Contacts of the helix formed by residues 1176 - 1190 (chain M) in PDB entry 6G0L
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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1174M ASN* 3.8 22.9 - - - +
1175M TRP* 1.3 84.2 - - - +
1177M LYS* 1.3 64.8 + - - +
1178M GLU* 3.3 13.5 + - - +
1179M GLU* 2.5 31.8 + - - +
1180M ASP* 3.3 22.1 + - - +
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Residues in contact with LYS1177 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1160M LEU* 4.7 15.5 - - + -
1161M GLY 2.8 30.2 + - - +
1162M ASN* 3.9 7.7 - - - +
1163M ASN 4.4 8.7 - - - +
1164M THR* 3.7 26.2 + - - +
1176M THR* 1.3 75.7 - - - +
1178M GLU* 1.3 62.3 + - + +
1180M ASP* 3.0 11.9 + - - +
1181M GLU* 2.9 49.0 + - + +
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Residues in contact with GLU1178 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1176M THR* 3.3 11.3 + - - +
1177M LYS* 1.3 81.2 - - + +
1179M GLU* 1.3 61.7 + - - +
1181M GLU* 3.3 21.1 + - - +
1182M LYS* 2.9 47.7 + - + +
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Residues in contact with GLU1179 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1174M ASN* 4.4 10.4 + - - +
1175M TRP* 3.6 46.8 - - + -
1176M THR* 2.5 42.2 + - - +
1177M LYS 3.2 0.2 - - - -
1178M GLU* 1.3 78.2 - - - +
1180M ASP* 1.3 57.2 + - - +
1182M LYS* 4.5 3.5 - - - +
1183M LEU* 2.9 32.6 + - - +
1204M LEU 6.0 1.6 - - - +
1206M ILE* 4.4 17.5 - - + +
1209M LYS* 4.6 8.8 - - + -
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Residues in contact with ASP1180 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1160M LEU* 4.4 15.4 - - + +
1165M PRO* 4.0 20.1 - - + +
1175M TRP* 2.5 37.0 + - - -
1176M THR 3.3 12.1 - - - +
1177M LYS* 3.0 14.1 + - - +
1179M GLU* 1.3 77.0 - - - +
1181M GLU* 1.3 61.2 + - - +
1183M LEU* 3.7 7.3 + - - +
1184M LEU* 3.5 25.6 + - - +
1256M ARG* 4.8 2.0 + - - -
1260M LEU* 3.9 27.9 - - + +
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Residues in contact with GLU1181 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1158M PHE* 3.2 31.1 - - + +
1159M SER* 3.6 20.3 + - - -
1160M LEU* 3.4 35.4 + - + -
1161M GLY 4.8 0.5 + - - -
1177M LYS* 2.9 36.3 + - + +
1178M GLU* 3.3 24.8 + - - +
1180M ASP* 1.3 80.3 - - - +
1182M LYS* 1.3 66.3 + - + +
1183M LEU 3.5 0.3 + - - -
1184M LEU* 3.6 12.6 + - - +
1185M ILE* 3.7 12.9 + - - +
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Residues in contact with LYS1182 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1156M LEU* 2.9 46.1 + - - +
1158M PHE 5.9 2.2 + - - -
1178M GLU* 2.9 34.5 + - + +
1179M GLU* 4.5 3.4 - - - +
1181M GLU* 1.3 79.3 - - + +
1183M LEU* 1.3 63.2 + - - +
1184M LEU 3.3 0.4 - - - -
1185M ILE* 3.4 24.5 + - + +
1186M GLY 4.0 1.4 + - - -
1203M PHE 4.6 11.8 + - - +
1204M LEU* 3.3 48.2 - - + +
1206M ILE* 6.0 1.1 - - + -
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Residues in contact with LEU1183 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1175M TRP* 3.6 32.1 - - + -
1179M GLU 2.9 19.6 + - - +
1180M ASP 3.9 5.4 - - - +
1181M GLU 3.2 0.6 - - - -
1182M LYS* 1.3 78.4 - - - +
1184M LEU* 1.3 60.6 + - + +
1185M ILE 3.4 0.7 + - - -
1186M GLY* 3.6 8.8 + - - -
1187M VAL* 3.7 11.9 + - + +
1195M TRP* 4.1 27.6 - - + -
1198M ILE* 4.8 7.6 - - + +
1204M LEU* 5.5 0.9 - - - -
1206M ILE* 4.6 17.9 - - + -
1210M ILE* 5.7 0.2 - - + -
1253M LEU* 5.4 1.1 - - + +
1256M ARG* 5.3 4.3 - - + -
1257M VAL* 3.7 27.1 - - + +
1260M LEU* 3.9 17.3 - - + -
