Contacts of the helix formed by residues 998 - 1019 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695B ILE* 4.1 2.9 - - - -
992B ILE 5.6 3.9 + - - +
994B SER 4.7 4.1 + - - +
995B PRO* 3.2 23.6 + - + +
996B LEU 3.3 1.4 + - - -
997B PHE* 1.3 75.4 - - - +
999B THR* 1.3 57.1 + - - +
1000B LYS* 3.1 9.5 + - - +
1001B GLN* 2.7 47.9 + - + +
1002B TYR* 2.8 28.6 + - - +
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Residues in contact with THR 999 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563B LEU 4.9 2.9 - - - +
564B MET* 6.2 0.2 - - - -
566B SER* 4.4 8.8 - - - -
567B ILE* 4.8 10.0 - - + +
570B MET* 3.5 25.9 - - - +
695B ILE* 3.9 14.8 - - + -
696B GLY 3.7 23.6 - - - +
697B ASP* 4.2 15.8 + - - +
699B ALA* 5.9 3.0 - - + +
700B ASN* 6.1 1.0 - - - +
997B PHE 3.5 4.4 + - - +
998B ASN* 1.3 73.6 + - - +
1000B LYS* 1.3 63.9 + - - +
1002B TYR* 3.6 6.4 - - - +
1003B THR* 2.9 29.5 + - - -
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Residues in contact with LYS1000 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B MET* 3.6 43.4 + - + +
571B HIS 5.4 0.8 + - - -
572B ASN* 5.8 1.0 - - - +
998B ASN* 3.1 7.2 + - - +
999B THR* 1.3 83.3 + - - +
1001B GLN* 1.3 64.0 + - - +
1003B THR* 3.3 1.8 + - - -
1004B MET* 3.2 46.2 + - + +
730C ASP* 3.5 42.8 + - + +
791C GLY 5.9 0.2 + - - -
792C PHE* 4.9 11.4 - - + +
793C SER* 4.6 14.6 + - - +
815C ARG 3.9 19.8 + - - -
816C THR* 5.5 1.2 - - - +
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Residues in contact with GLN1001 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691B HIS* 4.3 14.6 + - - -
995B PRO* 3.5 38.4 - - - +
998B ASN* 2.7 30.6 + - + +
1000B LYS* 1.3 71.5 - - - +
1002B TYR* 1.3 68.2 + - - +
1004B MET* 3.1 20.4 + - + +
1005B GLU* 3.1 24.1 + - + +
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Residues in contact with TYR1002 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B ILE* 4.0 25.4 - - + -
652B TRP* 3.1 25.9 + + - -
689B MET* 3.5 28.3 - - + +
692B THR 3.7 7.6 - - - -
693B PHE* 2.5 25.5 + - - +
694B PHE 3.3 23.6 - - - -
695B ILE* 3.6 28.9 - - + -
995B PRO 5.4 3.3 + - - +
998B ASN 2.8 18.9 + - - +
999B THR* 3.6 4.0 - - - +
1001B GLN* 1.3 75.3 - - - +
1003B THR* 1.3 67.4 + - - +
1005B GLU* 2.9 19.1 + - - +
1006B LEU* 3.0 21.2 + - + -
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Residues in contact with THR1003 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B ILE* 3.4 25.1 - - + +
570B MET* 3.6 37.1 - - - +
571B HIS* 3.8 27.6 - - + +
999B THR 2.9 21.8 + - - -
1000B LYS 3.6 4.5 - - - -
1002B TYR* 1.3 77.1 - - - +
1004B MET* 1.3 54.1 + - + +
1006B LEU* 3.1 8.4 + - - +
1007B GLU* 2.7 38.2 + - - +
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Residues in contact with MET1004 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B MET 5.7 0.7 - - - +
1000B LYS* 3.2 40.3 + - - +
1001B GLN* 3.1 13.1 + - + +
1003B THR* 1.3 78.1 - - + +
1005B GLU* 1.3 60.3 + - + +
1007B GLU* 3.3 19.8 + - - +
1008B ARG* 3.1 28.1 + - - +
790C ASN 3.6 13.2 - - - +
791C GLY* 3.2 38.1 - - - +
792C PHE* 3.5 27.8 - - + +
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Residues in contact with GLU1005 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689B MET* 3.7 16.9 - - + +
690B PRO* 3.6 34.8 - - + +
