Contacts of the helix formed by residues 976 - 997 (chain A) in PDB entry 4EI4
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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972A LYS 5.3 0.2 - - - -
974A LYS 3.8 5.0 + - - +
975A ILE* 1.3 76.0 - - - +
977A LEU* 1.3 64.8 + - - +
978A LYS* 3.5 13.7 + - - +
979A GLN* 3.0 27.1 + - - +
980A GLN* 3.1 13.9 + - - +
1077A TYR* 4.3 3.1 - - - -
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Residues in contact with LEU 977 (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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976A ASN* 1.3 75.3 - - - +
978A LYS* 1.3 62.3 + - - +
980A GLN* 3.2 20.4 + - + +
981A LEU* 3.0 51.4 + - + +
1075A LEU* 4.2 17.7 - - + -
1077A TYR* 4.9 0.8 + - - -
1119A ASN 4.9 5.2 - - - +
1121A PRO* 3.6 34.8 - - + -
1124A VAL* 4.4 8.5 - - + -
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Residues in contact with LYS 978 (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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976A ASN* 3.1 17.0 + - - +
977A LEU* 1.3 78.5 - - - +
979A GLN* 1.3 61.5 + - - +
981A LEU* 3.3 4.6 + - - -
982A LYS* 3.1 49.6 + - - +
1153A LEU* 3.0 51.7 + - + +
1154A LYS* 5.3 2.0 - - - +
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Residues in contact with GLN 979 (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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974A LYS 5.2 1.6 - - - +
975A ILE* 3.7 27.8 - - + -
976A ASN* 3.0 18.1 + - - +
978A LYS* 1.3 79.9 - - - +
980A GLN* 1.3 61.7 + - - +
982A LYS* 3.3 27.3 + - - +
983A TYR* 3.1 38.8 + - + -
1014A GLU* 3.3 21.5 + - + +
1015A HIS* 3.3 32.5 + - - +
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Residues in contact with GLN 980 (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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975A ILE* 3.8 13.9 - - + -
976A ASN 3.1 8.2 + - - +
977A LEU* 3.2 28.1 + - + +
979A GLN* 1.3 75.4 - - - +
981A LEU* 1.3 60.9 + - + +
983A TYR* 3.2 3.1 + - - -
984A ALA* 2.9 23.6 + - - +
1071A LEU* 6.0 0.4 - - - -
1074A LEU* 2.9 57.9 + - + +
1075A LEU* 3.7 28.2 + - + +
1077A TYR* 3.4 33.9 + - - -
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Residues in contact with LEU 981 (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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977A LEU* 3.0 40.9 + - + +
978A LYS* 3.3 6.2 + - - +
980A GLN* 1.3 78.2 - - + +
982A LYS* 1.3 56.2 + - - +
984A ALA* 3.4 6.4 + - + +
985A VAL* 3.0 34.2 + - - +
1071A LEU* 5.4 4.5 - - + -
1075A LEU* 5.5 1.8 - - + -
1124A VAL* 4.0 26.9 - - + -
1149A PHE* 4.0 27.5 - - + +
1152A LEU* 4.3 24.2 - - + +
1153A LEU* 3.8 23.6 - - + -
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Residues in contact with LYS 982 (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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978A LYS* 3.1 47.9 + - - +
979A GLN* 3.5 33.8 + - - +
980A GLN 3.2 0.2 - - - -
981A LEU* 1.3 74.5 - - - +
983A TYR* 1.3 64.5 + - - +
985A VAL* 3.5 6.2 + - - +
986A GLN* 3.1 34.0 + - - +
1015A HIS* 5.3 7.8 + - + +
1153A LEU* 4.1 17.0 - - + -
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Residues in contact with TYR 983 (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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964A LEU* 4.3 14.8 - - + -
967A TYR* 3.8 9.1 - + - -
968A LEU* 4.5 5.8 - - + -
975A ILE* 3.6 27.6 - - + +
979A GLN* 3.1 37.2 + - + -
980A GLN* 3.2 7.2 + - - +
