Contacts of the helix formed by residues 677 - 702 (chain A) in PDB entry 4BEJ
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 677 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A PRO* 4.1 21.4 - - - +
675A THR 3.9 0.8 + - - -
676A GLU* 1.3 72.8 - - - +
678A GLU* 1.3 59.0 + - - +
679A ASP* 2.5 34.0 + - - -
680A MET* 3.2 22.6 + - - +
681A ALA* 2.8 29.0 + - - +
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Residues in contact with GLU 678 (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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675A THR* 6.3 1.3 - - + -
676A GLU 3.5 6.0 + - - +
677A SER* 1.3 73.4 + - - +
679A ASP* 1.3 62.7 + - - +
681A ALA* 4.2 6.6 - - - +
682A GLN* 3.4 26.0 + - - +
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Residues in contact with ASP 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A SER* 2.5 27.2 + - - -
678A GLU* 1.3 79.4 - - - +
680A MET* 1.3 80.0 + - - +
682A GLN* 3.1 29.6 - - - +
683A ARG* 3.6 21.3 + - - +
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Residues in contact with MET 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A TYR* 5.2 4.9 - - + -
456A ARG* 3.4 60.3 - - + +
458A PRO* 5.1 2.2 - - - -
676A GLU* 5.3 3.1 - - + -
677A SER* 3.3 33.0 - - - +
679A ASP* 1.3 83.9 + - - +
681A ALA* 1.3 59.9 + - - +
682A GLN 3.4 0.9 - - - -
683A ARG* 3.3 44.0 - - - +
684A ARG* 4.0 11.9 + - - +
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Residues in contact with ALA 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A GLU* 4.0 21.1 - - + +
677A SER 2.8 23.6 + - - +
678A GLU* 3.6 6.9 + - - +
679A ASP 3.4 0.6 - - - -
680A MET* 1.3 75.5 - - - +
682A GLN* 1.3 60.0 + - - +
684A ARG* 3.8 11.8 + - - +
685A LYS* 3.1 38.0 + - - +
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Residues in contact with GLN 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678A GLU 3.4 16.4 + - - +
679A ASP* 3.1 28.2 - - - +
681A ALA* 1.3 77.3 - - - +
683A ARG* 1.3 60.8 + - + +
684A ARG 3.2 1.8 - - - -
685A LYS* 3.0 10.3 + - - +
686A GLU* 2.9 46.0 + - + +
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Residues in contact with ARG 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A TYR* 3.5 38.1 + - + +
679A ASP* 3.6 24.7 + - - +
680A MET* 3.3 40.2 - - - +
682A GLN* 1.3 82.7 - - + +
684A ARG* 1.3 65.5 + - - +
686A GLU* 3.4 12.7 + - - +
687A ALA* 3.2 21.8 + - - +
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Residues in contact with ARG 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 5.2 9.5 - - + +
322A TYR* 3.7 46.6 + - + +
323A GLY 5.1 0.2 - - - +
324A GLU* 4.0 26.3 + - - +
326A VAL* 5.5 0.2 - - - +
676A GLU* 2.6 40.0 + - - -
680A MET* 4.1 7.2 + - - +
681A ALA* 3.8 13.9 + - - +
682A GLN 3.2 0.8 - - - -
683A ARG* 1.3 81.2 - - - +
685A LYS* 1.3 83.8 + - + +
687A ALA* 3.5 1.4 + - - +
688A ALA* 3.0 30.1 + - + +
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Residues in contact with LYS 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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681A ALA* 3.1 27.6 + - - +
682A GLN* 3.0 11.7 + - - +
684A ARG* 1.3 101.6 - - - +
686A GLU* 1.3 63.1 + - + +
687A ALA 3.1 1.6 - - - -
688A ALA* 4.2 5.3 - - + +
689A ASP* 3.2 36.8 + - - +
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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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18A VAL* 4.5 7.5 - - - +
315A TYR* 4.9 1.0 - - - -
682A GLN* 2.9 33.2 + - + +
683A ARG* 3.8 11.2 - - - +
