Contacts of the helix formed by residues 1176 - 1190 (chain W) in PDB entry 5O9G
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 THR1176 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1174W ASN* 3.8 22.2 - - - +
1175W TRP* 1.3 83.6 - - - +
1177W LYS* 1.3 66.0 + - - +
1178W GLU* 3.3 13.0 + - - +
1179W GLU* 2.5 32.3 + - - +
1180W ASP* 3.3 21.9 + - - +
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Residues in contact with LYS1177 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1160W LEU* 4.7 15.7 - - + -
1161W GLY 2.8 30.2 + - - +
1162W ASN* 3.9 8.5 - - - +
1163W ASN 4.4 8.1 - - - +
1164W THR* 3.8 26.3 + - - +
1165W PRO* 6.2 1.6 - - + -
1176W THR* 1.3 75.5 - - - +
1178W GLU* 1.3 63.1 + - + +
1180W ASP* 3.0 12.1 + - - +
1181W GLU* 2.9 48.0 + - + +
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Residues in contact with GLU1178 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1176W THR* 3.3 11.8 - - - +
1177W LYS* 1.3 80.8 - - + +
1179W GLU* 1.3 60.9 + - - +
1181W GLU* 3.3 22.3 + - - +
1182W LYS* 2.9 47.6 + - + +
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Residues in contact with GLU1179 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1174W ASN* 4.4 11.4 + - - +
1175W TRP* 3.6 46.9 - - + -
1176W THR* 2.5 41.9 + - - +
1177W LYS 3.2 0.2 - - - -
1178W GLU* 1.3 78.4 - - - +
1180W ASP* 1.3 58.2 + - - +
1182W LYS* 4.5 3.8 - - - +
1183W LEU* 2.9 32.1 + - - +
1204W LEU 6.0 1.8 - - - +
1206W ILE* 4.4 17.2 - - + +
1209W LYS* 4.6 8.8 - - + -
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Residues in contact with ASP1180 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1160W LEU* 4.3 15.6 - - + +
1165W PRO* 4.0 20.6 - - + +
1175W TRP* 2.5 37.3 + - - -
1176W THR 3.3 12.2 + - - +
1177W LYS* 3.0 14.6 + - + +
1179W GLU* 1.3 77.9 - - - +
1181W GLU* 1.3 61.8 + - - +
1183W LEU* 3.7 7.9 + - - +
1184W LEU* 3.5 24.9 + - - +
1256W ARG* 4.8 1.9 + - - -
1260W LEU* 3.9 27.7 - - + +
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Residues in contact with GLU1181 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1158W PHE* 3.2 30.1 - - + +
1159W SER* 3.6 20.9 + - - -
1160W LEU* 3.4 36.6 + - + -
1161W GLY 4.8 0.5 + - - -
1177W LYS* 2.9 36.7 + - + +
1178W GLU* 3.7 25.3 - - - +
1180W ASP* 1.3 80.0 - - - +
1182W LYS* 1.3 67.4 + - + +
1183W LEU 3.5 0.5 + - - -
1184W LEU* 3.6 12.5 + - - +
1185W ILE* 3.7 12.4 + - - +
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Residues in contact with LYS1182 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1156W LEU* 2.9 46.3 + - - +
1158W PHE 5.8 2.4 + - - +
1178W GLU* 2.9 33.2 + - + +
1179W GLU* 4.5 3.6 - - - +
1181W GLU* 1.3 78.5 - - + +
1183W LEU* 1.3 63.4 + - - +
1184W LEU 3.3 0.4 - - - -
1185W ILE* 3.4 24.8 + - + +
1186W GLY 4.0 1.6 + - - -
1203W PHE 4.6 11.4 + - - +
1204W LEU* 3.3 47.4 - - + +
1206W ILE* 6.0 0.9 - - + -
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Residues in contact with LEU1183 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1175W TRP* 3.6 31.4 - - + -
1179W GLU 2.9 19.0 + - - +
1180W ASP 3.9 4.9 - - - +
1181W GLU 3.2 0.6 - - - -
1182W LYS* 1.3 80.4 - - - +
1184W LEU* 1.3 60.9 + - + +
1185W ILE 3.4 0.9 + - - -
1186W GLY* 3.6 8.8 + - - -
1187W VAL* 3.7 11.9 + - + +
1195W TRP* 4.1 27.4 - - + -
1198W ILE* 4.8 7.7 - - + +
1204W LEU* 5.5 1.3 - - - -
1206W ILE* 4.6 18.6 - - + -
1210W ILE* 5.7 0.2 - - + -
1253W LEU* 5.4 1.8 - - + +
1256W ARG* 5.3 4.9 - - + -
1257W VAL* 3.7 26.2 - - + +
1260W LEU* 3.9 16.8 - - + -
