Contacts of the helix formed by residues 984 - 1007 (chain B) in PDB entry 3CQC
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 SER 984 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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982B ASP 3.5 2.4 + - - -
983B PHE* 1.3 76.0 - - - +
985B GLU* 1.3 59.6 + - - +
986B ASP* 3.5 12.6 + - - +
987B MET* 3.3 27.1 + - - +
988B LEU* 2.8 28.6 + - - +
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Residues in contact with GLU 985 (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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983B PHE 5.6 0.2 - - - +
984B SER* 1.3 73.9 - - - +
986B ASP* 1.3 61.6 + - - +
988B LEU* 4.0 9.7 - - + +
989B GLN* 3.0 28.4 + - - +
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Residues in contact with ASP 986 (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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984B SER* 3.2 13.8 + - - +
985B GLU* 1.3 74.0 + - - +
987B MET* 1.3 69.3 + - + +
989B GLN* 2.8 19.5 + - - +
990B GLU* 3.0 11.7 + - - +
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Residues in contact with MET 987 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
983B PHE* 3.9 25.1 - - + -
984B SER* 3.3 17.3 + - - +
986B ASP* 1.3 78.2 - - + +
988B LEU* 1.3 63.1 + - - +
990B GLU* 3.2 12.0 + - - +
991B LYS* 3.1 59.1 + - - +
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Residues in contact with LEU 988 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894A LYS* 5.5 5.6 - - - -
978B ALA* 3.9 38.4 - - + +
979B LEU* 4.5 24.7 - - + +
981B SER 5.5 3.1 - - - +
983B PHE* 3.7 20.1 - - + +
984B SER 2.8 23.0 + - - +
985B GLU* 4.0 9.4 - - + +
987B MET* 1.3 71.2 - - - +
989B GLN* 1.3 66.3 + - - +
991B LYS* 3.0 7.2 + - + +
992B ILE* 2.9 34.1 + - + +
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Residues in contact with GLN 989 (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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985B GLU 3.0 20.5 + - - +
986B ASP* 2.8 14.7 + - - +
988B LEU* 1.3 73.1 - - - +
990B GLU* 1.3 58.3 + - - +
992B ILE* 3.0 33.2 - - - +
993B GLU* 3.1 19.0 + - + +
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Residues in contact with GLU 990 (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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986B ASP 3.0 9.4 + - - +
987B MET* 3.4 15.9 - - - +
988B LEU 3.2 0.2 - - - -
989B GLN* 1.3 74.1 - - - +
991B LYS* 1.3 66.4 + - + +
993B GLU* 2.8 24.4 + - - +
994B GLU* 2.8 45.7 + - - +
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Residues in contact with LYS 991 (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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950B HIS* 3.9 29.3 + - + +
978B ALA* 4.7 9.6 - - + -
983B PHE* 3.9 27.8 - - + -
987B MET* 3.1 48.5 - - - +
988B LEU* 3.0 7.9 + - + +
990B GLU* 1.3 84.7 + - - +
992B ILE* 1.3 58.7 + - - +
994B GLU* 3.4 15.8 + - - +
995B MET* 2.9 34.6 + - - +
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Residues in contact with ILE 992 (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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884A GLU* 4.2 8.5 - - - +
889A TYR* 3.8 27.6 - - + +
975B LYS* 4.5 15.9 - - + -
978B ALA* 5.9 1.3 - - + +
979B LEU* 4.8 10.3 - - + -
988B LEU* 2.9 24.9 + - + +
989B GLN* 3.0 40.8 - - - +
991B LYS* 1.3 74.5 - - - +
993B GLU* 1.3 57.7 + - - +
995B MET* 3.6 9.3 - - - +
996B ALA* 3.0 27.4 + - + +
