Contacts of the helix formed by residues 996 - 1017 (chain A) in PDB entry 3NZ0
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 GLY 996 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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994A SER 4.2 1.2 + - - -
995A ILE* 1.3 77.9 - - - +
997A LEU* 1.3 66.2 + - - -
998A ALA* 3.3 3.4 - - - -
999A GLN* 3.1 8.8 + - - +
1000A LEU* 3.1 19.1 + - - +
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Residues in contact with LEU 997 (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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996A GLY* 1.3 70.5 - - - -
998A ALA* 1.3 64.3 + - - +
1000A LEU* 3.2 13.5 + - + +
1001A LEU* 2.9 51.4 + - + +
1095A LEU* 4.7 17.7 - - + -
1139A LYS 5.2 3.1 - - - +
1140A CYS* 5.9 0.7 - - - -
1141A PRO* 3.6 38.8 - - + -
1144A VAL* 4.9 2.9 - - + -
1176A TYR* 3.7 27.8 - - + +
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Residues in contact with ALA 998 (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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996A GLY 3.3 1.2 - - - -
997A LEU* 1.3 79.0 - - - +
999A GLN* 1.3 57.5 + - - +
1001A LEU* 3.3 5.9 + - - +
1002A LEU 2.9 22.0 + - - -
1173A HIS* 3.0 28.9 - - + +
1176A TYR* 3.7 33.0 + - - +
1177A ARG* 3.9 14.8 - - + +
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Residues in contact with GLN 999 (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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995A ILE* 3.5 19.7 - - + -
996A GLY* 3.1 7.3 + - - +
998A ALA* 1.3 76.6 - - - +
1000A LEU* 1.3 60.4 + - - +
1002A LEU* 3.1 28.1 + - - +
1003A PHE* 2.9 54.4 + - + -
1006A GLN* 5.6 0.3 + - - -
1035A ARG* 3.5 37.0 - - - +
1173A HIS* 5.4 0.4 - - - -
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Residues in contact with LEU1000 (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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990A LEU* 3.7 21.5 - - + -
995A ILE* 3.7 21.5 - - + +
996A GLY 3.1 15.0 + - - +
997A LEU* 3.5 16.4 - - + +
999A GLN* 1.3 76.8 - - - +
1001A LEU* 1.3 57.8 + - - +
1003A PHE* 3.4 11.0 + - + +
1004A ALA* 3.1 21.8 + - - +
1091A LEU* 5.1 0.2 - - - +
1094A LEU* 3.5 43.6 - - + +
1095A LEU* 4.4 21.8 - - + -
1097A HIS* 3.6 23.1 - - + +
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Residues in contact with LEU1001 (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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997A LEU* 2.9 33.2 + - + +
998A ALA 3.6 7.0 - - - +
999A GLN 3.2 0.2 - - - -
1000A LEU* 1.3 73.9 - - - +
1002A LEU* 1.3 60.8 + - - +
1004A ALA* 3.3 4.5 + - - +
1005A GLN* 2.9 28.6 + - - +
1091A LEU* 4.5 12.1 - - + -
1095A LEU* 4.8 1.8 - - + -
1144A VAL* 4.1 24.7 - - + -
1147A LEU* 5.9 0.4 - - + -
1169A LEU* 4.3 24.0 - - + +
1172A VAL* 3.1 43.1 - - + +
1173A HIS* 4.0 14.4 - - + +
1176A TYR* 4.0 9.4 - - + -
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Residues in contact with LEU1002 (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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998A ALA 2.9 12.7 + - - +
999A GLN* 3.4 34.1 - - - +
1001A LEU* 1.3 74.0 - - - +
1003A PHE* 1.3 64.2 + - - +
1005A GLN* 3.3 26.2 + - - +
1006A GLN* 3.0 50.7 + - + +
1173A HIS* 3.9 28.9 - - + +
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Residues in contact with PHE1003 (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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986A LEU* 3.6 29.2 - - + -
989A TYR* 4.6 10.8 - + - -
990A LEU* 4.3 5.8 - - + -
