Contacts of the helix formed by residues 999 - 1020 (chain A) in PDB entry 1Y6A
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 THR 999 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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933A PHE* 3.8 7.9 - - - -
934A VAL* 3.0 26.2 - - + +
935A PRO 3.6 6.7 - - - +
936A TYR* 4.6 10.3 - - - -
997A PHE* 4.1 9.2 - - + +
998A LEU* 1.3 80.5 - - - +
1000A LEU* 1.3 64.7 + - - +
1001A GLU* 3.3 16.0 + - - +
1002A HIS* 3.0 33.2 + - + +
1003A LEU* 3.2 14.0 + - - +
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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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933A PHE* 4.1 10.2 - - + -
935A PRO* 3.0 35.2 + - + +
936A TYR* 3.9 20.6 - - + -
999A THR* 1.3 75.3 - - - +
1001A GLU* 1.3 62.3 + - - +
1003A LEU* 3.2 4.6 + - + +
1004A ILE* 2.9 35.9 + - + +
1097A PHE* 4.3 12.3 - - + -
1128A TYR 3.7 23.1 - - - +
1130A THR* 3.8 29.6 - - + -
1165A ASN* 3.9 14.6 - - - +
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Residues in contact with GLU1001 (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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935A PRO 4.7 0.4 + - - -
999A THR* 3.3 11.4 + - - +
1000A LEU* 1.3 78.7 - - - +
1002A HIS* 1.3 59.5 + - + +
1005A CYS* 2.9 34.7 + - + +
1162A LEU* 3.3 34.2 - - - +
1165A ASN* 2.8 42.9 + - - +
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Residues in contact with HIS1002 (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 PHE 3.6 16.3 + - - -
998A LEU* 3.7 26.1 - - + +
999A THR* 3.0 48.8 + - - +
1001A GLU* 1.3 81.0 - - + +
1003A LEU* 1.3 57.9 + - + +
1005A CYS* 3.2 6.9 + - - +
1006A TYR* 2.9 44.0 + - + -
1038A ASN* 3.8 30.7 + - - -
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Residues in contact with LEU1003 (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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926A LEU* 3.9 15.5 - - + -
933A PHE* 3.6 27.4 - - + -
998A LEU* 4.5 8.3 - - + -
999A THR 3.2 11.3 + - - +
1000A LEU* 3.9 4.5 - - + +
1002A HIS* 1.3 78.6 - - + +
1004A ILE* 1.3 60.4 + - - +
1006A TYR* 3.5 5.4 + - + +
1007A SER* 2.8 28.6 + - - -
1096A ILE* 3.7 26.4 - - + +
1097A PHE* 3.5 38.8 - - + -
1099A LEU* 3.8 26.9 - - + -
1128A TYR* 4.7 4.3 - - + +
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Residues in contact with ILE1004 (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* 2.9 26.9 + - + +
1003A LEU* 1.3 72.6 - - - +
1005A CYS* 1.3 60.0 + - - +
1007A SER* 3.2 4.4 + - - -
1008A PHE* 2.9 28.8 + - - +
1097A PHE* 3.9 19.7 - - + -
1130A THR* 5.0 9.9 - - + +
1133A MET* 4.4 15.9 - - + -
1158A LEU* 4.1 10.1 - - + +
1161A LEU* 4.4 12.6 - - + +
1162A LEU* 3.8 36.1 - - + +
1165A ASN* 3.9 30.3 - - + +
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Residues in contact with CYS1005 (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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1001A GLU* 2.9 24.2 + - + +
1002A HIS* 3.3 7.6 - - - +
1004A ILE* 1.3 73.8 - - - +
1006A TYR* 1.3 68.7 + - + +
1007A SER 3.3 0.2 + - - -
1008A PHE* 3.3 3.4 + - - +
1009A GLN* 3.0 52.5 + - - +
1038A ASN* 4.8 6.7 - - - -
1162A LEU* 3.7 22.5 - - + +
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Residues in contact with TYR1006 (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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922A LEU* 4.0 18.4 - - + -
925A TYR* 4.2 8.2 - + - -
926A LEU* 4.1 20.2 - - + -
