Contacts of the helix formed by residues 1189 - 1203 (chain B) in PDB entry 5JPM
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 GLY1189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1136B ASP* 3.1 27.8 + - - -
1187B LEU 3.8 0.6 + - - -
1188B LEU* 1.3 77.6 - - - +
1190B ALA* 1.3 62.0 + - - -
1191B HIS* 3.3 2.9 - - - -
1192B ALA* 3.8 3.9 - - - +
1193B ALA* 2.8 28.6 + - - +
1220B MET* 4.3 0.9 - - - -
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Residues in contact with ALA1190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1189B GLY* 1.3 72.5 - - - -
1191B HIS* 1.3 62.4 + - - +
1193B ALA* 3.5 1.6 + - - +
1194B ALA* 3.1 19.2 + - - +
1217B LEU* 4.3 2.8 - - - +
1220B MET* 4.0 22.6 - - + +
1230B TRP* 4.7 12.3 - - + -
1231B GLY 3.4 26.9 - - - +
1232B SER* 5.8 0.7 - - - -
1264B THR* 3.4 18.7 - - + +
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Residues in contact with HIS1191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1126B ARG* 4.6 12.4 + - + +
1127B SER* 6.3 0.8 - - - -
1140B ALA* 4.0 24.6 - - + +
1189B GLY* 3.3 0.6 - - - -
1190B ALA* 1.3 79.5 - - - +
1192B ALA* 1.3 62.6 + - - +
1194B ALA* 3.4 1.7 + - - +
1195B ILE* 3.2 28.3 + - + +
1260B LEU* 3.8 27.5 - - + +
1263B GLU* 3.7 32.3 + - + +
1264B THR* 3.4 28.4 - - - +
1267B TYR* 4.6 10.1 - + - -
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Residues in contact with ALA1192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1136B ASP* 3.9 41.5 - - + +
1139B VAL* 4.4 10.5 - - + +
1140B ALA* 4.5 2.5 - - + -
1188B LEU* 4.3 8.5 - - + -
1189B GLY 3.3 10.5 + - - +
1191B HIS* 1.3 84.1 + - - +
1193B ALA* 1.3 55.7 + - - +
1195B ILE* 3.3 9.2 - - - +
1196B THR* 2.6 35.3 + - - -
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Residues in contact with ALA1193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1188B LEU* 4.4 9.3 - - + +
1189B GLY 2.8 18.8 + - - +
1190B ALA 3.9 3.6 - - - +
1192B ALA* 1.3 75.6 - - - +
1194B ALA* 1.3 60.0 + - - +
1196B THR* 3.4 6.0 + - - -
1197B ALA* 3.0 28.6 + - - +
1213B ALA* 5.2 1.8 - - - +
1216B ASN* 4.0 20.2 - - - +
1217B LEU* 4.0 18.7 - - + +
1220B MET* 4.3 12.1 - - + -
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Residues in contact with ALA1194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1190B ALA 3.1 18.1 + - - +
1191B HIS 3.8 2.9 - - - +
1192B ALA 3.3 0.2 - - - -
1193B ALA* 1.3 76.8 - - - +
1195B ILE* 1.3 62.0 + - - +
1197B ALA* 3.3 4.2 + - - +
1198B TYR* 3.2 18.0 + - - +
1217B LEU* 3.8 18.7 - - + +
1264B THR* 3.3 35.2 - - + +
1267B TYR* 3.8 16.8 - - + +
1268B ALA* 4.2 4.9 - - + +
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Residues in contact with ILE1195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1140B ALA* 3.5 33.9 - - + +
1143B ALA* 3.8 10.8 - - + -
1144B PHE* 3.7 22.7 - - + +
1147B ILE* 3.8 16.5 - - + +
1191B HIS* 3.2 18.2 + - + +
1192B ALA* 3.3 17.5 - - - +
1194B ALA* 1.3 76.0 - - - +
1196B THR* 1.3 63.6 + - - +
1198B TYR 3.5 1.1 + - - +
1199B ALA* 2.9 26.9 + - - +
1267B TYR* 3.9 39.4 - - + +
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Residues in contact with THR1196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1139B VAL* 3.5 19.4 - - - +
1143B ALA* 4.1 11.5 - - - +
1179B LEU* 4.3 16.4 - - + +
1183B ALA* 4.3 22.7 - - + -
1188B LEU* 4.4 4.2 - - + +
1192B ALA 2.6 24.8 + - - -
1193B ALA* 3.7 7.4 - - - -
1194B ALA 3.2 0.2 - - - -
