Contacts of the helix formed by residues 1086 - 1103 (chain O) in PDB entry 5X0X
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 ALA1086 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059O CYS* 3.2 27.8 - - + +
1062O PRO* 3.8 8.1 - - + -
1083O TRP 3.2 1.2 + - - -
1084O ARG 2.9 6.2 - - - +
1085O VAL* 1.3 82.8 - - - +
1087O GLY* 1.3 64.0 + - - +
1088O LYS 4.0 0.7 - - - +
1089O PHE* 3.2 34.5 - - + +
1090O GLU* 3.1 23.9 + - - +
1316O ARG* 5.3 2.2 - - - -
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Residues in contact with GLY1087 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1013O CYS* 5.0 1.3 - - - -
1014O LYS 5.0 0.2 + - - -
1059O CYS* 3.0 19.3 - - - -
1086O ALA* 1.3 69.0 - - - +
1088O LYS* 1.3 58.1 + - - +
1091O LEU* 2.3 45.2 + - - +
1213O THR* 5.0 4.5 - - - -
1316O ARG* 3.1 33.0 - - - +
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Residues in contact with LYS1088 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1058O ILE 5.5 0.2 - - - +
1059O CYS* 3.9 17.8 - - + +
1060O ASN* 3.3 23.0 - - - +
1086O ALA* 3.2 1.5 - - + +
1087O GLY* 1.3 75.8 - - - +
1089O PHE* 1.3 68.7 + - + +
1091O LEU* 3.6 3.6 - - - +
1092O LEU* 2.9 37.3 + - - +
1110O PHE* 3.5 12.6 - - + -
1115O ILE* 3.5 27.6 - - + +
1119O MET* 4.8 4.3 - - + -
1181O PHE* 3.7 32.5 - - + -
1182O ASP* 2.5 43.5 + - - -
1211O LEU* 5.3 5.2 - - + -
1213O THR* 5.9 0.2 - - - +
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Residues in contact with PHE1089 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059O CYS 4.1 3.8 - - - -
1060O ASN 4.7 1.8 - - - -
1062O PRO* 4.0 20.6 - - + -
1083O TRP* 3.1 17.7 - - + +
1086O ALA* 3.2 29.9 + - + -
1087O GLY 3.4 0.4 - - - -
1088O LYS* 1.3 78.6 - - + +
1090O GLU* 1.3 69.5 + - - +
1092O LEU* 2.9 7.1 + - - +
1093O ASP 2.8 17.0 + - - -
1115O ILE* 4.2 17.7 - - + -
1118O ILE* 3.3 40.4 - - + -
1119O MET* 3.2 43.7 - - + -
1122O PHE* 2.9 35.9 - + + -
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Residues in contact with GLU1090 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083O TRP* 3.5 21.4 + - + -
1084O ARG* 3.7 12.8 - - - +
1086O ALA 3.1 13.8 + - - +
1089O PHE* 1.3 78.1 - - - +
1091O LEU* 1.3 76.1 + - - +
1093O ASP* 2.7 18.5 + - - +
1094O ARG* 2.9 34.2 + - - +
1314O LYS 3.6 17.5 - - - +
1315O SER* 3.4 27.8 - - - +
1316O ARG* 3.7 29.4 + - - +
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Residues in contact with LEU1091 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011O VAL* 5.0 2.5 - - + -
1013O CYS* 3.6 26.5 - - - -
1087O GLY 2.3 35.8 + - - +
1088O LYS* 3.6 0.9 - - - +
1090O GLU* 1.3 85.8 + - - +
1092O LEU* 1.3 58.8 + - - +
1094O ARG* 3.0 11.4 + - + +
1095O ILE* 2.9 52.4 + - + +
1211O LEU* 4.2 31.6 - - + -
1278O LEU* 5.8 4.9 - - + -
1283O ILE* 5.5 5.6 - - + -
1316O ARG* 3.8 16.6 - - - +
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Residues in contact with LEU1092 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088O LYS* 2.9 21.8 + - - +
1089O PHE* 3.4 6.3 - - - +
1091O LEU* 1.3 75.5 - - - +
1093O ASP* 1.3 59.7 + - - +
1095O ILE* 3.5 23.8 - - + -
1096O LEU* 2.8 66.8 + - + +
1108O ILE* 4.7 10.8 - - + -
1119O MET* 3.8 35.7 - - + -
1122O PHE* 3.8 7.0 - - + -
1179O ILE* 5.1 7.0 - - + -
1181O PHE* 4.5 18.4 - - + -
1211O LEU* 5.1 6.3 - - + -
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Residues in contact with ASP1093 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083O TRP* 3.5 39.1 - - + -
1089O PHE 2.8 5.1 + - - -
1090O GLU 2.7 17.7 + - - +
1092O LEU* 1.3 72.0 - - - +
1094O ARG* 1.3 61.1 + - - +
1097O PRO* 3.2 20.3 - - - +
1122O PHE* 3.3 14.7 - - + -
1125O TYR* 5.6 3.5 - - - -
1126O ILE* 4.0 19.6 - - - +
1309O GLU* 4.3 5.0 - - - +
1314O LYS* 3.5 20.3 - - - +
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Residues in contact with ARG1094 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090O GLU* 2.9 27.7 + - - +
1091O LEU* 3.2 13.0 - - + +
1093O ASP* 1.3 79.2 + - - +
1095O ILE* 1.3 69.5 + - + +
1097O PRO* 3.1 17.2 - - - +
1098O LYS* 4.3 12.6 - - - +
1278O LEU* 3.9 30.2 - - + +
1280O ASP* 3.8 27.4 + - - +
1283O ILE* 4.3 6.7 - - + -
1304O ARG* 5.4 1.6 + - - +