998A LEU* 3.6 19.4 - - + +
1002A HIS* 2.9 39.4 + - + +
1003A LEU* 3.8 13.7 - - + +
1005A CYS* 1.3 73.6 - - + +
1007A SER* 1.3 57.7 + - - +
1009A GLN* 3.4 3.8 + - - +
1010A VAL* 3.0 34.8 + - - +
1034A LEU* 4.1 9.1 - - + +
1038A ASN* 2.5 50.2 + - + -
1040A VAL* 3.5 31.4 - - + +
1096A ILE* 4.2 13.9 - - + -
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Residues in contact with SER1007 (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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1003A LEU 2.8 17.6 + - - -
1004A ILE* 3.4 11.9 - - - -
1005A CYS 3.2 0.2 - - - -
1006A TYR* 1.3 78.5 - - - +
1008A PHE* 1.3 61.8 + - - +
1010A VAL* 3.5 1.5 + - - -
1011A ALA 3.1 17.3 + - - -
1089A PHE* 3.4 13.3 - - - -
1093A LEU* 3.3 30.0 - - - +
1096A ILE* 3.6 12.1 - - - +
1097A PHE* 3.4 13.7 - - - -
1158A LEU* 3.5 14.2 - - - +
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Residues in contact with PHE1008 (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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1004A ILE 2.9 16.3 + - - +
1005A CYS* 3.5 7.2 - - - +
1007A SER* 1.3 74.5 - - - +
1009A GLN* 1.3 66.5 + - + +
1011A ALA* 3.2 4.9 + - - +
1012A LYS* 2.9 61.4 + - + +
1155A VAL* 3.5 32.1 - - + -
1158A LEU* 3.9 15.4 - - + +
1159A GLY* 3.5 31.9 - - - -
1162A LEU* 3.7 23.6 - - + -
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Residues in contact with GLN1009 (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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894A LEU* 5.3 1.6 - - - +
895A ASN* 2.9 45.2 + - - +
1005A CYS* 3.0 40.9 + - - +
1006A TYR* 3.4 2.6 + - - -
1008A PHE* 1.3 84.1 - - + +
1010A VAL* 1.3 58.3 + - - +
1012A LYS* 3.3 4.7 + - + +
1013A GLY 2.9 24.6 + - - -
1038A ASN 2.8 24.4 + - - -
1039A VAL* 3.4 10.4 - - - +
1040A VAL* 3.1 32.6 + - + +
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Residues in contact with VAL1010 (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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895A ASN* 5.3 0.7 - - - -
922A LEU* 5.3 2.7 - - + -
1006A TYR 3.0 22.9 + - - +
1007A SER* 3.9 0.7 - - - +
1009A GLN* 1.3 75.2 - - - +
1011A ALA* 1.3 56.9 + - - +
1013A GLY* 3.2 1.7 + - - -
1014A MET* 2.8 29.6 + - + +
1027A LEU* 4.4 5.2 - - + -
1032A ILE* 3.9 39.7 - - + -
1040A VAL* 4.1 6.3 - - + -
1042A ILE* 3.7 12.9 - - + +
1089A PHE* 3.6 27.6 - - + -
1092A LEU* 4.0 24.7 - - + -
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Residues in contact with ALA1011 (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 SER 3.1 14.3 + - - +
1008A PHE 3.2 9.2 + - - +
1010A VAL* 1.3 76.5 - - - +
1012A LYS* 1.3 57.6 + - - +
1014A MET* 3.3 1.2 + - - +
1015A GLU* 2.7 30.5 + - - +
1089A PHE* 3.8 17.5 - - + -
1151A PHE* 4.2 10.5 - - + +
1154A LEU* 4.3 6.7 - - + -
1155A VAL* 3.5 22.4 - - + +
1158A LEU* 3.9 12.3 - - + -
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Residues in contact with LYS1012 (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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893A HIS* 3.8 17.4 + - + +
894A LEU* 6.3 0.8 - - - +
895A ASN* 3.8 15.3 + - - +
1008A PHE* 2.9 49.5 + - + +
1009A GLN* 3.5 9.2 - - + +
1011A ALA* 1.3 75.6 - - - +
1013A GLY* 1.3 58.5 + - - +
1015A GLU* 3.4 8.9 + - - +
1016A PHE* 3.0 27.9 + - - +
1155A VAL* 3.6 25.8 - - + -
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Residues in contact with GLY1013 (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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893A HIS* 4.3 7.2 - - - -