1195B ILE* 1.3 75.6 - - - +
1197B ALA* 1.3 60.6 + - - +
1199B ALA* 3.3 1.2 + - - +
1200B LEU* 2.9 46.5 + - + +
1213B ALA* 5.1 2.7 - - + -
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Residues in contact with ALA1197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1193B ALA 3.0 17.2 + - - +
1194B ALA 3.3 5.6 + - - +
1196B THR* 1.3 78.1 - - - +
1198B TYR* 1.3 55.6 + - - +
1200B LEU* 3.5 2.0 + - - +
1201B SER* 2.8 33.1 + - - -
1213B ALA* 4.5 21.0 - - + +
1217B LEU* 3.8 14.6 - - + -
1271B HIS* 3.1 30.3 + - + +
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Residues in contact with TYR1198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084B LYS* 6.3 1.1 - - - -
1147B ILE* 3.5 40.8 - - + -
1151B HIS* 4.4 7.9 + + - -
1194B ALA 3.2 11.3 + - - +
1195B ILE 4.0 2.9 - - - +
1197B ALA* 1.3 73.7 - - - +
1199B ALA* 1.3 57.1 + - - +
1201B SER* 4.3 1.3 - - - -
1202B LEU* 2.7 61.9 + - + +
1267B TYR* 3.8 33.4 - + + +
1270B LEU* 3.5 57.5 - - + +
1271B HIS* 3.7 6.4 - - - +
1274B LEU* 4.4 14.5 - - + +
1310B ASP* 5.6 1.7 + - - -
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Residues in contact with ALA1199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1143B ALA* 3.8 11.7 - - + +
1146B THR* 3.7 23.9 + - - +
1147B ILE* 3.7 17.7 - - + +
1176B ASN* 5.1 0.6 - - - +
1179B LEU* 4.4 1.8 - - + -
1195B ILE 2.9 19.2 + - - +
1196B THR* 3.3 4.7 + - - +
1198B TYR* 1.3 77.5 - - - +
1200B LEU* 1.3 59.4 + - + +
1201B SER 3.2 0.2 - - - -
1202B LEU* 4.8 0.2 - - - -
1203B THR* 2.4 41.3 + - - +
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Residues in contact with LEU1200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1176B ASN* 4.5 13.2 - - + +
1179B LEU* 3.9 33.0 - - + +
1180B GLY* 4.7 13.0 - - - -
1183B ALA* 5.2 2.2 - - + -
1196B THR* 2.9 26.4 + - + +
1197B ALA* 3.7 4.7 - - - +
1199B ALA* 1.3 75.7 - - - +
1201B SER* 1.3 56.7 + - - +
1203B THR* 2.9 19.9 - - - +
1205B ALA* 3.4 24.5 + - + +
1209B LEU* 3.9 37.9 - - + +
1210B LEU* 3.9 14.5 - - - +
1213B ALA* 4.2 13.7 - - + -
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Residues in contact with SER1201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1197B ALA 2.8 12.2 + - - -
1198B TYR* 3.9 5.2 - - - -
1199B ALA 3.2 0.2 - - - -
1200B LEU* 1.3 79.3 + - - +
1202B LEU* 1.3 65.9 + - - +
1203B THR 3.4 5.1 - - - +
1204B LYS* 4.2 12.1 - - - +
1210B LEU* 4.8 13.6 - - - +
1271B HIS* 2.8 37.4 + - - -
1274B LEU* 3.4 29.3 - - - +
1275B HIS* 4.4 5.8 - - - +
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Residues in contact with LEU1202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1147B ILE* 3.7 24.5 - - + +
1150B HIS* 3.4 42.1 + - + +
1151B HIS* 3.5 33.4 - - + +
1198B TYR* 2.7 42.5 + - + +
1199B ALA* 4.3 2.0 - - - +
1201B SER* 1.3 75.3 - - - +
1203B THR* 1.3 59.9 + - + +
1204B LYS* 3.7 11.8 + - - +
1274B LEU* 3.6 16.7 - - + +
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Residues in contact with THR1203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1146B THR* 4.5 8.7 - - - +
1147B ILE* 5.8 0.4 - - - -
1150B HIS* 3.6 37.5 - - + -
1172B ILE* 3.9 22.2 - - + -
1176B ASN* 3.3 25.6 + - - +
1199B ALA 2.4 24.1 + - - +
1200B LEU* 2.9 17.5 - - - +
1201B SER 3.6 1.9 - - - -
1202B LEU* 1.3 76.7 - - + +
1204B LYS* 1.3 55.0 + - - +
1205B ALA 2.7 15.6 + - - -
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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