Contacts of the helix formed by residues 981 - 1000 (chain A) in PDB entry 5Y36
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 TYR 981 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A ALA* 5.9 0.4 - - - -
974A LYS* 3.7 8.2 + - - -
979A ASN* 2.8 18.8 + - - +
980A ASN* 1.3 82.4 - - + +
982A HIS* 1.4 61.6 + - - +
983A HIS 3.6 2.1 + - - -
984A ALA* 3.7 14.9 + - + +
985A HIS* 4.4 8.3 + - + -
1092A VAL* 5.5 7.4 - - + -
1094A ILE* 3.4 42.4 - - + -
1225A GLU* 3.5 13.7 - - + -
1226A LEU 3.0 38.0 + - - -
1316A THR* 3.0 49.2 + - + -
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Residues in contact with HIS 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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967A ARG* 3.9 13.2 - - - -
974A LYS* 3.0 48.9 + - + +
976A ARG* 3.9 26.4 + - + -
979A ASN* 3.6 15.3 + - - +
980A ASN 3.3 3.2 + - - -
981A TYR* 1.4 77.5 - - - +
983A HIS* 1.3 72.2 + + + +
984A ALA 3.3 0.9 + - - -
985A HIS 3.6 6.4 + - - -
986A ASP* 2.6 27.7 + - - +
1401A MG 2.7 18.2 - - - -
33D C 3.0 14.0 + - - -
34D A 2.5 21.7 + - - -
35D T 4.5 6.7 - - + +
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Residues in contact with HIS 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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10A ALA* 3.2 17.3 + - + +
11A ILE 4.1 1.8 - - - -
12A GLY* 3.4 23.6 - - - -
15A SER* 3.3 37.6 + - - -
17A GLY* 3.5 22.7 - - - +
50A ALA* 4.3 5.3 - - + +
976A ARG* 4.4 6.0 + - - -
981A TYR 3.6 0.8 - - - -
982A HIS* 1.3 80.9 - + + +
984A ALA* 1.3 63.9 + - - +
986A ASP* 3.5 4.7 - - - +
987A ALA* 2.9 27.5 + - - +
1401A MG 3.1 22.0 - - - -
34D A 3.8 3.8 - - - -
35D T 3.0 29.2 + - - -
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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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17A GLY* 4.8 0.2 - - - -
18A TRP 4.3 0.4 - - - +
48A ILE* 3.2 31.5 - - + +
49A GLY 3.6 26.0 + - - +
50A ALA* 4.2 2.2 - - - +
981A TYR 3.7 12.5 + - - +
982A HIS 3.3 0.4 + - - -
983A HIS* 1.3 76.9 - - - +
985A HIS* 1.4 64.5 + - + +
987A ALA* 3.8 2.9 + - - +
988A TYR* 3.4 13.0 + - - +
1092A VAL* 4.0 21.8 - - + -
1094A ILE* 4.2 5.4 - - + -
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Residues in contact with HIS 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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48A ILE* 5.1 3.4 - - + -
967A ARG* 5.2 2.2 - - - +
972A PHE* 5.7 8.5 - + + -
974A LYS* 2.8 37.1 + - + +
979A ASN* 5.1 4.7 - - - -
981A TYR* 4.4 8.5 + - + -
982A HIS 3.6 1.4 + - - -
983A HIS 3.3 0.4 - - - -
984A ALA* 1.4 80.2 - - + +
986A ASP* 1.3 66.4 + - - +
988A TYR* 3.4 8.7 + + + +
989A LEU* 3.1 32.4 + - + +
1086A VAL* 3.8 24.4 + - + +
1087A LEU* 3.7 48.7 + - + +
1092A VAL* 5.0 12.4 - - + +
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Residues in contact with ASP 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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10A ALA* 3.7 9.2 - - + -
762A GLU* 5.3 2.9 - - - +
967A ARG* 2.7 43.7 + - - +
974A LYS* 4.5 1.0 - - - -
982A HIS* 2.6 25.4 + - - +
983A HIS 3.5 7.0 - - - +
985A HIS* 1.3 75.6 - - - +
987A ALA* 1.3 57.2 + - - +
989A LEU* 3.3 5.9 + - - +
990A ASN* 2.8 37.7 + - - +
1401A MG 2.0 35.6 - - - -
33D C 4.6 0.2 - - - +
34D A 4.8 0.2 + - - -
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Residues in contact with ALA 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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8A GLY* 3.3 30.7 - - - +