691B HIS* 5.8 0.7 - - - +
1001B GLN* 3.1 23.1 + - + +
1002B TYR* 2.9 10.8 + - - +
1004B MET* 1.3 76.6 - - + +
1006B LEU* 1.3 66.7 + - - +
1007B GLU 3.0 1.1 - - - -
1008B ARG* 3.0 34.1 + - - +
1009B LEU* 3.0 22.7 + - - +
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Residues in contact with LEU1006 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550B TYR* 3.6 14.1 - - + +
567B ILE* 4.5 12.3 - - + -
571B HIS* 4.6 3.1 - - + -
652B TRP* 4.4 30.3 - - + +
668B ILE* 4.2 20.2 - - + -
689B MET* 3.8 19.6 - - - +
1002B TYR* 3.0 20.7 + - + +
1003B THR* 3.2 10.8 - - - +
1005B GLU* 1.3 76.0 - - - +
1007B GLU* 1.3 58.5 + - - +
1009B LEU* 3.4 5.3 + - + +
1010B TYR* 3.0 67.1 + - + +
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Residues in contact with GLU1007 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570B MET 4.9 0.5 - - - +
571B HIS* 2.8 31.9 + - + +
572B ASN* 2.7 35.6 + - - +
576B PHE* 3.2 33.0 - - + -
1003B THR* 2.7 18.5 + - - +
1004B MET* 3.4 30.2 + - - +
1005B GLU 3.0 0.4 - - - -
1006B LEU* 1.3 71.3 - - - +
1008B ARG* 1.3 65.7 + - - +
1010B TYR* 3.2 6.9 + - - +
1011B LEU* 3.1 28.1 + - + +
791C GLY 4.9 2.8 - - - +
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Residues in contact with ARG1008 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004B MET 3.1 16.0 + - - +
1005B GLU* 3.0 35.3 + - - +
1007B GLU* 1.3 74.4 - - - +
1009B LEU* 1.3 64.6 + - - +
1011B LEU* 2.9 12.3 + - - +
1012B GLN* 2.8 41.5 + - + +
1028B LYS* 4.9 14.6 - - - +
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Residues in contact with LEU1009 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668B ILE* 4.2 18.4 - - + -
687B ALA* 3.7 36.6 - - + +
688B TYR 3.5 31.6 - - - +
689B MET* 4.2 15.0 - - - -
1005B GLU 3.0 11.6 + - - +
1006B LEU* 3.7 6.3 - - + +
1008B ARG* 1.3 79.7 - - - +
1010B TYR* 1.3 62.6 + - + +
1012B GLN* 3.3 16.5 + - - +
1013B MET* 3.1 32.9 + - + +
1026B MET* 4.2 16.6 - - + +
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Residues in contact with TYR1010 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546B LEU* 3.9 10.3 - - + -
548B VAL* 3.9 25.6 - - + -
550B TYR* 3.0 40.4 + - - -
571B HIS* 4.0 6.7 - + - -
576B PHE* 4.1 6.7 - + + -
625B ILE* 3.7 37.8 - - + +
627B VAL* 3.5 10.9 - - + +
650B ALA* 5.8 0.4 - - + -
652B TRP* 5.2 0.5 - - - -
668B ILE* 4.4 13.7 - - + +
1006B LEU* 3.0 48.3 + - + +
1007B GLU* 3.4 11.4 - - - +
1008B ARG 3.1 0.2 - - - -
1009B LEU* 1.3 77.7 - - + +
1011B LEU* 1.3 62.0 + - - +
1013B MET* 3.2 17.3 + - + +
1014B TRP* 3.0 20.8 + - - +
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Residues in contact with LEU1011 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539B LEU* 5.7 5.6 - - + -
546B LEU* 4.4 15.0 - - + -
575B LYS* 5.4 13.7 - - + +
576B PHE* 3.5 27.6 - - + -
1007B GLU* 3.1 17.9 + - + +
1008B ARG* 2.9 9.4 + - - +
1010B TYR* 1.3 80.1 - - - +
1012B GLN* 1.3 62.3 + - - +
1014B TRP* 3.8 10.8 - - + +
1015B GLU* 3.0 43.4 + - + +
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Residues in contact with GLN1012 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008B ARG* 2.8 29.5 + - + +
1009B LEU* 3.4 20.0 - - - +
1011B LEU* 1.3 77.9 - - - +
1013B MET* 1.3 63.6 + - - +
1015B GLU* 3.8 5.6 - - - +
1016B HIS* 3.2 23.4 + - - +
