 + - - -
686A LYS 3.9 4.0 - - - -
687A GLN 3.0 1.2 - - - -
688A LEU* 1.3 77.1 - - - +
690A SER* 1.3 56.3 + - - +
692A LEU* 3.2 6.0 + - - +
693A LYS* 2.8 35.8 + - - +
750A THR* 4.7 16.6 - - - -
751A VAL* 3.8 12.9 - - - +
754A GLU* 4.7 1.3 - - - +
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Residues in contact with SER 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627A PRO* 5.0 6.6 - - - +
631A HIS* 3.3 25.9 + - - -
686A LYS* 3.3 13.1 + - - -
687A GLN* 2.9 9.2 + - - -
689A GLY* 1.3 72.1 - - - +
691A ILE* 1.3 66.1 + - - +
693A LYS* 4.2 3.8 - - - -
694A THR* 2.8 30.0 + - - -
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Residues in contact with ILE 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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661A PRO* 3.9 24.4 - - + +
664A VAL* 3.3 43.3 - - + -
665A TRP* 3.7 33.2 - - + +
668A ILE* 4.2 6.1 - - + -
687A GLN* 2.7 28.1 + - + +
688A LEU* 4.0 6.5 - - - +
690A SER* 1.3 71.7 - - - +
692A LEU* 1.3 64.1 + - - +
694A THR* 3.0 9.9 + - - -
695A ASN* 2.9 35.0 + - - +
178B GLU* 5.9 1.1 - - - +
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Residues in contact with LEU 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A TRP* 4.2 21.1 - - + -
688A LEU* 3.1 23.3 + - + +
689A GLY 3.5 3.6 - - - +
691A ILE* 1.3 78.6 - - - +
693A LYS* 1.3 56.2 + - - +
695A ASN* 2.8 30.5 + - - +
696A VAL* 2.8 18.0 + - + +
713A ILE* 4.9 1.6 - - + -
717A MET* 3.9 25.4 - - + -
751A VAL* 3.4 28.9 - - + +
754A GLU* 4.0 12.1 - - + -
755A THR* 3.2 30.1 - - - +
758A LEU* 4.5 11.7 - - + -
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Residues in contact with LYS 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A ASN* 6.1 0.6 - - - +
439A GLU* 3.6 35.3 + - - -
628A GLN* 5.6 9.8 - - + +
631A HIS* 3.4 31.0 - - + +
689A GLY 2.8 22.8 + - - +
690A SER* 3.3 2.9 + - - -
692A LEU* 1.3 72.1 - - - +
694A THR* 1.3 61.7 + - - +
696A VAL* 3.3 7.7 + - - +
697A ARG* 3.1 23.7 + - - +
750A THR* 4.5 4.7 - - - +
754A GLU* 2.7 51.1 + - + +
757A LYS* 5.3 2.2 - - - +
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Residues in contact with THR 694 (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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630A VAL* 5.0 6.1 - - - +
631A HIS* 3.2 18.8 + - + +
634A TYR* 3.7 42.3 - - + +
658A MET* 4.9 2.9 - - + -
661A PRO* 4.3 18.4 - - + -
690A SER* 2.8 19.8 + - - -
691A ILE* 3.2 10.8 - - - -
693A LYS* 1.3 75.2 - - - +
695A ASN* 1.3 62.9 + - - +
696A VAL 3.3 0.2 + - - -
697A ARG* 3.3 5.4 + - - +
698A ALA* 3.2 21.7 + - - +
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Residues in contact with ASN 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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658A MET* 3.1 29.5 - - - +
661A PRO* 5.4 0.6 - - - +
665A TRP* 5.7 0.2 - - - -
691A ILE* 2.9 30.6 + - - +
692A LEU* 2.8 14.6 + - - +
694A THR* 1.3 78.0 - - - +
696A VAL* 1.3 59.3 + - - +
698A ALA* 4.6 0.2 - - - -
699A CYS* 3.3 23.0 + - - +
706A PHE* 3.2 24.2 - - - -
709A GLN* 3.4 11.7 + - - +
713A ILE* 4.0 23.9 - - - +
758A LEU* 3.6 17.8 - - + +
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Residues in contact with VAL 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A LEU 2.8 17.8 + - - +
693A LYS 3.6 7.6 - - - +
694A THR 3.2 0.8 - - - -
695A ASN* 1.3 76.5 - - - +