982A LYS* 1.3 73.9 - - - +
984A ALA* 1.3 59.7 + - - +
986A GLN* 3.0 9.9 + - - +
987A ILE* 2.8 37.1 + - + +
1011A VAL* 5.4 0.7 - - + -
1013A SER 3.7 3.3 + - - -
1014A GLU* 2.7 30.3 + - - -
1016A GLN 4.1 11.2 - - - -
1017A VAL* 3.7 37.7 - - + -
1074A LEU* 3.9 24.9 - - + -
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Residues in contact with ALA 984 (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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980A GLN 2.9 13.8 + - - +
981A LEU* 3.5 12.3 - - - +
983A TYR* 1.3 75.7 - - - +
985A VAL* 1.3 62.9 + - - +
987A ILE* 3.3 4.6 + - - +
988A CYS* 2.9 30.2 + - - -
1067A PHE* 3.8 9.6 - - + -
1071A LEU* 3.8 26.5 - - + -
1074A LEU* 4.1 5.5 - - + +
1149A PHE* 3.9 19.3 - - + -
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Residues in contact with VAL 985 (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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981A LEU 3.0 21.9 + - - +
982A LYS* 3.7 7.0 - - - +
984A ALA* 1.3 74.6 - - - +
986A GLN* 1.3 61.2 + - + +
988A CYS* 3.2 8.3 + - - +
989A LYS* 2.9 54.1 + - + +
1146A ILE* 4.3 14.6 - - + +
1149A PHE* 3.4 29.2 - - + -
1150A GLU* 4.3 14.8 - - + +
1153A LEU* 4.2 13.7 - - + -
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Residues in contact with GLN 986 (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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936A ASN* 3.5 40.0 + - - +
982A LYS* 3.1 24.3 + - - +
983A TYR* 3.0 10.0 + - - +
985A VAL* 1.3 75.5 - - + +
987A ILE* 1.3 65.4 + - - +
989A LYS* 3.4 4.4 + - + -
990A GLY* 3.1 18.0 + - - -
1015A HIS 2.8 24.6 + - - -
1016A GLN* 3.4 5.2 - - - +
1017A VAL* 2.8 40.8 + - + +
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Residues in contact with ILE 987 (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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964A LEU* 4.6 8.1 - - + -
983A TYR* 2.8 28.1 + - + +
984A ALA* 3.6 11.0 - - - +
986A GLN* 1.3 72.0 - - - +
988A CYS* 1.3 61.8 + - - +
990A GLY* 3.4 1.4 + - - -
991A MET* 3.1 31.6 + - + +
1004A LEU* 4.1 24.5 - - + -
1009A VAL* 4.1 29.4 - - + -
1017A VAL* 4.0 13.9 - - + -
1019A ILE* 4.0 11.2 - - + +
1067A PHE* 3.7 24.5 - - + -
1070A THR* 4.5 13.0 - - + -
1071A LEU* 6.5 0.2 - - - -
1074A LEU* 5.0 6.5 - - + -
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Residues in contact with CYS 988 (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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984A ALA 2.9 17.6 + - - +
985A VAL* 3.5 8.7 - - - +
987A ILE* 1.3 77.2 - - - +
989A LYS* 1.3 56.9 + - - +
991A MET* 3.3 1.0 + - - +
992A ASP* 2.8 31.7 + - - +
1067A PHE* 3.4 29.2 - - - -
1142A PHE* 3.8 28.7 - - + +
1145A LEU* 3.9 16.6 - - - -
1146A ILE* 3.6 20.2 - - + -
1149A PHE* 4.1 5.2 - - - -
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Residues in contact with LYS 989 (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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934A HIS* 3.6 20.0 + - + +
935A GLU* 5.4 7.4 + - - +
936A ASN* 4.0 9.4 - - - +
985A VAL* 2.9 38.4 + - + +
986A GLN* 3.8 7.4 - - + +
987A ILE 3.3 0.4 - - - -
988A CYS* 1.3 75.3 - - - +
990A GLY* 1.3 62.7 + - - +
992A ASP* 3.9 3.8 - - - +
993A TYR* 3.1 23.0 + - - +
1146A ILE* 3.9 21.8 - - + -
1150A GLU* 4.2 15.5 + - - -
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Residues in contact with GLY 990 (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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934A HIS* 3.8 17.4 - - - -