685A LYS* 1.3 76.1 - - - +
687A ALA* 1.3 58.3 + - - +
689A ASP* 4.7 1.7 - - - +
690A MET* 3.3 23.4 + - - +
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Residues in contact with ALA 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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315A TYR* 4.1 17.1 - - + +
318A LEU* 4.6 8.7 - - + -
319A LEU* 4.8 9.6 - - + +
322A TYR* 4.0 20.0 - - + +
683A ARG 3.2 16.3 + - - +
684A ARG* 3.8 4.0 - - - +
685A LYS 3.1 0.6 - - - -
686A GLU* 1.3 76.9 - - - +
688A ALA* 1.3 60.3 + - - +
689A ASP 3.3 1.3 - - - -
690A MET* 3.7 5.2 - - - +
691A LEU* 2.9 32.6 + - - +
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Residues in contact with ALA 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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319A LEU* 3.7 25.5 - - + +
684A ARG* 3.0 19.1 + - + +
685A LYS* 4.2 6.1 - - + +
687A ALA* 1.3 76.2 - - - +
689A ASP* 1.3 61.5 + - - +
691A LEU* 3.6 3.0 + - - +
692A LYS* 3.1 27.4 + - - +
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Residues in contact with ASP 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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17A THR* 6.5 0.4 - - + -
18A VAL* 4.7 12.2 - - + +
685A LYS* 3.2 21.8 + - - +
686A GLU* 4.7 3.0 - - - +
687A ALA 3.3 0.4 - - - -
688A ALA* 1.3 80.5 - - - +
690A MET* 1.3 64.0 + - - +
692A LYS* 3.4 8.6 + - - +
693A ALA* 3.1 22.5 + - - +
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Residues in contact with MET 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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15A PHE* 3.5 32.3 - - + -
18A VAL* 3.5 31.3 - - + +
19A GLY 4.2 9.6 - - - +
22A ILE* 4.7 12.6 - - + -
23A ILE* 4.0 10.8 - - + -
315A TYR* 3.4 36.6 - - + +
686A GLU 3.3 20.3 + - - +
687A ALA 3.3 4.9 + - - +
689A ASP* 1.3 75.1 - - - +
691A LEU* 1.3 65.2 + - - +
693A ALA* 3.4 1.7 + - - +
694A LEU* 3.1 33.4 + - + +
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Residues in contact with LEU 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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312A ALA* 3.2 33.0 - - + +
315A TYR* 4.0 9.4 - - + -
316A GLN* 3.4 42.4 - - + +
319A LEU* 3.9 23.8 - - + -
687A ALA 2.9 18.3 + - - +
688A ALA 3.9 3.1 - - - +
690A MET* 1.3 73.5 - - - +
692A LYS* 1.3 67.5 + - - +
694A LEU* 3.1 10.0 + - - +
695A GLN* 3.0 45.9 + - + +
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Residues in contact with LYS 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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688A ALA 3.1 19.7 + - - +
689A ASP* 3.4 11.7 - - - +
691A LEU* 1.3 76.8 - - - +
693A ALA* 1.3 60.0 + - - +
695A GLN* 3.3 21.3 + - - +
696A GLY* 2.9 32.6 + - - -
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Residues in contact with ALA 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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14A VAL* 3.6 22.9 - - - +
15A PHE* 3.5 23.7 - - + -
17A THR* 6.4 0.4 - - + -
18A VAL* 4.2 7.9 - - + -
689A ASP 3.1 11.2 + - - +
690A MET 3.7 7.0 - - - +
692A LYS* 1.3 79.1 - - - +
694A LEU* 1.3 54.3 + - - +
696A GLY* 3.1 2.0 + - - +
697A ALA* 2.7 36.6 + - - +
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Residues in contact with LEU 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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15A PHE* 4.2 11.2 - - + -
23A ILE* 4.4 4.0 - - + -
308A ILE* 3.7 27.4 - - + +
311A LEU* 3.7 51.6 - - + +
312A ALA* 3.8 17.0 - - + +
