Contacts of the helix formed by residues 998 - 1019 (chain A) in PDB entry 4AY6
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 ASN 998 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695A ILE* 4.0 2.7 - - - -
992A ILE 5.6 4.1 + - - +
994A SER 4.6 4.3 + - - +
995A PRO* 3.1 23.9 + - + +
996A LEU 3.2 1.2 + - - -
997A PHE* 1.3 74.7 - - - +
999A THR* 1.3 59.1 + - - +
1000A LYS* 3.2 9.3 + - - +
1001A GLN* 2.7 48.2 + - - +
1002A TYR* 2.8 29.8 + - - +
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Residues in contact with THR 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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563A LEU 4.9 2.5 - - - +
566A SER* 4.5 8.0 - - - -
567A ILE* 4.6 9.0 - - + +
570A MET* 3.4 25.3 - - - +
695A ILE* 3.9 13.9 - - + -
696A GLY 3.6 25.1 - - - +
697A ASP* 4.2 16.2 - - - +
699A ALA* 6.0 2.5 - - + +
700A ASN* 6.1 1.2 - - - +
997A PHE 3.6 3.6 + - - +
998A ASN* 1.3 70.1 - - - +
1000A LYS* 1.3 61.6 + - - +
1002A TYR* 3.6 6.5 - - - +
1003A THR* 2.9 33.4 + - - -
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Residues in contact with LYS1000 (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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570A MET* 3.4 45.8 + - + +
571A HIS 5.4 0.6 + - - -
572A ASN* 5.8 1.6 - - - +
998A ASN* 3.2 7.0 + - - +
999A THR* 1.3 78.0 + - - +
1001A GLN* 1.3 66.7 + - - +
1003A THR* 3.2 3.7 + - - -
1004A MET* 3.1 52.0 + - + +
730D ASP* 3.5 42.7 + - + +
733D ALA* 6.0 3.4 - - + -
791D GLY 5.7 0.8 + - - -
792D PHE* 4.8 11.1 - - + +
793D SER* 5.0 11.9 + - - +
815D ARG 4.2 17.2 + - - -
816D THR* 5.8 0.6 - - - +
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Residues in contact with GLN1001 (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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691A HIS* 4.4 13.5 + - - -
995A PRO* 3.4 39.3 - - - +
998A ASN* 2.7 29.7 + - + +
1000A LYS* 1.3 71.0 - - - +
1002A TYR* 1.3 68.1 + - - +
1004A MET* 3.3 13.0 + - + +
1005A GLU* 3.3 30.7 + - + +
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Residues in contact with TYR1002 (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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567A ILE* 3.9 27.8 - - + -
652A TRP* 3.0 27.1 + + - -
689A MET* 3.6 29.1 - - + +
692A THR 3.7 7.4 - - - -
693A PHE* 2.5 24.5 + - - +
694A PHE 3.2 26.7 - - - -
695A ILE* 3.7 24.5 - - + -
995A PRO 5.4 2.0 + - - +
998A ASN 2.8 19.5 + - - +
999A THR* 3.6 4.7 - - - +
1000A LYS 3.2 0.2 - - - -
1001A GLN* 1.3 76.0 - - - +
1003A THR* 1.3 66.1 + - - +
1005A GLU* 3.0 9.4 + - - +
1006A LEU* 3.0 28.2 + - + +
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Residues in contact with THR1003 (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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567A ILE* 3.4 23.4 - - + +
570A MET* 3.5 41.1 - - - +
571A HIS* 3.8 22.0 - - + +
999A THR 2.9 22.6 + - - -
1000A LYS 3.2 5.3 + - - -
1002A TYR* 1.3 79.0 - - - +
1004A MET* 1.3 53.2 + - + +
1006A LEU* 3.0 9.9 + - - +
1007A GLU* 2.7 40.4 + - - +
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Residues in contact with MET1004 (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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570A MET 5.8 0.2 - - - +
1000A LYS* 3.1 37.8 + - - +
1001A GLN* 3.8 11.7 - - - +
1002A TYR 3.3 0.2 - - - -
1003A THR* 1.3 77.3 - - + +
1005A GLU* 1.3 60.2 + - + +
1007A GLU* 3.4 21.0 + - - +
1008A ARG* 3.0 28.1 + - - +
790D ASN 3.5 24.5 - - - +
791D GLY* 3.6 21.1 - - - +
792D PHE* 3.6 35.9 - - + -