995A ILE* 4.3 10.5 - - + -
999A GLN* 2.9 47.8 + - + -
1000A LEU* 3.5 18.8 - - + +
1002A LEU* 1.3 75.9 - - - +
1004A ALA* 1.3 57.1 + - - +
1006A GLN* 3.3 4.5 + - - -
1007A ILE* 3.0 33.3 + - - +
1031A LEU* 3.5 27.4 - - + -
1035A ARG* 3.4 32.8 - - + -
1037A VAL* 3.6 15.3 - - + +
1094A LEU* 4.0 10.3 - - + -
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Residues in contact with ALA1004 (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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1000A LEU 3.1 13.7 + - - +
1001A LEU* 3.5 11.2 - - - +
1002A LEU 3.3 0.2 - - - -
1003A PHE* 1.3 76.7 - - - +
1005A GLN* 1.3 62.3 + - - +
1007A ILE* 3.2 6.4 + - - +
1008A CYS* 3.0 26.5 + - - -
1087A PHE* 3.6 17.1 - - + -
1091A LEU* 3.9 25.1 - - + -
1094A LEU* 4.0 8.0 - - + +
1169A LEU* 4.0 10.5 - - + -
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Residues in contact with GLN1005 (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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1001A LEU 2.9 19.7 + - - +
1002A LEU* 3.5 24.9 - - - +
1004A ALA* 1.3 73.5 - - - +
1006A GLN* 1.3 58.0 + - - +
1008A CYS* 3.2 5.0 + - - +
1009A GLU* 2.7 57.6 + - - +
1166A ILE* 4.3 13.5 - - + +
1169A LEU* 4.0 18.8 - - + +
1170A LYS* 3.3 45.6 - - + +
1173A HIS* 4.3 7.6 + - - +
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Residues in contact with GLN1006 (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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958A HIS* 3.5 39.2 - - + +
999A GLN* 5.6 0.4 + - - -
1002A LEU* 3.0 48.8 + - + +
1003A PHE* 3.7 6.2 - - - +
1005A GLN* 1.3 75.5 - - + +
1007A ILE* 1.3 66.2 + - - +
1009A GLU* 3.4 12.1 + - - +
1010A GLY 3.1 17.2 + - - -
1035A ARG 3.8 6.5 + - - +
1036A LEU* 3.4 24.6 - - - +
1037A VAL* 2.9 36.8 + - + +
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Residues in contact with ILE1007 (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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986A LEU* 4.1 16.6 - - + -
1003A PHE 3.0 24.2 + - - +
1004A ALA* 3.2 11.9 + - - +
1006A GLN* 1.3 74.2 - - - +
1008A CYS* 1.3 59.2 + - - +
1010A GLY 3.3 1.9 + - - -
1011A MET* 2.9 34.9 + - + +
1024A LEU* 4.0 23.3 - - + -
1029A VAL* 4.0 20.6 - - + -
1037A VAL* 3.8 20.2 - - + -
1039A ILE* 3.6 6.9 - - + +
1087A PHE* 3.9 21.1 - - + -
1090A THR* 4.2 16.2 - - + -
1094A LEU* 4.5 4.7 - - + -
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Residues in contact with CYS1008 (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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1004A ALA 3.0 10.2 + - - +
1005A GLN 3.2 8.9 + - - +
1007A ILE* 1.3 77.2 - - - +
1009A GLU* 1.3 52.7 + - - +
1012A ALA* 2.8 35.5 + - - +
1087A PHE* 3.3 39.0 - - - -
1162A PHE* 3.7 30.1 - - + +
1165A LEU* 3.8 8.7 - - + -
1166A ILE* 4.0 15.7 - - + -
1169A LEU* 3.5 14.1 - - + -
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Residues in contact with GLU1009 (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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956A HIS* 3.8 11.5 + - + +
957A GLU* 4.7 4.0 - - - +
958A HIS* 3.3 28.0 + - + -
1005A GLN* 2.7 48.8 + - - +
1006A GLN* 3.7 10.4 - - - +
1007A ILE 3.3 0.2 - - - -
1008A CYS* 1.3 75.0 - - - +
1010A GLY* 1.3 58.0 + - - +
1012A ALA* 3.5 2.6 + - - +
1013A TYR* 3.1 26.5 + - - +
1166A ILE* 3.8 31.1 - - + +
1170A LYS* 4.1 4.3 + - - -
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Residues in contact with GLY1010 (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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956A HIS* 4.0 9.4 - - - -