315A TYR* 3.7 24.5 - - + -
690A MET* 3.1 37.4 + - + +
691A LEU* 3.1 6.9 + - - +
693A ALA* 1.3 76.0 - - - +
695A GLN* 1.3 61.5 + - - +
697A ALA 3.5 0.2 + - - -
698A SER* 3.1 22.0 + - - -
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Residues in contact with GLN 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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312A ALA* 5.4 6.7 - - + -
316A GLN* 3.7 10.1 + - - -
691A LEU* 3.0 50.7 + - + +
692A LYS* 3.4 21.4 - - + +
694A LEU* 1.3 76.3 - - - +
696A GLY* 1.3 61.2 + - - +
698A SER* 3.2 16.4 + - - -
699A GLN* 3.3 16.6 + - - +
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Residues in contact with GLY 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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14A VAL* 5.0 5.2 - - - -
692A LYS* 2.9 23.1 + - - +
693A ALA* 3.1 5.3 + - - -
695A GLN* 1.3 76.5 - - - +
697A ALA* 1.3 59.9 + - - +
699A GLN* 3.3 15.5 + - - +
700A ILE* 3.4 22.1 + - - +
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Residues in contact with ALA 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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11A LEU* 3.7 16.9 - - + +
14A VAL* 4.3 4.3 - - + +
15A PHE* 3.4 30.5 - - + -
308A ILE* 4.3 9.9 - - + -
693A ALA 2.7 19.7 + - - +
694A LEU 3.7 4.7 - - - +
696A GLY* 1.3 72.7 - - - +
698A SER* 1.3 65.0 + - - +
700A ILE* 3.2 11.8 + - - +
701A ILE* 3.1 25.8 + - - +
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Residues in contact with SER 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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305A LYS* 4.6 10.7 + - - +
308A ILE* 4.4 8.9 - - - +
309A ASN* 3.8 21.9 + - - -
694A LEU 3.1 10.5 + - - -
695A GLN* 3.2 13.0 + - - -
697A ALA* 1.3 79.4 - - - +
699A GLN* 1.3 63.0 + - - +
701A ILE* 3.0 9.1 + - - +
702A ALA* 2.8 28.5 + - - +
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Residues in contact with GLN 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695A GLN 3.3 10.4 + - - +
696A GLY* 3.3 11.1 + - - +
698A SER* 1.3 82.4 + - - +
700A ILE* 1.3 63.4 + - + +
702A ALA* 3.2 28.1 + - - +
703A GLU* 5.3 2.3 - - - +
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Residues in contact with ILE 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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7A VAL* 4.0 25.9 - - + +
10A LYS* 3.9 42.4 - - + +
11A LEU* 4.6 5.6 - - + +
14A VAL* 3.5 32.1 - - + -
696A GLY 3.4 13.4 + - - +
697A ALA* 3.2 11.8 + - - +
698A SER 3.1 0.4 - - - -
699A GLN* 1.3 78.8 - - + +
701A ILE* 1.3 60.6 - - - +
702A ALA 3.4 0.5 + - - -
703A GLU* 3.8 22.4 + - - +
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Residues in contact with ILE 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 4.2 9.9 - - + -
11A LEU* 3.5 34.3 - - + -
301A LEU* 3.7 27.8 - - + -
304A LEU* 4.6 5.4 - - + -
305A LYS* 3.5 39.6 - - + -
308A ILE* 4.4 11.0 - - + -
697A ALA 3.1 15.7 + - - +
698A SER* 3.0 11.5 + - - +
700A ILE* 1.3 71.4 - - - +
702A ALA* 1.3 52.0 + - - +
703A GLU 2.7 26.6 + - - +
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Residues in contact with ALA 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A LYS* 5.5 5.4 - - - +
698A SER* 2.8 13.2 + - - +
699A GLN* 3.3 31.0 - - - +
700A ILE 3.2 1.6 - - - -
701A ILE* 1.3 74.2 - - - +
703A GLU* 1.3 59.9 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
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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