Contacts of the helix formed by residues 866 - 886 (chain A) in PDB entry 3CMM
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 ILE 866 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLN* 3.9 23.8 - - + +
25A VAL* 4.5 11.4 - - + -
26A LEU* 4.1 20.2 - - + -
54A ASN 6.2 0.2 - - - +
58A ALA* 5.1 1.6 - - + -
372A GLN* 4.1 15.9 - - - +
375A LEU* 4.1 20.6 - - + -
480A ASN* 4.9 3.1 - - - -
481A ARG* 4.1 6.3 - - - -
568A THR* 5.8 0.2 + - - -
570A GLY 3.6 25.9 + - - +
571A THR* 4.9 0.4 - - - +
865A ALA* 1.3 77.5 - - - +
867A ALA* 1.3 69.8 + - + +
868A THR* 3.1 17.7 + - + +
869A THR* 3.6 13.1 + - - +
870A THR* 3.1 19.5 + - - -
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Residues in contact with ALA 867 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLN* 5.5 0.2 + - - -
53A LYS* 5.4 0.4 - - - -
54A ASN* 3.4 22.0 - - + +
57A LEU* 4.1 20.4 - - + -
448A GLU* 5.2 3.2 - - - +
480A ASN* 4.1 5.3 + - - +
481A ARG* 3.7 32.3 - - - +
866A ILE* 1.3 75.8 - - + +
868A THR* 1.3 63.2 + - - +
870A THR* 3.2 5.5 + - - -
871A SER* 2.9 28.3 + - - +
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Residues in contact with THR 868 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ASN* 4.3 12.3 + - - +
368A GLY* 3.2 36.1 + - - +
371A ALA* 3.8 9.2 - - - +
372A GLN* 2.7 42.1 + - + +
375A LEU* 4.8 4.4 - - - +
866A ILE* 3.0 16.3 - - + +
867A ALA* 1.3 81.2 - - - +
869A THR* 1.3 74.9 + - - +
872A LEU* 3.4 8.8 + - - +
901A LEU* 3.6 14.1 - - + -
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Residues in contact with THR 869 (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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568A THR* 3.9 14.6 - - + -
570A GLY 2.9 23.0 + - - +
571A THR* 3.3 22.4 + - - +
572A LYS 3.5 27.6 - - - +
573A GLY* 4.2 4.0 - - - +
866A ILE* 3.6 10.5 + - - +
868A THR* 1.3 85.4 - - - +
870A THR* 1.3 59.2 + - - +
872A LEU* 3.6 2.7 + - - +
873A VAL* 3.0 31.3 + - + +
899A VAL* 4.8 5.6 - - + -
901A LEU* 4.0 8.5 - - + +
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Residues in contact with THR 870 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ALA* 3.4 46.6 - - + +
445A ILE* 3.6 16.8 - - + +
448A GLU* 3.8 8.1 - - + -
481A ARG* 5.0 2.7 - - - +
568A THR* 4.3 18.4 + - - +
865A ALA* 5.4 1.0 - - - +
866A ILE 3.1 15.0 + - - -
867A ALA* 3.2 12.5 + - - -
869A THR* 1.3 75.2 - - - +
871A SER* 1.3 60.0 + - - +
873A VAL* 3.4 1.2 + - - +
874A THR* 2.8 34.5 + - - -
76B GLY* 5.8 0.2 - - - -
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Residues in contact with SER 871 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLU* 3.5 15.9 - - - -
53A LYS* 2.9 25.5 + - - -
54A ASN* 3.2 22.9 + - - -
364A ALA* 3.6 17.0 - - - +
368A GLY* 4.1 0.4 - - - -
448A GLU* 3.3 16.5 + - - +
867A ALA 2.9 9.3 + - - -
868A THR 3.9 2.7 - - - -
870A THR* 1.3 71.9 - - - +
872A LEU* 1.3 53.0 + - - +
874A THR* 3.2 2.4 + - - -
875A GLY* 2.8 33.3 + - - -
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Residues in contact with LEU 872 (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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364A ALA 3.8 9.8 + - - -
365A PHE* 3.5 52.3 - - + +
368A GLY* 4.3 1.5 - - - -
369A LEU* 3.6 21.5 - - + +
868A THR 3.4 14.6 + - - +
869A THR* 3.7 5.4 - - - +
870A THR 3.4 0.2 - - - -
871A SER* 1.3 77.2 - - - +
873A VAL* 1.3 67.5 + - + +
875A GLY* 3.1 2.9 + - - -
876A LEU* 3.0 36.8 + - + +
899A VAL* 3.9 17.5 - - + -
901A LEU* 3.9 15.5 - - + -
906A PHE* 3.9 10.1 - - + -
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Residues in contact with VAL 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A ILE* 4.6 4.9 - - + -