9A LEU* 3.8 4.3 - - - -
10A ALA* 3.8 2.3 - - - +
17A GLY 3.6 7.0 - - - +
18A TRP* 3.5 25.6 - - - +
19A ALA* 4.0 1.3 - - - +
983A HIS 2.9 17.1 + - - +
984A ALA 3.9 1.1 - - - +
986A ASP* 1.3 73.9 - - - +
988A TYR* 1.4 60.1 + - - +
990A ASN* 3.4 11.9 + - - +
991A ALA* 3.1 20.4 + - - +
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Residues in contact with TYR 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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19A ALA* 3.4 17.1 - - + +
20A VAL 5.4 1.6 - - - -
21A ILE* 3.6 29.2 - - + +
28A PRO* 6.0 2.0 - - + -
48A ILE* 3.6 28.5 - - + -
972A PHE* 6.3 0.2 - + - -
984A ALA 3.4 9.3 + - - +
985A HIS* 3.4 13.2 + + + +
986A ASP 3.3 0.4 - - - -
987A ALA* 1.4 77.2 - - - +
989A LEU* 1.3 69.1 + - + +
991A ALA* 3.2 6.9 + - - +
992A VAL* 3.0 43.3 + - + +
1074A TRP* 5.7 2.8 - - - -
1082A THR* 4.7 9.0 - - - +
1083A VAL* 3.5 47.4 + - + +
1086A VAL* 5.1 11.0 - - + -
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Residues in contact with LEU 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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963A VAL* 4.8 14.6 - - + -
966A PHE* 5.0 12.1 - - + -
967A ARG* 3.6 29.6 - - - +
970A PHE* 4.1 28.9 - - + -
972A PHE* 3.8 26.7 - - + -
985A HIS* 3.1 20.2 + - + +
986A ASP* 3.7 4.7 - - - +
988A TYR* 1.3 88.4 - - + +
990A ASN* 1.3 58.3 + - - +
992A VAL* 3.3 10.9 + - + +
993A VAL* 3.0 38.4 + - + +
1083A VAL* 4.4 2.9 - - + -
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Residues in contact with ASN 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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9A LEU 3.4 19.4 + - - -
10A ALA* 3.7 10.9 - - - +
760A VAL* 3.2 29.3 - - + +
762A GLU* 3.0 43.3 + - - +
958A LEU* 3.4 12.9 - - - +
963A VAL* 4.3 7.8 - - - +
986A ASP* 2.8 22.2 + - - +
987A ALA* 3.5 6.9 - - - +
988A TYR 3.3 0.2 - - - -
989A LEU* 1.3 76.6 - - - +
991A ALA* 1.4 56.9 + - - +
993A VAL* 4.0 0.5 - - - +
994A GLY 3.0 26.3 + - - -
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Residues in contact with ALA 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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6A SER* 4.3 5.3 + - - +
7A ILE* 3.9 7.2 - - - -
8A GLY* 3.6 28.4 - - - +
19A ALA 4.7 2.2 - - - +
21A ILE* 3.6 20.4 - - + -
760A VAL* 4.3 7.2 - - - -
987A ALA 3.1 10.1 + - - +
988A TYR* 3.2 8.9 + - - +
990A ASN* 1.4 74.3 - - - +
992A VAL* 1.3 61.1 + - - +
995A THR* 2.8 32.3 + - - -
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Residues in contact with VAL 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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21A ILE* 3.4 17.0 - - + -
966A PHE* 5.1 11.2 - - + -
970A PHE* 5.9 5.4 - - + -
988A TYR* 3.0 33.9 + - + +
989A LEU* 3.3 16.4 + - + +
991A ALA* 1.3 76.3 - - - +
993A VAL* 1.4 61.7 + - + +
996A ALA* 3.0 31.2 + - + +
1074A TRP* 3.4 38.6 - - + -
1083A VAL* 5.5 4.0 - - + -
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Residues in contact with VAL 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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958A LEU* 3.9 29.4 - - + -
962A LEU* 5.0 11.2 - - + +
963A VAL* 5.5 6.3 - - + -
966A PHE* 3.7 44.0 - - + -
989A LEU* 3.0 26.3 + - + +
990A ASN 4.0 2.5 - - - +
992A VAL* 1.4 71.1 - - + +
994A GLY* 1.4 66.1 + - - +
996A ALA* 3.1 7.9 + - + +
997A LEU* 3.0 39.5 + - + +
1046A PHE* 5.9 3.4 - - + -