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Residues in contact with GLU 993 (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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989B GLN* 3.1 20.2 + - - +
990B GLU* 2.8 15.4 + - + +
992B ILE* 1.3 77.7 - - - +
994B GLU* 1.3 56.7 + - - +
995B MET 2.8 4.0 - - - -
996B ALA* 2.7 26.8 + - - +
997B GLU* 3.0 34.9 + - - +
1000B ARG* 4.0 14.9 + - - -
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Residues in contact with GLU 994 (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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950B HIS* 5.5 0.2 + - - -
954B LEU* 3.4 28.6 - - + +
990B GLU* 2.8 43.1 + - - +
991B LYS* 3.6 22.3 + - - +
993B GLU* 1.3 72.3 - - - +
995B MET* 1.3 62.1 + - - +
997B GLU* 3.8 12.2 - - - +
998B GLN* 3.7 18.5 + - - +
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Residues in contact with MET 995 (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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950B HIS* 3.4 34.1 - - + -
954B LEU* 4.6 9.4 - - + -
971B LEU* 4.1 38.4 - - + +
974B SER* 3.8 4.7 - - - +
975B LYS* 3.8 42.4 - - + -
978B ALA* 4.8 3.4 - - + -
991B LYS 2.9 25.0 + - - +
992B ILE* 3.6 8.7 - - - +
993B GLU 2.8 0.2 - - - -
994B GLU* 1.3 78.5 - - + +
996B ALA* 1.3 61.0 + - - +
997B GLU 3.1 1.6 - - - -
998B GLN* 3.2 6.7 + - - +
999B GLU* 2.9 28.2 + - + +
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Residues in contact with ALA 996 (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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884A GLU* 5.7 10.1 - - + -
975B LYS* 6.1 2.2 - - - +
992B ILE* 3.0 17.7 + - + +
993B GLU* 2.7 16.9 + - - +
995B MET* 1.3 73.6 - - - +
997B GLU* 1.3 62.2 + - - +
999B GLU* 3.4 8.8 + - - +
1000B ARG* 2.9 54.2 + - - +
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Residues in contact with GLU 997 (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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993B GLU* 3.0 36.9 + - - +
994B GLU* 3.8 14.5 - - - +
996B ALA* 1.3 77.5 - - - +
998B GLN* 1.3 62.6 + - - +
1000B ARG* 2.6 55.1 + - - +
1001B PHE* 3.2 7.1 + - - +
1057B TYR* 4.3 9.8 + - + +
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Residues in contact with GLN 998 (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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954B LEU* 4.3 8.6 - - + +
958B ASN* 3.1 31.8 + - - +
967B LYS* 3.9 20.4 - - - +
971B LEU* 3.4 30.1 - - + -
994B GLU 3.7 10.7 + - - +
995B MET* 3.2 11.6 + - - +
997B GLU* 1.3 79.6 - - - +
999B GLU* 1.3 62.0 + - - +
1001B PHE* 3.5 13.6 + - - +
1002B LEU* 3.2 23.9 + - + +
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Residues in contact with GLU 999 (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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884A GLU* 5.8 8.3 - - + -
971B LEU* 4.6 8.3 - - + +
975B LYS* 5.9 3.8 - - - +
995B MET* 2.9 16.9 + - + +
996B ALA* 3.7 10.1 - - - +
997B GLU 3.1 0.2 - - - -
998B GLN* 1.3 74.8 - - - +
1000B ARG* 1.3 60.7 + - + +
1002B LEU* 3.9 6.1 - - - +
1003B LEU* 3.0 29.2 + - - +
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Residues in contact with ARG1000 (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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993B GLU* 4.0 7.4 + - - -
996B ALA* 2.9 54.5 + - - +
997B GLU* 2.6 44.4 + - - +
999B GLU* 1.3 74.8 - - - +
1001B PHE* 1.3 69.0 + - - +
1003B LEU* 3.0 24.6 + - + +
1004B HIS* 3.6 15.2 + - - +
1057B TYR* 4.1 11.9 - - - +
