Contacts of the helix formed by residues 1258 - 1276 (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 PRO1258 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1256B GLN 4.3 2.2 - - - +
1257B ALA* 1.3 94.1 - - + +
1259B ALA* 1.3 66.7 + - - +
1260B LEU* 3.2 5.8 - - + +
1261B TRP* 3.2 51.8 + - + +
1262B ILE* 3.4 10.9 + - - +
1300B ARG* 4.7 2.0 - - + -
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Residues in contact with ALA1259 (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* 4.4 12.3 + - - +
1258B PRO* 1.3 73.2 - - - +
1260B LEU* 1.3 62.8 + - - +
1262B ILE* 3.3 6.1 + - - +
1263B GLU* 3.1 23.2 + - - +
1300B ARG* 3.6 24.2 - - + +
1301B SER* 5.0 3.8 - - - +
1304B ASP* 3.4 26.2 - - - +
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Residues in contact with LEU1260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1126B ARG* 4.1 47.2 - - + +
1127B SER* 5.8 2.5 - - - -
1128B MET 5.9 2.9 - - - +
1191B HIS* 3.8 37.0 - - + +
1232B SER* 4.9 13.7 - - - +
1258B PRO* 3.2 5.6 - - + +
1259B ALA* 1.3 78.7 - - - +
1261B TRP* 1.3 73.1 + - + +
1263B GLU* 3.5 0.9 + - - +
1264B THR* 2.8 32.1 + - - +
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Residues in contact with TRP1261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1222B GLN* 5.5 2.7 - - - -
1229B TYR* 4.2 28.5 - + - -
1230B TRP 3.7 14.2 - - - +
1231B GLY* 3.5 17.7 - - - -
1232B SER* 3.3 39.9 - - - +
1234B THR* 5.8 4.7 - - + -
1257B ALA* 3.8 24.7 - - + -
1258B PRO* 3.2 34.0 + - + +
1260B LEU* 1.3 85.2 - - + +
1262B ILE* 1.3 66.1 + - - +
1264B THR* 3.3 2.6 + - - -
1265B THR* 3.1 28.4 + - - +
1288B TRP* 4.3 7.6 - + + -
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Residues in contact with ILE1262 (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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1257B ALA* 3.9 10.5 - - + +
1258B PRO 3.4 14.8 - - - +
1259B ALA 3.3 6.8 + - - +
1261B TRP* 1.3 77.4 - - - +
1263B GLU* 1.3 60.0 + - - +
1265B THR* 3.3 6.0 - - - +
1266B ALA* 3.1 23.4 + - - +
1288B TRP* 3.9 11.0 - - + -
1289B LEU* 3.9 10.7 - - + +
1292B GLN* 3.7 42.8 - - + +
1299B PHE* 3.6 28.0 - - + -
1300B ARG* 4.3 13.9 - - + +
1304B ASP* 4.2 12.3 - - + -
1308B ALA* 4.1 9.6 - - + -
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Residues in contact with GLU1263 (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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1077B TRP* 5.9 0.2 - - - -
1124B LEU* 5.0 2.9 - - - +
1126B ARG* 2.7 39.0 + - - +
1144B PHE* 6.1 0.2 - - - -
1191B HIS* 3.7 17.4 + - + +
1259B ALA 3.1 14.8 + - - +
1260B LEU 4.0 3.4 - - - +
1262B ILE* 1.3 75.1 - - - +
1264B THR* 1.3 65.9 + - - +
1266B ALA* 3.5 5.9 + - - +
1267B TYR* 3.2 33.4 + - + -
1303B GLN* 3.7 17.3 - - - +
1304B ASP* 3.9 12.2 + - + +
1307B ILE* 3.5 34.1 - - + +
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Residues in contact with THR1264 (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* 3.4 32.5 - - + +
1191B HIS* 3.4 26.1 + - - +
1194B ALA* 3.3 17.1 - - + +
1230B TRP* 3.6 28.9 - - + +
1260B LEU* 2.8 25.1 + - - +
1261B TRP* 3.8 4.2 - - - -
1262B ILE 3.3 0.2 - - - -
1263B GLU* 1.3 77.4 - - - +