566A SER* 3.5 31.2 - - - +
567A GLY 4.3 5.4 - - - +
568A THR* 4.1 10.8 - - + -
573A GLY* 3.9 29.6 - - - -
574A ASN* 4.0 13.5 - - - +
575A THR* 3.8 4.8 + - - +
869A THR* 3.0 22.7 + - + +
870A THR 4.0 2.7 - - - +
872A LEU* 1.3 86.2 - - + +
874A THR* 1.3 61.1 + - - +
876A LEU* 3.3 6.0 + - + +
877A VAL* 3.2 21.5 + - - +
899A VAL* 5.1 4.0 - - + -
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Residues in contact with THR 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A ILE* 4.0 18.4 - - - +
448A GLU* 3.4 21.5 - - + +
449A MET* 3.5 43.3 - - - +
452A ASN* 3.9 4.7 - - - +
870A THR 2.8 18.5 + - - -
871A SER* 3.7 3.6 - - - -
873A VAL* 1.3 76.7 - - - +
875A GLY* 1.3 59.7 + - - +
877A VAL* 3.3 7.9 + - - +
878A ASN* 2.7 43.2 + - - +
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Residues in contact with GLY 875 (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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361A GLY* 3.4 27.7 - - - +
364A ALA* 3.6 12.3 - - - +
365A PHE* 4.3 2.5 - - - -
452A ASN* 4.6 1.6 - - - -
871A SER 2.8 17.5 + - - -
872A LEU 3.1 4.9 + - - -
874A THR* 1.3 73.9 - - - +
876A LEU* 1.3 61.5 + - - +
878A ASN 3.3 1.9 + - - -
879A LEU* 3.2 25.3 + - - +
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Residues in contact with LEU 876 (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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365A PHE* 3.8 21.8 - - + -
391A PHE* 4.1 17.0 - - + -
575A THR* 4.2 16.6 - - + +
872A LEU* 3.0 34.4 + - + +
873A VAL* 3.3 10.5 + - + +
875A GLY* 1.3 73.1 - - - +
877A VAL* 1.3 65.2 + - - +
879A LEU* 3.3 12.6 + - + +
880A GLU* 3.2 24.1 + - - +
897A GLY* 4.9 7.2 - - - -
899A VAL* 4.1 14.1 - - + -
908A PHE* 3.6 41.1 - - + -
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Residues in contact with VAL 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A MET* 3.9 22.9 - - + -
540A THR* 4.7 1.6 - - + -
564A LEU* 3.8 35.7 - - + +
565A GLU 4.3 4.7 - - - +
566A SER* 3.7 24.7 - - - +
575A THR* 3.6 17.0 - - + +
873A VAL 3.2 17.2 + - - +
874A THR* 3.4 10.3 - - - +
875A GLY 3.2 0.2 - - - -
876A LEU* 1.3 77.4 - - - +
878A ASN* 1.3 57.7 + - - +
880A GLU* 3.0 11.7 + - - +
881A LEU* 2.8 23.7 + - - +
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Residues in contact with ASN 878 (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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361A GLY* 4.3 7.2 - - - +
449A MET* 2.7 36.8 - - - +
452A ASN* 3.3 32.3 + - - +
453A TRP* 3.1 18.9 + - - -
456A LEU* 3.5 15.6 - - + +
874A THR* 2.7 23.4 + - - +
875A GLY 3.3 4.9 + - - +
877A VAL* 1.3 77.0 - - - +
879A LEU* 1.3 58.6 + - - +
881A LEU* 3.3 21.9 + - - +
882A TYR* 3.5 19.4 - - + -
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Residues in contact with LEU 879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LEU* 4.1 11.0 - - + -
359A ILE* 4.1 3.6 - - + -
361A GLY* 4.0 22.4 - - - +
362A VAL* 3.8 21.5 - - + -
365A PHE* 5.4 0.7 - - + -
391A PHE* 3.7 35.4 - - + -
393A SER* 3.8 14.8 - - - +
396A SER* 2.7 23.9 + - - +
875A GLY 3.2 15.0 + - - +
876A LEU* 3.7 16.6 - - + +
877A VAL 3.2 0.6 - - - -
878A ASN* 1.3 75.0 - - - +
880A GLU* 1.3 65.4 + - - +
882A TYR* 3.9 22.3 + - + +
883A LYS* 3.7 7.8 - - - +
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Residues in contact with GLU 880 (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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393A SER* 5.4 0.3 + - - -
564A LEU* 4.3 5.8 - - + +
575A THR* 4.9 6.0 - - + +
