Contacts of the helix formed by residues 976 - 997 (chain B) in PDB entry 4E5W
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 976 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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974B LYS 4.0 3.7 + - - -
975B ILE* 1.3 74.9 - - - +
977B LEU* 1.3 65.4 + - - +
978B LYS* 3.5 15.2 + - - +
979B GLN* 3.1 24.6 + - - +
980B GLN* 3.0 24.0 + - - +
1077B TYR* 4.2 3.8 - - - -
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Residues in contact with LEU 977 (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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976B ASN* 1.3 74.1 - - - +
978B LYS* 1.3 58.9 + - - +
980B GLN* 3.1 13.9 + - - +
981B LEU* 2.9 53.0 + - + +
1075B LEU* 3.8 28.5 - - + -
1077B TYR* 4.8 1.2 + - - -
1119B ASN 5.2 4.3 - - - +
1120B CYS* 5.7 0.4 - - - -
1121B PRO* 3.7 35.7 - - + -
1124B VAL* 4.5 3.1 - - + -
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Residues in contact with LYS 978 (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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976B ASN* 3.3 16.4 + - - +
977B LEU* 1.3 79.1 - - - +
979B GLN* 1.3 62.3 + - - +
981B LEU* 3.4 2.5 + - - -
982B LYS* 3.1 47.2 + - - +
1153B LEU* 3.6 42.6 + - + +
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Residues in contact with GLN 979 (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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974B LYS 5.3 1.3 - - - +
975B ILE* 3.9 19.3 - - + -
976B ASN* 3.1 23.1 + - - +
978B LYS* 1.3 72.0 - - - +
980B GLN* 1.3 59.7 + - - +
982B LYS* 3.3 29.3 + - - +
983B TYR* 3.1 50.2 + - + +
1014B GLU* 3.3 23.4 + - + +
1015B HIS* 3.6 32.7 + - - +
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Residues in contact with GLN 980 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968B LEU* 5.5 0.2 - - + -
975B ILE* 3.9 13.9 - - + -
976B ASN 3.0 12.3 + - - +
977B LEU* 3.4 25.6 + - - +
979B GLN* 1.3 75.9 - - - +
981B LEU* 1.4 59.1 + - - +
983B TYR* 3.2 7.4 + - - +
984B ALA* 3.0 25.9 + - - +
1071B LEU* 5.9 1.1 - - + -
1074B LEU* 3.0 47.9 + - + +
1075B LEU* 3.6 31.9 + - + +
1077B TYR* 3.3 37.1 + - - -
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Residues in contact with LEU 981 (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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977B LEU* 2.9 38.2 + - + +
978B LYS* 3.8 5.4 - - - +
980B GLN* 1.4 74.3 - - - +
982B LYS* 1.4 60.5 + - - +
984B ALA* 3.3 5.2 + - - +
985B VAL* 3.0 31.2 + - - +
1071B LEU* 5.1 4.5 - - + -
1075B LEU* 5.1 3.4 - - + -
1124B VAL* 3.9 41.7 - - + -
1149B PHE* 4.0 22.6 - - + +
1152B LEU* 4.3 23.3 - - + +
1153B LEU* 3.9 22.7 - - + -
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Residues in contact with LYS 982 (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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978B LYS* 3.1 44.1 + - - +
979B GLN* 3.3 34.0 + - - +
981B LEU* 1.4 72.8 - - - +
983B TYR* 1.4 65.1 + - - +
985B VAL* 3.3 5.4 + - - +
986B GLN* 3.1 38.2 + - - +
1015B HIS 6.1 0.2 - - - +
1153B LEU* 4.1 21.1 - - + -
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Residues in contact with TYR 983 (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 LEU* 4.0 20.9 - - + -
967B TYR* 3.8 8.0 - + - -
968B LEU* 4.2 4.5 - - + -
975B ILE* 3.4 32.2 - - + +
979B GLN* 3.1 29.5 + - + -
980B GLN* 3.2 8.5 + - - +
982B LYS* 1.4 74.2 - - - +