895A ASN* 3.9 17.4 - - - +
896A VAL* 4.4 1.6 - - - +
1009A GLN 2.9 13.6 + - - -
1010A VAL 3.5 3.8 - - - -
1012A LYS* 1.3 75.6 - - - +
1014A MET* 1.3 55.6 + - - +
1016A PHE* 3.3 6.2 - - - +
1017A LEU* 3.0 29.5 + - - +
1042A ILE* 3.6 18.2 - - - -
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Residues in contact with MET1014 (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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1010A VAL* 2.8 22.4 + - + +
1011A ALA 3.8 0.2 - - - +
1013A GLY* 1.3 70.7 - - - +
1015A GLU* 1.3 66.3 + - - +
1017A LEU* 3.1 25.7 + - + +
1018A ALA* 2.9 25.6 + - - +
1024A HIS* 4.1 11.0 - - + +
1027A LEU* 3.6 31.6 - - + -
1042A ILE* 3.9 11.0 - - + -
1082A ILE* 4.0 9.0 - - + -
1085A ASP* 3.5 28.5 - - + +
1151A PHE* 3.4 45.0 - - + -
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Residues in contact with GLU1015 (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 ALA 2.7 21.1 + - - +
1012A LYS* 3.4 10.4 + - - +
1014A MET* 1.3 71.4 - - - +
1016A PHE* 1.3 64.2 + - - +
1018A ALA* 3.4 4.2 + - - +
1019A SER* 3.0 24.5 + - - -
1151A PHE* 3.7 16.9 - - + +
1152A SER* 2.8 39.9 + - - +
1155A VAL* 3.7 23.5 - - + +
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Residues in contact with PHE1016 (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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890A ILE* 3.4 42.2 - - + -
891A GLY 3.7 7.9 - - - -
892A HIS 3.4 23.8 - - - -
893A HIS* 3.5 41.5 - + + +
896A VAL* 4.2 11.2 - - + -
1012A LYS 3.0 13.6 + - - +
1013A GLY 3.3 11.2 - - - +
1014A MET 3.1 0.2 - - - -
1015A GLU* 1.3 76.8 - - - +
1017A LEU* 1.3 68.0 + - + +
1019A SER* 2.7 26.4 + - - -
1020A ARG* 3.1 25.2 + - + +
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Residues in contact with LEU1017 (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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890A ILE* 3.9 37.5 - - + -
896A VAL* 4.3 5.4 - - + -
1013A GLY 3.0 17.6 + - - +
1014A MET* 3.1 31.8 + - + +
1016A PHE* 1.3 81.0 - - + +
1018A ALA* 1.3 60.6 - - - +
1020A ARG* 3.1 11.1 + - - +
1022A CYS* 2.9 40.1 + - + +
1024A HIS* 4.4 11.4 - - + +
1042A ILE* 4.3 13.7 - - + -
1044A ASP* 3.6 28.3 - - + +
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Residues in contact with ALA1018 (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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1014A MET 2.9 16.4 + - - +
1015A GLU* 3.6 7.4 - - - +
1017A LEU* 1.3 77.2 - - - +
1019A SER* 1.3 56.6 + - - +
1021A LYS* 2.8 23.2 + - - +
1022A CYS 4.0 11.6 + - - -
1082A ILE* 3.7 28.2 - - + +
1151A PHE* 4.8 4.5 - - + -
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Residues in contact with SER1019 (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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1015A GLU* 3.0 13.9 + - - -
1016A PHE* 2.7 28.3 + - - -
1018A ALA* 1.3 71.9 - - - +
1020A ARG* 1.3 71.5 + - - +
1021A LYS* 3.1 14.6 + - - +
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Residues in contact with ARG1020 (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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889A HIS* 2.9 56.6 + - - +
890A ILE* 3.0 31.4 + - + +
1016A PHE* 3.1 34.0 + - + +
1017A LEU* 3.1 7.3 + - - +
1019A SER* 1.3 84.5 + - - +
1021A LYS* 1.3 82.1 + - - +
1022A CYS* 3.5 15.2 + - - -
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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