958A HIS* 3.9 18.0 - - - +
959A ILE* 3.9 7.5 - - - +
1006A GLN 3.1 10.5 + - - -
1007A ILE 3.7 2.7 - - - -
1009A GLU* 1.3 75.3 - - - +
1011A MET* 1.3 57.9 + - - +
1013A TYR* 3.3 4.3 + - - +
1014A LEU* 2.9 26.3 + - - +
1039A ILE* 3.8 16.4 - - - -
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Residues in contact with MET1011 (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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1007A ILE* 2.9 21.3 + - + +
1010A GLY* 1.3 73.4 - - - +
1012A ALA* 1.3 61.3 + - - +
1014A LEU* 3.3 16.9 + - + +
1015A HIS* 2.9 40.6 + - - +
1021A HIS* 3.8 16.2 - - + -
1024A LEU* 4.0 23.8 - - + -
1039A ILE* 3.8 21.1 - - + -
1083A ASP* 3.4 41.5 - - + +
1162A PHE* 3.5 33.9 - - + -
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Residues in contact with ALA1012 (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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1008A CYS 2.8 22.6 + - - +
1009A GLU 3.7 4.7 - - - +
1011A MET* 1.3 72.5 - - - +
1013A TYR* 1.3 62.8 + - - +
1015A HIS* 3.5 4.9 + - - +
1016A ALA* 3.0 22.9 + - - +
1162A PHE* 3.7 16.3 - - + +
1163A GLU* 3.8 29.7 - - + +
1166A ILE* 4.0 15.3 - - + -
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Residues in contact with TYR1013 (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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953A THR 3.9 3.1 + - - -
954A LEU* 3.6 25.3 - - + -
955A TYR* 2.9 41.5 + - - +
956A HIS* 3.4 46.0 - + + +
959A ILE* 4.1 5.8 - - + -
1009A GLU 3.1 10.2 + - - +
1010A GLY 3.4 10.5 - - - +
1012A ALA* 1.3 73.8 - - - +
1014A LEU* 1.3 69.3 + - - +
1016A ALA* 3.1 23.4 + - + +
1017A GLN* 3.3 39.2 + - + +
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Residues in contact with LEU1014 (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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950A ILE* 5.4 0.2 - - + -
954A LEU* 3.7 29.8 - - + -
959A ILE* 4.9 5.4 - - + -
1010A GLY 2.9 16.6 + - - +
1011A MET* 3.5 24.9 - - + +
1013A TYR* 1.3 77.8 - - - +
1015A HIS* 1.3 59.5 + - + +
1017A GLN* 3.0 21.8 + - - +
1019A TYR* 3.3 45.9 + - + +
1020A ILE 4.2 0.7 - - - -
1021A HIS* 3.6 41.1 - - + +
1042A PHE* 3.8 16.8 - - + -
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Residues in contact with HIS1015 (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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1011A MET* 2.9 26.2 + - + +
1012A ALA* 3.9 5.6 - - - +
1014A LEU* 1.3 73.5 - - + +
1016A ALA* 1.3 60.8 + - - +
1018A HIS* 3.0 26.0 + - - -
1019A TYR 3.2 20.0 - - - -
1080A TYR* 3.2 58.5 - + + +
1083A ASP* 2.9 24.6 + - + +
1084A VAL* 4.9 1.3 - - + +
1162A PHE* 3.5 30.8 + + + +
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Residues in contact with ALA1016 (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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1012A ALA 3.0 14.7 + - - +
1013A TYR* 3.1 20.8 + - + +
1015A HIS* 1.3 76.0 - - - +
1017A GLN* 1.3 67.1 + - - +
1018A HIS* 3.2 10.8 + - - -
1163A GLU* 5.7 2.2 - - - +
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Residues in contact with GLN1017 (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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953A THR* 4.4 10.3 + - - -
954A LEU* 4.0 7.6 - - + -
1013A TYR* 3.4 49.4 + - + +
1014A LEU 3.0 9.0 + - - +
1016A ALA* 1.3 85.5 - - - +
1018A HIS* 1.3 70.7 + - - +
1019A TYR* 3.5 26.6 + - + -
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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