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Residues in contact with GLY 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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758A ASN* 4.2 3.6 + - - -
760A VAL* 3.7 26.9 - - - +
956A ILE* 4.3 16.2 - - - +
958A LEU* 4.8 2.0 - - - +
990A ASN 3.0 10.9 + - - -
993A VAL* 1.4 78.2 - - - +
995A THR* 1.3 61.2 + - - +
997A LEU* 3.6 21.4 + - - +
998A ILE* 3.8 9.0 + - - +
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Residues in contact with THR 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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6A SER* 2.9 24.3 + - - +
23A ASP* 6.2 0.2 - - - +
757A GLU* 4.8 3.1 - - - +
758A ASN* 3.4 22.2 + - - +
760A VAL* 4.4 1.1 - - - +
991A ALA* 2.8 24.4 + - - -
992A VAL 3.9 2.7 - - - -
994A GLY* 1.3 73.2 - - - +
996A ALA* 1.3 63.5 + - - +
998A ILE* 3.3 10.7 - - - +
999A LYS* 3.3 38.1 - - + +
1073A VAL* 5.7 1.3 - - + -
1074A TRP* 4.6 12.8 - - + -
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Residues in contact with ALA 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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966A PHE* 6.2 2.0 - - + -
992A VAL* 3.0 21.9 + - + +
993A VAL* 3.4 8.7 - - - +
995A THR* 1.3 75.4 - - - +
997A LEU* 1.4 60.7 + - - +
998A ILE 3.4 0.5 + - - -
999A LYS* 3.6 16.9 + - - +
1000A LYS* 4.3 4.7 + - - +
1045A PHE* 4.8 5.2 - - - -
1046A PHE* 4.6 21.7 - - + -
1073A VAL* 5.4 0.2 - - - -
1074A TRP* 3.4 26.9 - - + +
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Residues in contact with LEU 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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956A ILE* 6.0 4.0 - - + -
958A LEU* 4.4 12.6 - - + -
962A LEU* 4.8 10.8 - - + -
993A VAL* 3.0 36.4 + - + +
994A GLY* 3.8 13.5 - - - +
995A THR 3.3 0.2 - - - -
996A ALA* 1.4 74.8 - - - +
998A ILE* 1.3 58.6 + - - +
999A LYS 3.6 0.2 - - - -
1000A LYS 3.4 17.5 - - - +
1002A PRO* 3.6 26.0 - - + +
1045A PHE* 3.9 26.0 - - + -
1046A PHE* 4.4 11.0 - - + -
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Residues in contact with ILE 998 (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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757A GLU* 4.4 13.7 - - + +
758A ASN* 3.7 28.9 - - - +
954A LYS* 3.5 29.2 - - + +
956A ILE* 5.3 4.3 - - + -
994A GLY 3.8 4.8 + - - +
995A THR 3.3 13.0 + - - +
997A LEU* 1.3 76.2 - - + +
999A LYS* 1.4 68.3 + - + +
1000A LYS* 3.3 5.9 + - - -
1001A TYR* 4.8 3.0 + - + +
1002A PRO* 6.3 1.8 - - + -
1068A GLU* 5.3 3.8 - - - +
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Residues in contact with LYS 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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23A ASP* 5.0 10.2 + - - -
757A GLU* 2.7 41.1 + - - +
995A THR* 3.3 31.6 + - - +
996A ALA 3.6 8.8 + - - +
998A ILE* 1.4 76.9 - - + +
1000A LYS* 1.3 56.7 + - - +
1066A ASN 5.0 1.8 - - - +
1067A GLY* 3.8 1.5 - - - -
1068A GLU* 3.1 31.9 + - - +
1073A VAL* 4.0 40.2 - - + -
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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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996A ALA 4.3 3.2 + - - +
997A LEU 3.4 12.3 - - - +
998A ILE 3.3 1.3 - - - -
999A LYS* 1.3 80.2 - - - +
1001A TYR* 1.3 73.4 + - - +
1002A PRO 3.3 2.4 - - - -
1003A LYS* 5.3 14.6 - - - +
1045A PHE* 3.5 19.0 - - + -
1065A THR* 5.4 9.3 + - - +
1066A ASN* 3.3 26.9 - - - +
1067A GLY 4.2 11.2 + - - -
1068A GLU* 3.9 17.7 - - + +
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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