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Residues in contact with GLU1005 (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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689A MET* 3.7 17.2 - - + +
690A PRO* 3.5 34.3 - - + +
691A HIS* 5.9 0.7 - - - +
1001A GLN* 3.3 23.2 + - + +
1002A TYR* 3.0 10.8 + - - +
1004A MET* 1.3 74.9 - - + +
1006A LEU* 1.3 68.4 + - - +
1007A GLU 3.0 0.9 - - - -
1008A ARG* 3.0 33.4 + - - +
1009A LEU* 2.9 23.9 + - - +
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Residues in contact with LEU1006 (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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550A TYR* 3.7 13.5 - - - +
567A ILE* 4.5 11.0 - - + -
571A HIS* 4.7 2.7 - - + -
652A TRP* 4.3 30.3 - - + +
668A ILE* 4.2 20.6 - - + -
689A MET* 3.9 21.0 - - - +
1002A TYR* 3.0 20.3 + - + +
1003A THR* 3.0 10.7 + - - +
1005A GLU* 1.3 77.4 - - - +
1007A GLU* 1.3 62.3 + - - +
1009A LEU* 3.4 6.1 + - + +
1010A TYR* 3.0 59.2 + - + +
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Residues in contact with GLU1007 (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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570A MET 5.1 0.3 - - - +
571A HIS* 3.0 30.7 + - + +
572A ASN* 2.6 40.0 + - - +
576A PHE* 3.4 32.5 - - + -
1003A THR* 2.7 16.9 + - - +
1004A MET* 3.4 28.8 + - - +
1005A GLU 3.0 0.2 - - - -
1006A LEU* 1.3 74.1 - - - +
1008A ARG* 1.3 68.5 + - - +
1010A TYR* 3.0 8.3 + - - +
1011A LEU* 3.0 24.6 + - + +
791D GLY 4.6 3.5 - - - +
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Residues in contact with ARG1008 (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 MET 3.0 17.1 + - - +
1005A GLU* 3.0 37.3 + - - +
1007A GLU* 1.3 73.5 - - - +
1009A LEU* 1.3 64.5 + - - +
1011A LEU* 2.9 22.7 + - + +
1012A GLN* 3.0 26.0 + - - +
1028A LYS* 4.8 17.0 - - - +
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Residues in contact with LEU1009 (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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668A ILE* 4.1 25.4 - - + -
687A ALA* 3.7 39.0 - - + +
688A TYR 3.5 28.3 - - - +
689A MET* 4.3 9.9 - - - -
1005A GLU 2.9 18.0 + - - +
1006A LEU* 3.7 7.2 - - + +
1008A ARG* 1.3 73.1 - - - +
1010A TYR* 1.3 62.4 + - + +
1012A GLN* 3.6 15.2 + - - +
1013A MET* 3.0 34.3 + - + +
1026A MET* 4.3 14.8 - - + +
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Residues in contact with TYR1010 (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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546A LEU* 3.9 15.3 - - + -
548A VAL* 4.0 23.1 - - + -
550A TYR* 3.1 39.6 + - - -
571A HIS* 3.9 9.2 - + - -
576A PHE* 4.0 6.5 - + + -
625A ILE* 3.7 34.1 - - + +
627A VAL* 3.6 10.9 - - + +
650A ALA* 5.8 0.7 - - + -
652A TRP* 5.2 0.7 - - - -
668A ILE* 4.4 13.5 - - + +
1006A LEU* 3.0 49.0 + - + +
1007A GLU* 3.3 11.9 - - - +
1008A ARG 3.0 0.2 + - - -
1009A LEU* 1.3 76.3 - - + +
1011A LEU* 1.3 65.8 + - - +
1013A MET* 3.1 17.4 + - + +
1014A TRP* 3.0 17.8 + - - +
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Residues in contact with LEU1011 (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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539A LEU* 5.8 6.1 - - + -
546A LEU* 4.4 15.3 - - + -
575A LYS* 5.5 12.3 - - + +
576A PHE* 3.5 32.3 - - + -
1007A GLU* 3.0 13.4 + - + +
1008A ARG* 2.9 10.6 + - - +
1010A TYR* 1.3 80.0 - - - +
1012A GLN* 1.3 58.4 + - - +
1014A TRP* 3.6 9.8 - - + +
1015A GLU* 2.9 45.8 + - + +
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Residues in contact with GLN1012 (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 ARG* 3.0 26.3 + - + +
1009A LEU* 3.7 19.6 + - - +