1026B MET* 3.9 36.6 + - - +
1028B LYS* 4.1 28.4 + - - +
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Residues in contact with MET1013 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625B ILE* 4.5 4.3 - - + -
648B ILE* 3.5 27.8 - - + +
650B ALA* 4.5 6.7 - - + -
666B TYR* 3.7 43.7 + - + -
668B ILE* 4.2 16.2 - - + -
687B ALA* 3.5 31.4 - - + -
1009B LEU* 3.1 22.6 + - + +
1010B TYR* 3.3 22.9 - - + +
1012B GLN* 1.3 80.7 - - - +
1014B TRP* 1.3 60.5 + - - +
1016B HIS* 3.5 2.9 - - - +
1017B TYR* 3.1 17.7 + - - +
1026B MET* 4.0 14.5 - - + -
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Residues in contact with TRP1014 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536B PRO 3.7 17.7 - - - -
537B LYS 3.8 7.2 - - - -
538B ASP* 3.8 19.2 - - - +
539B LEU* 3.6 40.7 - - + +
546B LEU* 4.0 18.6 - - + -
624B HIS* 3.6 34.8 - + + -
625B ILE* 5.0 0.9 - - + -
647B PRO* 4.1 7.4 - - + -
648B ILE* 3.9 12.5 - - + +
1010B TYR 3.0 14.4 + - - +
1011B LEU* 3.8 11.0 - - + +
1012B GLN 3.2 0.4 - - - -
1013B MET* 1.3 75.5 - - - +
1015B GLU* 1.3 83.2 + - - +
1017B TYR* 3.0 33.9 + + - -
1018B ALA* 2.7 34.6 + - + +
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Residues in contact with GLU1015 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011B LEU* 3.0 32.9 + - + +
1012B GLN* 3.8 6.1 - - - +
1014B TRP* 1.3 86.0 + - - +
1016B HIS* 1.3 55.5 + - - +
1018B ALA* 3.0 8.3 + - - +
1019B ALA* 2.7 37.3 + - - +
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Residues in contact with HIS1016 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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859A PRO* 3.1 40.4 - - + +
860A ASN* 3.8 13.8 + - - -
666B TYR* 4.0 8.5 - - - -
1012B GLN 3.2 14.7 + - - +
1013B MET 3.5 4.5 - - - +
1014B TRP 3.1 0.2 - - - -
1015B GLU* 1.3 78.7 - - - +
1017B TYR* 1.3 62.5 + - + +
1019B ALA* 3.3 5.8 - - - +
1021B ASN* 3.0 57.4 + - + +
1022B LYS 2.9 27.1 + - - -
1023B PRO* 4.2 1.1 - - + -
1024B ASP 3.7 7.4 + - - -
1026B MET* 3.5 22.4 - - + -
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Residues in contact with TYR1017 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535B HIS* 3.9 11.5 + - - +
536B PRO 3.5 18.6 + - - -
537B LYS* 4.6 11.6 - - + +
647B PRO* 3.5 31.5 - - + +
648B ILE* 3.9 14.6 - - + -
1013B MET 3.1 11.7 + - - +
1014B TRP* 3.0 40.3 + + - +
1016B HIS* 1.3 75.1 - - + +
1018B ALA* 1.3 64.7 + - - +
1019B ALA 3.1 2.2 - - - -
1020B GLY* 3.0 20.5 + - - -
1021B ASN 3.5 19.7 - - - +
1023B PRO* 6.4 2.0 - - + -
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Residues in contact with ALA1018 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537B LYS* 4.2 16.8 - - - +
538B ASP* 5.8 0.2 - - - -
1014B TRP* 2.7 43.0 + - + +
1015B GLU* 3.5 9.9 - - - +
1017B TYR* 1.3 79.5 - - - +
1019B ALA* 1.3 61.7 + - - +
1020B GLY* 3.0 2.1 + - - -
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Residues in contact with ALA1019 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
977A LEU* 5.5 7.4 - - - +
1015B GLU 2.7 12.2 + - - +
1016B HIS* 3.3 16.2 - - - +
1017B TYR 3.1 0.4 - - - -
1018B ALA* 1.3 78.1 - - - +
1020B GLY* 1.3 54.7 + - - +
1021B ASN* 3.3 16.4 + - - +
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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