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Residues in contact with PHE1001 (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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967B LYS* 5.5 2.5 - - - -
997B GLU 3.2 6.4 + - - +
998B GLN* 3.7 15.9 - - - +
1000B ARG* 1.3 77.8 - - - +
1002B LEU* 1.3 89.5 + - + +
1004B HIS* 3.0 29.5 + - - +
1005B GLN* 4.0 4.3 + - + -
1025B VAL* 4.6 6.5 - - + -
1026B LEU 3.4 25.6 - - - -
1027B THR* 4.4 1.8 - - - -
1028B ALA 4.0 20.0 - - - -
1031B LEU* 4.6 8.2 - - + +
1054B LEU* 4.3 8.5 - - + -
1057B TYR* 3.8 48.3 + + + -
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Residues in contact with LEU1002 (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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964B PHE* 3.4 29.0 - - + -
967B LYS* 3.8 33.0 - - + -
968B LYS* 4.1 24.5 - - + +
971B LEU* 3.5 28.7 - - + -
998B GLN* 3.2 14.1 + - + +
999B GLU* 4.1 4.7 - - - +
1001B PHE* 1.3 105.4 - - + +
1003B LEU* 1.3 63.1 + - - +
1004B HIS 3.1 0.2 + - - -
1005B GLN* 3.3 3.1 + - - +
1006B GLU* 3.0 23.5 + - - +
1025B VAL* 4.6 1.8 - - + -
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Residues in contact with LEU1003 (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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999B GLU 3.0 15.3 + - - +
1000B ARG* 3.0 17.9 + - + +
1002B LEU* 1.3 77.6 - - - +
1004B HIS* 1.3 60.4 + - + +
1006B GLU* 3.9 14.1 - - + -
1007B THR* 2.9 46.8 + - + -
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Residues in contact with HIS1004 (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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1000B ARG* 3.7 19.5 + - - +
1001B PHE* 3.0 14.7 + - - +
1003B LEU* 1.3 78.7 - - + +
1005B GLN* 1.3 64.8 - - - +
1006B GLU 3.1 1.1 - - - -
1007B THR* 3.1 7.4 + - - -
1008B LEU 3.6 0.5 + - - -
1031B LEU* 4.3 2.2 - - + -
1035B TYR* 3.0 31.0 + - + -
1050B LYS* 3.8 37.7 - - + +
1053B ASP* 4.2 20.0 - - + +
1054B LEU* 3.1 44.3 - - + +
1057B TYR* 4.6 8.0 - + - -
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Residues in contact with GLN1005 (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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964B PHE* 3.6 41.2 - - + +
1001B PHE* 4.0 3.7 + - + -
1002B LEU* 3.3 5.8 + - + +
1004B HIS* 1.3 78.5 - - - +
1006B GLU* 1.3 63.8 + - - +
1008B LEU* 3.4 26.9 + - + +
1023B MET* 3.8 17.7 - - - -
1024B PRO 3.0 23.2 + - - -
1025B VAL* 3.8 1.7 - - - +
1026B LEU* 2.9 41.3 + - - +
1031B LEU* 4.0 23.3 - - + +
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Residues in contact with GLU1006 (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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964B PHE* 3.0 26.3 - - + -
968B LYS* 3.7 24.3 + - + +
1002B LEU 3.0 18.7 + - - +
1003B LEU* 3.4 21.3 - - + +
1004B HIS 3.1 0.2 - - - -
1005B GLN* 1.3 80.2 - - - +
1007B THR* 1.3 59.8 + - + +
1008B LEU* 3.3 6.6 + - - +
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Residues in contact with THR1007 (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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1003B LEU* 2.9 36.7 + - + +
1004B HIS* 3.1 3.3 + - - -
1006B GLU* 1.3 75.3 - - + +
1008B LEU* 1.3 65.3 + - - +
1009B PRO* 3.1 6.9 - - - +
1035B TYR* 3.0 20.9 + - - -
1050B LYS* 3.1 20.1 + - + +
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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
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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