1010A TYR 3.2 0.2 - - - -
1011A LEU* 1.3 77.7 - - - +
1013A MET* 1.3 62.7 + - - +
1015A GLU* 3.6 6.7 + - - +
1016A HIS* 3.3 24.8 + - - +
1026A MET* 3.7 35.7 - - - +
1028A LYS* 3.9 31.9 + - - +
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Residues in contact with MET1013 (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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625A ILE* 4.5 9.0 - - + -
648A ILE* 3.4 24.8 - - + +
650A ALA* 4.4 4.3 - - + -
666A TYR* 3.6 43.3 + - + -
668A ILE* 4.2 13.0 - - + -
687A ALA* 3.5 31.2 - - + -
1009A LEU* 3.0 26.9 - - + +
1010A TYR* 3.2 24.9 - - - +
1012A GLN* 1.3 79.4 - - - +
1014A TRP* 1.3 62.8 + - - +
1016A HIS* 3.7 2.6 - - - +
1017A TYR* 3.1 17.5 + - - +
1026A MET* 4.2 16.6 - - + -
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Residues in contact with TRP1014 (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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536A PRO 3.8 10.8 - - - -
537A LYS 3.8 8.7 - - - -
538A ASP* 3.8 18.9 - - - +
539A LEU* 3.6 41.3 - - + +
546A LEU* 4.2 17.5 - - + -
624A HIS* 3.7 30.5 - + + -
625A ILE* 5.1 0.4 - - + -
647A PRO* 4.1 10.1 - - + -
648A ILE* 3.9 12.8 - - + -
1010A TYR 3.0 12.3 + - - +
1011A LEU* 3.6 14.1 - - + +
1012A GLN 3.2 0.2 - - - -
1013A MET* 1.3 74.9 - - - +
1015A GLU* 1.3 84.2 + - - +
1017A TYR* 2.9 42.2 + + - -
1018A ALA* 2.8 33.3 + - + +
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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 LEU* 2.9 33.0 + - + +
1012A GLN* 3.9 6.1 - - - +
1014A TRP* 1.3 86.9 - - - +
1016A HIS* 1.3 54.1 + - - +
1018A ALA* 3.1 6.4 + - - +
1019A ALA* 2.7 36.2 + - - +
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Residues in contact with HIS1016 (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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666A TYR* 4.0 9.0 - - - -
1012A GLN 3.3 15.6 + - - +
1013A MET 3.7 4.0 - - - +
1014A TRP 3.2 0.4 - - - -
1015A GLU* 1.3 79.6 - - - +
1017A TYR* 1.3 60.8 + - - +
1019A ALA* 3.4 4.0 - - - +
1021A ASN* 3.0 58.9 + - + +
1022A LYS 2.9 27.9 + - - -
1023A PRO* 4.2 0.7 - - + -
1024A ASP* 3.7 17.3 + - + +
1026A MET* 3.6 24.8 - - + +
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Residues in contact with TYR1017 (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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535A HIS* 3.9 11.8 + - - +
536A PRO 3.4 15.6 + - - -
537A LYS* 4.6 12.4 - - + +
647A PRO* 3.5 29.7 - - + +
648A ILE* 3.9 15.0 - - + -
1013A MET 3.1 10.1 + - - +
1014A TRP* 2.9 46.3 + + - +
1016A HIS* 1.3 76.7 - - + +
1018A ALA* 1.3 63.8 + - - +
1019A ALA 3.1 0.7 - - - -
1020A GLY* 3.0 20.7 + - - -
1021A ASN 3.4 17.0 + - - +
1022A LYS* 6.1 0.9 - - - -
1023A PRO* 6.4 2.9 - - + -
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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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537A LYS 4.2 13.0 - - - +
538A ASP* 5.8 0.4 - - - -
1014A TRP* 2.8 46.7 + - + +
1015A GLU* 3.6 9.2 - - - +
1017A TYR* 1.3 73.9 - - - +
1019A ALA* 1.3 61.0 + - - +
1020A GLY* 3.0 6.5 + - - -
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Residues in contact with ALA1019 (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 2.7 16.4 + - - +
1016A HIS* 3.4 2.9 - - - +
1017A TYR 3.1 0.2 - - - -
1018A ALA* 1.3 77.1 - - - +
1020A GLY* 1.3 56.4 + - - +
1021A ASN* 3.3 27.3 + - - +
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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
------------------------------------------------------------
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