697A ARG* 1.3 66.6 + - + +
699A CYS* 3.4 3.8 + - - +
700A LYS* 3.1 25.7 + - + +
754A GLU* 3.6 39.9 - - - +
757A LYS* 4.3 22.4 - - + +
758A LEU* 4.0 20.9 - - + +
761A GLY* 6.4 0.9 - - - -
765A ARG* 5.6 0.3 + - - -
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Residues in contact with ARG 697 (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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589A ILE* 5.2 0.6 - - - +
628A GLN* 4.7 11.1 + - - +
631A HIS* 3.4 39.9 - - + +
632A THR* 3.8 25.9 + - - +
634A TYR* 5.1 0.7 - - + -
635A GLU* 2.7 54.2 + - + +
693A LYS 3.1 18.8 - - - +
694A THR 3.3 4.6 + - - +
696A VAL* 1.3 80.4 - - - +
698A ALA* 1.3 66.6 + - - +
699A CYS 3.1 1.6 - - - -
700A LYS* 3.0 22.6 + - - +
701A ALA* 3.3 9.5 + - - +
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Residues in contact with ALA 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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634A TYR* 4.6 3.1 - - + -
635A GLU* 4.7 1.0 - - - +
638A GLY* 5.1 0.2 - - - -
657A TYR* 3.0 41.3 - - + +
658A MET* 4.0 14.6 - - - -
694A THR 3.2 14.8 + - - +
695A ASN 4.1 1.8 - - - +
697A ARG* 1.3 78.2 - - - +
699A CYS* 1.3 57.3 + - - +
701A ALA* 3.3 1.0 + - - +
702A VAL* 2.9 35.6 + - - +
706A PHE* 4.0 9.6 - - + -
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Residues in contact with CYS 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 ASN 3.3 17.7 + - - +
696A VAL* 3.6 5.6 - - - +
697A ARG 3.1 0.8 - - - -
698A ALA* 1.3 78.8 - - - +
700A LYS* 1.3 65.0 + - - +
703A GLY* 3.1 22.8 + - - -
706A PHE* 3.6 34.5 - - + -
758A LEU* 4.0 8.3 - - + -
761A GLY 4.3 5.4 - - - -
762A TRP* 3.7 41.5 - - - -
765A ARG* 4.3 4.9 + - - -
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Residues in contact with LYS 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A GLU* 3.6 27.6 + - - +
639A TYR* 4.5 10.2 - - - +
696A VAL* 3.1 13.9 + - + +
697A ARG* 3.0 17.3 + - - +
699A CYS* 1.3 78.4 - - - +
701A ALA* 1.3 57.8 + - - +
703A GLY 4.8 0.5 + - - -
765A ARG* 3.6 44.8 + - - +
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Residues in contact with ALA 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A ARG* 4.9 4.5 + - - -
635A GLU* 3.5 13.2 - - + +
638A GLY* 3.6 8.5 - - - +
639A TYR* 3.4 56.6 - - + +
642A GLY* 4.6 4.7 - - - -
697A ARG 3.3 9.6 + - - +
699A CYS 3.1 0.2 - - - -
700A LYS* 1.3 78.9 - - - +
702A VAL* 1.3 64.9 + - - +
703A GLY* 3.4 1.8 + - - -
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Residues in contact with VAL 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A GLY* 3.7 19.5 - - - +
641A ILE* 4.3 12.6 - - + -
642A GLY* 4.2 11.3 - - - -
650A GLN* 4.6 2.9 + - - +
654A ILE* 4.1 17.3 - - + -
657A TYR* 3.7 24.7 - - + -
698A ALA 2.9 25.2 + - - +
701A ALA* 1.3 74.3 - - - +
703A GLY* 1.3 61.2 + - - +
705A PRO* 3.7 15.2 - - + +
706A PHE* 3.7 34.5 - - + +
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Residues in contact with GLY 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699A CYS* 3.1 17.6 + - - +
700A LYS 5.3 0.2 - - - -
701A ALA 3.4 2.3 - - - -
702A VAL* 1.3 75.0 - - - +
704A HIS* 1.3 67.6 + - - +
705A PRO* 3.2 3.8 - - - -
706A PHE* 2.8 22.0 + - - +
762A TRP* 4.3 6.2 - - - -
765A ARG* 4.6 17.5 - - - -
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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