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Residues in contact with LEU1184 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1143W LEU* 4.2 19.6 - - + +
1146W LEU* 5.8 0.9 - - + -
1147W ILE* 5.6 5.3 - - + +
1158W PHE* 4.8 10.1 - - + -
1160W LEU* 4.7 12.1 - - + -
1180W ASP 3.5 16.2 - - - +
1181W GLU* 3.6 7.7 + - - +
1182W LYS 3.3 0.6 - - - -
1183W LEU* 1.3 77.1 - - + +
1185W ILE* 1.3 59.7 + - - +
1186W GLY 3.4 0.2 - - - -
1187W VAL* 3.4 7.4 + - + +
1188W PHE* 2.9 28.7 + - - +
1257W VAL* 4.4 17.5 - - + -
1260W LEU* 4.6 17.7 - - + -
1261W LEU* 4.0 23.1 - - + -
1264W LEU* 3.8 28.5 - - + -
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Residues in contact with ILE1185 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1147W ILE* 6.3 2.9 - - + -
1155W PRO* 3.4 34.3 - - + +
1156W LEU* 4.0 20.6 - - + -
1158W PHE* 5.9 4.0 - - + +
1181W GLU 3.7 12.8 - - - +
1182W LYS* 3.5 39.0 - - + +
1183W LEU 3.2 1.0 - - - -
1184W LEU* 1.3 75.2 - - - +
1186W GLY* 1.3 60.4 + - - +
1188W PHE* 3.1 7.0 + - + +
1189W LYS* 2.9 49.8 + - + +
1201W ASP* 5.6 2.0 - - - +
1204W LEU* 4.4 10.3 - - + -
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Residues in contact with GLY1186 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1182W LYS 4.0 3.8 + - - -
1183W LEU 3.6 6.8 + - - -
1184W LEU 3.4 0.4 - - - -
1185W ILE* 1.3 78.1 - - - +
1187W VAL* 1.3 58.7 + - - +
1189W LYS* 4.8 1.3 - - - -
1190W TYR* 2.9 40.4 + - - +
1191W GLY 3.2 5.4 + - - +
1198W ILE* 4.3 22.8 - - - +
1201W ASP* 5.6 2.2 - - - -
1204W LEU* 4.9 10.3 - - - +
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Residues in contact with VAL1187 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1140W LEU* 4.4 12.4 - - + +
1143W LEU* 3.9 17.3 - - + +
1144W LYS* 5.3 1.6 + - - -
1183W LEU* 3.7 15.3 - - + +
1184W LEU* 3.4 10.0 + - + +
1185W ILE 3.3 0.4 - - - -
1186W GLY* 1.3 77.7 - - - +
1188W PHE* 1.3 61.2 + - - +
1191W GLY* 3.2 24.6 - - - +
1192W TYR* 3.8 29.4 - - + +
1195W TRP* 5.9 1.8 - - + -
1198W ILE* 4.9 8.5 - - + -
1257W VAL* 3.9 32.3 - - + -
1261W LEU* 5.3 5.8 - - + -
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Residues in contact with PHE1188 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1143W LEU* 3.8 18.1 - - + +
1144W LYS* 2.7 63.3 + - + +
1147W ILE* 3.6 42.2 - - + -
1148W ASN* 3.2 26.0 - - - -
1151W TYR 5.6 0.4 - - - -
1152W LYS 6.2 0.4 - - - -
1155W PRO* 5.0 14.1 - - + -
1184W LEU 2.9 18.8 + - - +
1185W ILE* 3.1 8.0 + - - +
1187W VAL* 1.3 78.7 - - - +
1189W LYS* 1.3 71.5 + - + +
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Residues in contact with LYS1189 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343W ASN* 6.1 2.4 - - - +
1025W PHE* 4.8 7.8 - - - -
1144W LYS* 5.2 0.9 + - - -
1155W PRO* 5.7 7.4 - - + -
1185W ILE* 2.9 35.8 + - + +
1186W GLY* 5.4 0.7 - - - -
1188W PHE* 1.3 92.8 - - + +
1190W TYR* 1.3 90.9 + - + +
1201W ASP* 5.0 10.0 + - - +
1203W PHE* 5.3 11.7 - - - -
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Residues in contact with TYR1190 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339W GLN* 3.8 21.5 + - - +
343W ASN* 4.1 24.4 + - - -
1024W LYS* 4.0 2.3 - - - +
1025W PHE* 3.7 26.3 - - - -
1186W GLY* 2.9 22.9 + - - +
1189W LYS* 1.3 98.8 + - + +
1191W GLY* 1.3 59.4 + - - +
1194W SER* 4.0 27.5 + - - +
1197W GLN* 3.6 50.5 + - + +
1198W ILE* 5.1 3.1 - - + -
1201W ASP* 4.8 15.9 - - - +
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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