984B ALA* 1.3 57.0 + - - +
986B GLN* 3.2 8.7 + - - +
987B ILE* 2.9 37.3 + - + +
1011B VAL* 4.8 0.8 - - + +
1013B SER 4.1 2.3 + - - -
1014B GLU* 2.7 37.5 + - - -
1016B GLN 4.2 7.4 - - - -
1017B VAL* 3.7 32.9 - - + +
1074B LEU* 3.8 28.3 - - + -
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Residues in contact with ALA 984 (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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980B GLN 3.0 13.8 + - - +
981B LEU* 3.4 13.0 - - - +
982B LYS 3.3 0.2 - - - -
983B TYR* 1.3 75.8 - - - +
985B VAL* 1.3 56.8 + - - +
987B ILE* 3.4 0.8 + - - -
988B CYS* 3.0 34.5 + - - -
1067B PHE* 3.7 16.7 - - + -
1071B LEU* 3.8 27.6 - - + -
1074B LEU* 4.2 6.0 - - + +
1149B PHE* 4.0 11.7 - - + -
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Residues in contact with VAL 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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981B LEU 3.0 18.3 + - - +
982B LYS* 3.3 10.1 + - - +
984B ALA* 1.3 74.6 - - - +
986B GLN* 1.3 59.4 + - + +
988B CYS* 3.2 8.6 + - - +
989B LYS* 2.9 58.5 + - + +
1146B ILE* 4.3 17.9 - - + +
1149B PHE* 3.5 28.0 - - + -
1150B GLU* 4.5 7.9 - - + +
1153B LEU* 4.1 14.6 - - + -
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Residues in contact with GLN 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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935B GLU* 6.1 0.9 - - - +
936B ASN* 3.3 39.6 + - - +
982B LYS* 3.1 31.3 + - - +
983B TYR* 3.2 9.5 + - - +
985B VAL* 1.3 76.0 - - + +
987B ILE* 1.4 64.3 + - - +
989B LYS* 3.4 4.5 + - + +
990B GLY 3.1 19.1 + - - -
1015B HIS 3.0 22.4 + - - -
1016B GLN* 3.3 5.3 - - - +
1017B VAL* 2.8 38.1 + - + +
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Residues in contact with ILE 987 (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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936B ASN* 5.5 0.4 - - - -
964B LEU* 4.3 8.3 - - + -
983B TYR 2.9 22.3 + - - +
984B ALA* 3.8 5.6 - - - +
985B VAL 3.4 0.2 - - - -
986B GLN* 1.4 72.6 - - - +
988B CYS* 1.4 57.0 + - - +
990B GLY* 3.3 2.3 + - - -
991B MET* 2.9 30.3 + - + +
1004B LEU* 4.1 27.6 - - + -
1009B VAL* 4.0 34.8 - - + -
1017B VAL* 4.0 5.8 - - + -
1019B ILE* 3.9 10.7 - - + +
1067B PHE* 3.7 24.0 - - + -
1070B THR* 4.4 9.9 - - + -
1074B LEU* 4.0 23.6 - - + -
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Residues in contact with CYS 988 (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 ALA 3.0 18.1 + - - +
985B VAL* 3.5 8.3 - - - +
987B ILE* 1.4 77.4 - - - +
989B LYS* 1.3 52.2 + - - +
991B MET* 3.4 1.4 + - - +
992B ASP* 2.8 35.0 + - - +
1067B PHE* 3.4 31.0 - - - -
1142B PHE* 3.8 28.3 - - + +
1145B LEU* 3.9 16.4 - - - -
1146B ILE* 3.6 19.5 - - + -
1149B PHE* 4.1 5.2 - - - -
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Residues in contact with LYS 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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934B HIS* 3.7 21.3 + - + +
936B ASN* 4.1 7.0 - - - +
985B VAL* 2.9 44.0 + - + +
986B GLN* 3.7 7.0 - - + +
988B CYS* 1.3 68.7 - - - +
990B GLY* 1.3 66.5 + - - +
992B ASP* 3.3 3.5 + - - +
993B TYR* 3.0 24.3 + - - +
1146B ILE* 3.8 27.1 - - + -
1150B GLU* 4.2 9.7 + - - -
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Residues in contact with GLY 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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934B HIS* 3.8 17.5 - - - -