1308O GLU 4.5 1.6 + - - -
1309O GLU* 3.3 59.3 + - - +
1314O LYS 4.5 1.2 + - - -
1315O SER* 3.5 23.4 + - - -
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Residues in contact with ILE1095 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091O LEU* 2.9 47.7 + - + +
1092O LEU* 3.5 28.9 - - + -
1094O ARG* 1.3 77.9 - - + +
1096O LEU* 1.3 73.6 + - + +
1097O PRO 3.3 0.9 - - - -
1098O LYS* 3.3 25.9 + - - +
1099O LEU* 3.7 9.9 + - + +
1179O ILE* 4.7 15.0 - - + -
1209O LEU* 5.5 9.6 - - + -
1211O LEU* 5.6 4.3 - - + -
1283O ILE* 4.1 29.2 - - + -
1287O LEU* 4.7 7.3 - - + +
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Residues in contact with LEU1096 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092O LEU* 2.8 63.9 + - + +
1095O ILE* 1.3 76.5 - - + +
1097O PRO* 1.3 55.2 - - + +
1099O LEU* 2.6 47.1 + - + +
1100O LYS* 2.9 11.0 + - + +
1106O VAL* 4.8 7.0 - - + -
1108O ILE* 5.6 2.0 - - + -
1122O PHE* 4.2 4.9 - - + -
1123O LEU* 4.2 24.2 - - + -
1126O ILE* 5.1 1.3 - - + -
1128O ILE* 4.3 15.7 - - + -
1158O CYS* 4.2 23.1 - - - -
1179O ILE* 5.5 1.1 - - + -
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Residues in contact with PRO1097 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092O LEU 3.6 0.2 - - - +
1093O ASP* 3.2 21.3 - - - +
1094O ARG 3.1 16.6 - - - +
1095O ILE 3.3 0.4 - - - -
1096O LEU* 1.3 93.5 - - + +
1098O LYS* 1.3 62.9 + - + +
1100O LYS* 2.9 21.4 + - + +
1101O ALA* 2.9 13.0 + - - +
1126O ILE* 5.7 11.2 - - + -
1300O MET* 4.0 13.5 - - + +
1304O ARG* 5.4 6.1 - - - -
1309O GLU 6.1 0.4 - - - +
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Residues in contact with LYS1098 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094O ARG* 4.3 16.1 - - - +
1095O ILE* 3.5 13.2 - - - +
1097O PRO* 1.3 75.2 - - - +
1099O LEU* 1.3 58.4 + - - +
1101O ALA* 3.1 4.5 + - - +
1102O THR* 2.9 32.0 + - - +
1280O ASP* 3.2 26.0 + - - +
1283O ILE* 3.5 29.4 - - + +
1284O ASN* 3.2 21.0 + - - +
1287O LEU* 4.2 11.4 - - + -
1297O LEU* 3.6 17.8 - - + +
1300O MET* 3.9 10.9 - - + +
1304O ARG* 3.2 46.0 - - - +
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Residues in contact with LEU1099 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095O ILE* 4.2 9.2 - - + +
1096O LEU* 2.6 32.5 + - + +
1098O LYS* 1.3 70.4 - - - +
1100O LYS* 1.3 52.5 - - - +
1102O THR* 3.1 12.9 - - - +
1103O GLY* 2.4 38.6 + - - -
1104O HIS* 3.5 30.6 + - + +
1106O VAL* 3.6 26.9 - - + -
1157O LEU* 4.2 2.4 - - + +
1177O THR* 4.7 12.6 - - + +
1179O ILE* 5.1 6.1 - - + -
1287O LEU* 4.7 29.6 - - + +
1297O LEU* 6.0 0.7 - - + -
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Residues in contact with LYS1100 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096O LEU 2.9 6.3 + - - +
1097O PRO* 2.9 20.8 + - + +
1099O LEU* 1.3 76.7 - - - +
1101O ALA* 1.3 58.9 + - - +
1103O GLY* 3.7 6.8 + - - -
1126O ILE* 5.5 0.8 + - - +
1127O ASN 3.8 19.8 + - - -
1128O ILE* 4.6 24.4 - - + +
1129O LYS* 5.2 6.4 - - - +
1155O GLU 5.9 2.0 - - - -
1157O LEU* 3.6 27.5 - - + +
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Residues in contact with ALA1101 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097O PRO 2.9 7.1 + - - +
1098O LYS 3.4 8.3 - - - +
1100O LYS* 1.3 79.8 - - - +
1102O THR* 1.3 60.9 + - + +
1103O GLY* 3.2 1.5 + - - -
1296O VAL* 5.6 2.0 - - + +
1300O MET* 3.5 34.5 - - + -
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Residues in contact with THR1102 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1098O LYS 2.9 19.4 + - - +
1099O LEU* 3.1 12.6 - - - +
1101O ALA* 1.3 77.1 - - + +
1103O GLY* 1.3 65.1 + - - +
1104O HIS* 3.0 41.1 + - - +
1293O GLU* 5.5 3.4 - - + -
1296O VAL* 3.7 27.8 - - + -
1297O LEU* 3.7 24.5 - - + +
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Residues in contact with GLY1103 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1099O LEU 2.4 20.3 + - - -
1100O LYS 4.2 3.4 - - - -
1101O ALA 3.2 4.8 - - - -
1102O THR* 1.3 70.5 - - - +
1104O HIS* 1.3 61.2 + - - -
1105O ARG* 3.8 4.4 + - - +
1157O LEU* 4.0 25.2 - - - +
1176O ASP* 4.5 1.2 - - - +
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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