936A ASN* 4.3 5.2 - - - -
937A ILE* 3.9 7.8 - - - +
986A GLN 3.1 13.6 + - - -
987A ILE 3.9 2.5 - - - -
989A LYS* 1.3 76.7 - - - +
991A MET* 1.3 56.4 + - - +
993A TYR* 3.2 6.2 + - - +
994A LEU* 3.0 26.3 + - - +
1019A ILE* 3.9 18.2 - - - -
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Residues in contact with MET 991 (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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987A ILE* 3.1 22.0 + - + +
988A CYS 3.7 2.7 - - - +
990A GLY* 1.3 73.4 - - - +
992A ASP* 1.3 61.1 + - - +
994A LEU* 3.4 12.3 + - + +
995A GLY* 2.9 25.6 + - - -
1001A HIS* 3.7 22.0 - - + -
1004A LEU* 3.9 32.5 - - + -
1019A ILE* 3.9 18.2 - - + -
1063A ASP* 3.4 42.4 - - + +
1142A PHE* 3.5 26.2 - - + -
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Residues in contact with ASP 992 (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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988A CYS 2.8 18.0 + - - +
989A LYS* 3.9 6.7 - - - +
991A MET* 1.3 73.8 - - - +
993A TYR* 1.3 60.2 + - - +
995A GLY* 3.4 2.3 + - - +
996A SER* 2.9 30.6 + - - -
1142A PHE* 3.7 26.0 - - + +
1143A GLN* 3.4 33.6 + - - +
1146A ILE* 4.9 3.4 - - + -
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Residues in contact with TYR 993 (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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931A ASN 4.0 3.1 + - - -
932A LEU* 3.5 28.2 - - + +
933A TYR* 2.9 44.6 + - - -
934A HIS* 3.7 23.3 - + + -
937A ILE* 3.6 23.1 - - + -
989A LYS 3.1 14.3 + - - +
990A GLY 3.2 6.9 + - - +
992A ASP* 1.3 76.9 - - - +
994A LEU* 1.3 61.7 + - - +
996A SER* 2.5 23.1 + - - -
997A ARG* 3.1 58.4 + - + +
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Residues in contact with LEU 994 (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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932A LEU* 3.8 30.7 - - + -
937A ILE* 4.9 3.6 - - + -
990A GLY 3.0 13.4 + - - +
991A MET* 3.5 17.7 - - + +
993A TYR* 1.3 78.9 - - - +
995A GLY* 1.3 60.8 + - - +
997A ARG* 3.1 15.1 + - - +
999A TYR* 3.1 48.2 + - + +
1000A VAL 4.4 0.4 - - - -
1001A HIS* 3.6 49.6 - - + +
1019A ILE* 6.2 0.4 - - + -
1022A PHE* 4.0 12.3 - - + -
1025A THR* 4.5 5.4 - - + -
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Residues in contact with GLY 995 (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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991A MET 2.9 19.3 + - - -
992A ASP* 3.7 4.3 - - - -
994A LEU* 1.3 71.8 - - - +
996A SER* 1.3 56.3 + - - +
998A GLN* 3.1 18.7 + - - +
999A TYR 3.7 12.7 + - - -
1060A ILE* 3.8 30.3 - - - +
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Residues in contact with SER 996 (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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992A ASP* 2.9 15.7 + - - -
993A TYR* 2.5 25.1 + - - -
995A GLY* 1.3 72.3 - - - +
997A ARG* 1.3 74.9 + - - +
998A GLN* 3.1 14.3 + - - +
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Residues in contact with ARG 997 (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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931A ASN 5.1 5.3 + - - -
932A LEU* 4.4 6.1 - - + -
933A TYR* 5.3 5.5 - - - -
993A TYR* 3.1 64.6 + - + +
994A LEU* 3.1 9.5 + - - +
996A SER* 1.3 86.5 + - - +
998A GLN* 1.3 72.1 + - - +
999A TYR* 3.4 30.0 + - + -
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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