1265B THR* 1.3 62.7 + - - +
1267B TYR* 3.3 2.6 + - - -
1268B ALA* 3.1 17.7 + - - +
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Residues in contact with THR1265 (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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1228B LEU 3.9 11.4 + - - -
1230B TRP* 3.8 34.2 - - - +
1261B TRP 3.1 19.7 + - - +
1262B ILE 3.3 8.1 - - - +
1264B THR* 1.3 74.4 - - - +
1266B ALA* 1.3 62.2 + - - +
1268B ALA* 3.7 1.1 - - - +
1269B LEU* 2.9 28.9 + - - +
1285B ALA* 4.4 2.8 - - - +
1288B TRP* 3.5 25.5 - - + -
1289B LEU* 3.6 24.7 - - + +
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Residues in contact with ALA1266 (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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1262B ILE 3.1 20.3 + - - +
1263B GLU* 3.7 6.3 - - - +
1264B THR 3.2 0.2 - - - -
1265B THR* 1.3 75.8 - - - +
1267B TYR* 1.3 60.2 + - - +
1269B LEU* 3.3 2.2 + - - -
1270B LEU* 3.0 27.1 + - - +
1289B LEU* 4.8 5.6 - - + -
1307B ILE* 3.7 30.3 - - + +
1308B ALA* 3.8 14.4 - - + +
1311B ALA* 3.4 16.5 - - + +
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Residues in contact with TYR1267 (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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1144B PHE* 3.5 27.2 - - - -
1147B ILE* 4.5 5.3 - - + +
1191B HIS* 4.6 7.9 - + - -
1194B ALA* 3.8 18.6 - - + +
1195B ILE* 3.9 36.1 - - + -
1198B TYR* 3.8 34.6 - + + +
1263B GLU* 3.2 29.9 + - + -
1264B THR* 3.3 7.6 + - - +
1266B ALA* 1.3 78.9 - - - +
1268B ALA* 1.3 58.4 + - - +
1270B LEU* 3.3 8.5 + - + +
1271B HIS* 2.9 28.8 + - - +
1307B ILE* 3.3 43.1 - - + +
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Residues in contact with ALA1268 (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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1194B ALA* 4.2 2.8 - - + +
1217B LEU* 3.9 23.8 - - + -
1230B TRP* 3.6 39.0 - - + -
1264B THR 3.1 16.3 + - - +
1265B THR 3.7 2.5 - - - +
1266B ALA 3.3 0.4 - - - -
1267B TYR* 1.3 75.4 - - - +
1269B LEU* 1.3 57.6 + - - +
1271B HIS* 3.3 3.2 + - - +
1272B LEU* 2.9 36.6 + - + +
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Residues in contact with LEU1269 (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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1230B TRP* 5.4 0.6 - - - -
1265B THR 2.9 18.6 + - - +
1266B ALA* 3.7 4.7 - - - +
1267B TYR 3.3 0.4 - - - -
1268B ALA* 1.3 73.7 - - - +
1270B LEU* 1.3 66.1 + - - +
1272B LEU* 3.1 6.3 + - + -
1273B LEU* 3.1 37.7 + - + +
1282B ALA* 3.6 32.8 - - + +
1285B ALA* 4.1 15.0 - - + -
1286B SER* 3.3 31.0 - - - +
1289B LEU* 5.0 4.9 - - + -
1311B ALA* 3.3 35.9 - - + +
1312B LEU* 5.1 1.1 - - + -
1315B TYR* 4.0 1.3 - - + -
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Residues in contact with LEU1270 (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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1026B ARG* 5.8 0.2 - - - +
1198B TYR* 3.5 40.5 - - + +
1266B ALA 3.0 21.2 + - - +
1267B TYR* 3.7 14.8 - - + +
1269B LEU* 1.3 76.9 - - - +
1271B HIS* 1.3 61.9 + - - +
1272B LEU 3.5 0.2 + - - -
1273B LEU* 3.5 4.7 + - + +
1274B LEU* 3.4 31.9 + - + +