577A VAL* 3.6 28.9 - - + +
876A LEU 3.2 13.1 + - - +
877A VAL* 3.0 14.6 + - - +
879A LEU* 1.3 79.5 - - - +
881A LEU* 1.3 62.0 + - - +
882A TYR 3.3 0.7 - - - -
883A LYS* 2.9 47.3 + - + +
884A LEU* 3.5 8.8 + - - +
894A TYR* 3.2 10.6 - - - +
895A LYS* 2.6 52.2 + - - +
908A PHE* 5.8 0.9 - - - -
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Residues in contact with LEU 881 (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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432A ILE* 4.9 4.5 - - + -
449A MET* 4.9 0.4 - - + -
453A TRP* 3.5 28.7 - - + +
456A LEU* 4.5 11.4 - - + -
458A LEU* 3.8 17.7 - - + -
538A PHE* 3.5 31.9 - - + -
564A LEU* 4.0 16.6 - - + +
877A VAL 2.8 11.4 + - - +
878A ASN* 3.3 18.8 - - - +
879A LEU 3.3 0.4 - - - -
880A GLU* 1.3 77.7 - - - +
882A TYR* 1.3 70.2 + - + +
884A LEU* 3.1 18.1 + - - +
885A ILE* 3.2 31.6 + - + +
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Residues in contact with TYR 882 (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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359A ILE* 3.4 29.1 - - + +
360A PRO* 4.2 2.3 - - - +
361A GLY 5.0 1.4 + - - -
396A SER* 3.6 30.6 - - - +
420A GLN* 4.7 2.4 + - - -
424A PHE* 3.5 35.6 - + - -
428A PHE* 3.4 29.4 - + + -
429A GLN* 5.4 0.7 - - - -
432A ILE* 3.7 22.9 - - + -
456A LEU* 3.6 26.2 - - + +
878A ASN* 3.5 22.6 + - + -
879A LEU* 4.0 15.5 - - + +
880A GLU 3.3 0.6 - - - -
881A LEU* 1.3 80.4 - - + +
883A LYS* 1.3 64.1 + - - +
885A ILE* 3.1 7.4 + - - +
886A ASP* 3.1 19.2 + - - +
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Residues in contact with LYS 883 (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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393A SER* 4.6 5.9 + - - -
395A GLU* 3.5 35.8 + - - +
396A SER* 3.8 6.7 + - - +
879A LEU 3.7 16.8 - - - +
880A GLU* 2.9 48.6 + - - +
882A TYR* 1.3 76.4 - - - +
884A LEU* 1.3 60.8 + - - +
886A ASP 3.3 5.7 + - - -
888A LYS* 3.2 44.0 + - + +
893A GLN 3.0 26.6 + - - +
894A TYR* 3.7 20.1 + - + -
895A LYS* 3.6 13.5 - - - +
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Residues in contact with LEU 884 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A PHE* 3.8 40.6 - - + -
562A PRO* 3.6 31.9 - - + +
563A LEU 5.4 0.7 - - - +
564A LEU* 3.8 27.4 - - + -
577A VAL* 4.8 5.4 - - + -
578A ILE 5.2 0.7 - - - +
579A ILE* 4.1 23.3 - - + -
880A GLU 3.5 6.9 + - - +
881A LEU 3.1 9.5 + - - +
883A LYS* 1.3 73.9 - - - +
885A ILE* 1.3 62.0 + - + +
887A ASN* 2.9 29.8 + - - +
894A TYR* 4.2 11.2 - - + +
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Residues in contact with ILE 885 (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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403A PHE* 4.9 1.4 - - - -
428A PHE* 3.5 24.0 - - + -
431A LYS* 3.1 56.5 + - + +
432A ILE* 4.0 20.4 - - + -
435A SER* 3.3 26.5 - - - +
458A LEU* 5.5 0.2 - - + -
538A PHE* 3.9 21.3 - - + -
881A LEU* 3.4 25.1 - - + +
882A TYR* 3.1 9.6 + - - +
884A LEU* 1.3 76.3 - - - +
886A ASP* 1.3 57.8 + - - +
887A ASN* 3.3 4.2 + - - +
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Residues in contact with ASP 886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A PRO* 3.8 13.5 - - + -
399A ASP* 2.8 39.3 + - - +
402A ASN* 4.6 6.4 + - - +
403A PHE* 3.7 22.7 - - - -
428A PHE* 4.3 3.1 - - + -
882A TYR 3.1 12.4 + - - +
883A LYS 3.3 6.5 + - - +
884A LEU 3.2 0.8 - - - -
885A ILE* 1.3 75.2 - - - +
887A ASN* 1.3 71.7 - - - +
888A LYS* 3.0 25.1 + - + +
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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