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Residues in contact with LEU1184 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1143M LEU* 4.2 19.6 - - + +
1146M LEU* 5.8 0.7 - - + -
1147M ILE* 5.6 5.8 - - + -
1158M PHE* 4.8 9.4 - - + -
1160M LEU* 4.7 12.1 - - + -
1180M ASP 3.5 16.1 + - - +
1181M GLU* 3.6 7.7 + - - +
1182M LYS 3.3 0.8 - - - -
1183M LEU* 1.3 77.0 - - + +
1185M ILE* 1.3 60.9 + - + +
1186M GLY 3.4 0.2 - - - -
1187M VAL* 3.4 7.9 + - + +
1188M PHE* 2.9 28.5 + - - +
1257M VAL* 4.4 17.0 - - + -
1260M LEU* 4.6 17.5 - - + -
1261M LEU* 4.0 23.1 - - + -
1264M LEU* 3.8 28.7 - - + -
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Residues in contact with ILE1185 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1147M ILE* 6.3 2.7 - - + -
1155M PRO* 3.4 35.0 - - + +
1156M LEU* 4.0 20.0 - - + -
1158M PHE* 5.9 4.3 - - + +
1181M GLU 3.7 13.0 - - - +
1182M LYS* 3.5 39.0 - - + +
1183M LEU 3.2 1.0 - - - -
1184M LEU* 1.3 76.1 - - - +
1186M GLY* 1.3 60.3 + - - +
1188M PHE* 3.1 7.3 + - + +
1189M LYS* 2.9 49.9 + - + +
1201M ASP* 5.6 2.0 - - - +
1204M LEU* 4.4 9.9 - - + -
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Residues in contact with GLY1186 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1182M LYS 4.0 3.4 + - - -
1183M LEU 3.6 6.9 + - - -
1184M LEU 3.4 0.6 - - - -
1185M ILE* 1.3 79.7 - - - +
1187M VAL* 1.3 57.1 + - - +
1189M LYS* 4.8 0.9 - - - -
1190M TYR* 2.9 39.6 + - - +
1191M GLY 3.2 5.0 + - - +
1198M ILE* 4.3 22.6 - - - +
1201M ASP* 5.6 2.2 - - - -
1204M LEU* 4.9 10.3 - - - +
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Residues in contact with VAL1187 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1140M LEU* 4.4 12.6 - - + +
1143M LEU* 3.9 17.9 - - + +
1144M LYS* 5.3 1.6 + - - -
1183M LEU* 3.7 15.3 - - + +
1184M LEU* 3.4 9.4 + - + +
1185M ILE 3.3 0.4 - - - -
1186M GLY* 1.3 75.7 - - - +
1188M PHE* 1.3 62.2 + - - +
1191M GLY* 3.2 24.5 - - - +
1192M TYR* 3.8 30.1 - - + +
1195M TRP* 5.9 1.8 - - + -
1198M ILE* 4.9 8.3 - - + -
1257M VAL* 3.9 32.8 - - + -
1261M LEU* 5.3 5.6 - - + -
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Residues in contact with PHE1188 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1143M LEU* 3.8 17.4 - - + +
1144M LYS* 2.7 64.6 + - + +
1147M ILE* 3.6 43.5 - - + -
1148M ASN* 3.2 26.0 - - - -
1151M TYR 5.6 0.4 - - - -
1152M LYS 6.2 0.2 - - - -
1155M PRO* 5.0 14.6 - - + -
1184M LEU 2.9 17.5 + - - +
1185M ILE* 3.1 8.4 + - - +
1187M VAL* 1.3 78.4 - - - +
1189M LYS* 1.3 71.3 + - + +
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Residues in contact with LYS1189 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343M ASN* 6.1 2.4 - - - +
1025M PHE* 4.8 8.0 - - - -
1144M LYS* 5.2 0.7 + - - -
1155M PRO* 5.7 7.4 - - + -
1185M ILE* 2.9 36.4 + - + +
1186M GLY* 5.4 0.7 - - - -
1188M PHE* 1.3 94.4 - - + +
1190M TYR* 1.3 89.9 + - + +
1201M ASP* 5.0 10.4 + - - +
1203M PHE* 5.3 11.7 - - - -
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Residues in contact with TYR1190 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339M GLN* 3.8 21.7 + - - +
343M ASN* 4.1 24.4 + - - -
1024M LYS* 4.0 2.4 - - - +
1025M PHE* 3.7 25.9 - - - -
1186M GLY* 2.9 22.7 + - - +
1189M LYS* 1.3 100.4 + - + +
1191M GLY* 1.3 60.8 + - - +
1194M SER* 4.0 27.6 + - - +
1197M GLN* 3.6 51.0 + - + +
1198M ILE* 5.1 2.9 - - + -
1201M ASP* 4.8 16.4 - - + +
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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