936B ASN* 4.2 6.7 - - - -
937B ILE* 3.7 12.7 - - - +
986B GLN 3.1 13.6 + - - -
987B ILE 3.8 2.7 - - - -
989B LYS* 1.3 75.2 - - - +
991B MET* 1.3 56.6 + - - +
993B TYR* 3.4 5.0 + - - +
994B LEU* 3.1 23.6 + - - +
1019B ILE* 3.7 16.6 - - - +
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Residues in contact with MET 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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987B ILE* 2.9 22.1 + - + +
988B CYS 3.7 3.1 - - - +
990B GLY* 1.3 72.8 - - - +
992B ASP* 1.3 60.4 + - - +
994B LEU* 3.3 15.0 + - + +
995B GLY* 2.9 24.4 + - - -
1001B HIS* 3.8 19.5 - - + -
1004B LEU* 3.7 35.4 - - + -
1019B ILE* 3.7 18.4 - - + -
1063B ASP* 3.6 41.5 - - + +
1142B PHE* 3.6 28.0 - - + -
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Residues in contact with ASP 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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988B CYS 2.8 19.6 + - - +
989B LYS* 3.3 6.7 + - - +
991B MET* 1.3 74.5 - - - +
993B TYR* 1.3 59.6 + - - +
995B GLY* 3.3 3.1 + - - +
996B SER* 2.9 32.3 + - - -
1142B PHE* 3.8 24.1 + - + +
1143B GLN* 3.6 27.7 + - - +
1146B ILE* 4.7 3.6 - - + -
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Residues in contact with TYR 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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931B ASN 3.9 4.9 + - - -
932B LEU* 3.7 26.0 - - + -
933B TYR* 2.8 50.6 + - - +
934B HIS* 3.7 23.3 - + + -
937B ILE* 3.4 19.7 - - + -
989B LYS 3.0 16.6 + - - +
990B GLY 3.5 4.3 - - - +
992B ASP* 1.3 75.9 - - - +
994B LEU* 1.4 59.0 + - - +
996B SER* 2.7 23.6 + - - -
997B ARG* 3.2 52.0 + - - +
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Residues in contact with LEU 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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928B ILE* 4.8 0.2 - - + -
932B LEU* 3.8 29.4 - - + -
937B ILE* 5.1 2.5 - - + -
990B GLY 3.1 14.2 + - - +
991B MET* 3.5 17.5 - - + +
992B ASP 3.3 0.2 - - - -
993B TYR* 1.4 79.6 - - - +
995B GLY* 1.3 61.7 + - - +
997B ARG* 3.0 17.2 + - - +
999B TYR* 3.3 47.0 + - + +
1001B HIS* 3.7 49.4 - - + +
1019B ILE* 6.1 0.9 - - + -
1022B PHE* 4.3 10.1 - - + -
1025B THR* 4.3 7.6 - - + -
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Residues in contact with GLY 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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991B MET 2.9 15.3 + - - -
992B ASP* 3.3 4.9 + - - -
994B LEU* 1.3 75.3 - - - +
996B SER* 1.4 56.0 + - - +
998B GLN* 2.9 23.9 + - - +
999B TYR 3.8 12.7 + - - -
1060B ILE* 3.6 29.4 - - - +
1142B PHE* 6.4 0.2 - - - -
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Residues in contact with SER 996 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
992B ASP* 2.9 15.9 + - - -
993B TYR* 2.7 25.8 + - - -
995B GLY* 1.4 74.9 - - - +
997B ARG* 1.4 71.5 + - - +
998B GLN* 3.2 8.9 + - - +
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Residues in contact with ARG 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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931B ASN 5.4 3.0 + - - +
932B LEU* 4.3 16.6 - - + -
993B TYR* 3.2 56.6 + - + +
994B LEU 3.0 9.3 + - - +
996B SER* 1.4 82.7 + - - +
998B GLN* 1.3 69.4 + - - +
999B TYR* 3.4 28.7 + - + -
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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