1307B ILE* 4.5 9.0 - - + +
1310B ASP* 3.9 20.9 - - + +
1311B ALA* 3.7 31.2 - - + +
1314B ALA* 4.0 15.9 - - + -
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Residues in contact with HIS1271 (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* 3.1 26.6 + - + +
1198B TYR* 3.7 21.9 - - - +
1201B SER* 2.8 30.1 + - - -
1210B LEU 4.8 3.6 - - - -
1213B ALA* 5.9 0.4 - - + -
1214B HIS* 3.1 41.4 + - + +
1217B LEU* 4.0 10.5 - - + -
1267B TYR 2.9 17.4 + - - +
1268B ALA* 3.6 4.0 - - - +
1270B LEU* 1.3 75.5 - - - +
1272B LEU* 1.3 76.7 + - + +
1274B LEU* 3.5 1.6 + - - +
1275B HIS* 3.0 44.2 + + + +
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Residues in contact with LEU1272 (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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1214B HIS* 4.4 8.7 - - + -
1218B MET* 3.6 22.0 - - + -
1230B TRP* 4.8 11.2 - - + -
1268B ALA 2.9 23.5 + - - +
1269B LEU* 3.1 15.2 + - + +
1271B HIS* 1.3 95.4 - - + +
1273B LEU* 1.3 56.6 + - - +
1275B HIS* 4.7 2.5 - - - -
1276B GLU* 2.8 38.8 + - + +
1277B GLY 3.0 7.3 + - - +
1281B MET* 3.8 44.9 - - + +
1282B ALA* 3.8 8.3 - - + +
1285B ALA* 4.8 4.3 - - + -
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Residues in contact with LEU1273 (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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1269B LEU* 3.1 27.8 + - + +
1270B LEU* 4.0 6.7 - - + +
1271B HIS 3.4 0.2 - - - -
1272B LEU* 1.3 76.7 - - - +
1274B LEU* 1.3 66.9 + - + +
1277B GLY* 3.0 40.9 + - - +
1278B LYS* 4.3 4.3 - - - +
1282B ALA* 4.1 16.6 - - + -
1314B ALA* 3.6 20.6 - - + +
1315B TYR* 3.5 43.1 - - + +
1318B ALA* 4.6 9.2 - - + -
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Residues in contact with LEU1274 (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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1198B TYR* 4.4 12.3 - - + +
1201B SER* 3.4 32.5 - - - +
1202B LEU* 3.6 28.3 - - + +
1204B LYS* 5.8 3.4 - - - -
1270B LEU* 3.4 22.4 + - + +
1271B HIS 4.1 2.2 - - - +
1272B LEU 3.3 0.2 - - - -
1273B LEU* 1.3 84.0 - - + +
1275B HIS* 1.3 63.0 + - - +
1276B GLU 5.2 0.2 - - - -
1277B GLY 4.9 0.2 + - - -
1314B ALA* 6.5 1.1 - - + -
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Residues in contact with HIS1275 (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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1201B SER* 4.4 4.2 + - - +
1210B LEU* 3.5 36.8 - - + +
1211B GLY* 5.1 4.0 - - - -
1214B HIS* 3.8 43.1 + + + -
1271B HIS* 3.0 37.1 + + + +
1272B LEU* 4.2 2.2 - - - +
1274B LEU* 1.3 79.6 - - - +
1276B GLU* 1.3 69.5 + - + +
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Residues in contact with GLU1276 (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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1214B HIS* 5.7 6.4 + - + -
1272B LEU* 2.8 22.8 + - + +
1274B LEU 5.1 0.2 - - - -
1275B HIS* 1.3 87.6 - - + +
1277B GLY* 1.3 60.4 + - - +
1278B LYS 4.9 1.6 - - - +
1279B ALA* 3.3 27.4 - - + +
1281B MET* 4.7 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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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