Contacts of the helix formed by residues 1227 - 1239 (chain B) in PDB entry 1CJY
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 LEU1227 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1194B GLY 3.4 5.3 + - - -
1195B SER 3.3 9.7 - - - +
1196B GLY* 3.4 11.0 - - - +
1226B GLY* 1.3 75.9 - - - +
1228B SER* 1.3 85.9 + - - +
1229B GLY 3.1 3.3 + - - -
1230B SER* 3.2 10.4 + - - -
1231B THR* 4.0 4.9 + - - -
1330B THR* 3.9 16.6 - - + +
1346B TRP* 4.0 3.1 - - + -
1549B ASP* 4.2 0.4 - - - +
1550B SER* 3.9 17.0 - - - -
1551B GLY* 3.9 14.6 - - - +
1554B PHE 3.7 10.8 - - - +
1555B ASN* 3.5 32.3 - - - +
1556B LEU 3.7 0.9 - - - -
1557B PRO* 3.5 31.6 - - + -
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Residues in contact with SER1228 (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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1196B GLY* 3.6 7.0 - - - -
1197B GLY 4.0 6.9 + - - -
1227B LEU* 1.3 82.1 - - - +
1229B GLY* 1.3 66.0 + - - -
1231B THR* 2.8 35.7 + - - +
1232B TRP* 3.4 9.0 + - - -
1330B THR 5.2 0.8 + - - -
1393B TRP* 3.3 24.3 + - - +
1394B GLY* 4.1 2.4 - - - -
1397B PHE* 4.1 15.8 - - - -
1549B ASP* 3.5 28.0 + - - -
1550B SER 5.9 0.2 - - - +
1555B ASN* 5.1 1.6 - - - -
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Residues in contact with GLY1229 (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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1196B GLY* 3.8 3.4 - - - -
1198B GLY 3.6 23.6 - - - -
1201B ALA* 3.9 6.3 - - - -
1202B MET* 3.4 27.8 - - - +
1227B LEU 3.1 0.8 + - - -
1228B SER* 1.3 81.9 + - - +
1230B SER* 1.3 63.4 + - - +
1232B TRP* 3.3 20.8 + - - +
1233B TYR 3.5 0.7 + - - -
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Residues in contact with SER1230 (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 GLY* 3.0 30.9 - - - -
1195B SER 2.7 24.5 + - - -
1201B ALA* 4.1 1.2 + - - +
1205B PHE* 3.7 31.2 - - - +
1226B GLY* 4.1 4.9 - - - -
1227B LEU 3.2 5.3 + - - -
1229B GLY* 1.3 72.9 - - - +
1231B THR* 1.3 60.5 + - - +
1233B TYR* 3.1 7.0 + - - +
1234B MET* 2.9 32.3 + - - +
1576B PHE* 4.2 4.2 - - - -
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Residues in contact with THR1231 (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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1226B GLY 3.9 12.5 + - - -
1227B LEU* 3.8 4.6 + - - +
1228B SER 2.8 22.0 - - - +
1230B SER* 1.3 75.9 - - - +
1232B TRP* 1.3 78.8 + - + +
1234B MET* 3.3 6.3 + - - +
1235B SER* 2.9 28.4 + - - -
1329B PHE* 3.2 25.2 - - - +
1390B MET* 4.6 0.2 - - - -
1393B TRP* 3.0 42.9 - - + +
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Residues in contact with TRP1232 (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 GLY* 3.9 15.0 - - - -
1199B PHE* 3.8 35.4 - + - -
1202B MET* 3.9 14.8 - - - -
1228B SER* 3.4 9.9 + - - -
1229B GLY* 3.3 16.5 + - - +
1230B SER 3.3 0.6 - - - -
1231B THR* 1.3 92.8 - - + +
1233B TYR* 1.3 60.8 + - - +
1235B SER* 3.6 1.9 + - - -
1236B THR* 2.8 28.9 + - - -
1295B PHE* 3.7 31.2 - + - -
1299B ILE* 4.2 11.8 - - + +
1303B LEU* 3.9 6.5 - - + -
1390B MET* 2.9 45.6 + - + +
1394B GLY* 3.9 15.0 - - - +
1397B PHE* 3.6 25.6 - + - -
1683B PHE* 3.8 11.4 - + - -
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Residues in contact with TYR1233 (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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1202B MET* 3.8 32.0 - - + +
1205B PHE* 4.1 12.3 - + + -
1206B SER* 3.2 33.0 + - - -
1209B MET* 3.6 30.1 - - + -
1229B GLY 3.5 2.4 + - - -
1230B SER 3.1 9.4 + - - +
1232B TRP* 1.3 77.4 - - - +
1234B MET* 1.3 70.3 + - + +
1236B THR* 3.2 7.3 + - + -
1237B LEU* 2.9 54.5 + - + +
1248B PRO* 3.7 9.2 - - - +
1251B ILE* 5.2 5.6 - - + -
1252B ASN* 2.7 26.3 + - - -
1255B LEU* 4.9 12.8 - - + -
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Residues in contact with MET1234 (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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1205B PHE* 4.1 11.2 - - + -
1209B MET* 6.2 1.6 - - + -
1224B VAL* 3.2 48.5 - - + +
1225B ALA 4.1 0.2 - - - -
1226B GLY* 3.6 25.8 - - - -
1230B SER 2.9 19.6 + - - +
1231B THR* 3.8 4.0 - - - +
1233B TYR* 1.3 79.1 - - + +
1235B SER* 1.3 57.4 + - - +
1237B LEU* 3.1 4.2 + - + -
1238B TYR* 2.7 47.0 + - + +
1327B PRO* 3.8 12.6 - - + -
1328B LEU 3.3 22.0 - - - +
1329B PHE* 3.9 17.3 - - + -
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Residues in contact with SER1235 (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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1231B THR 2.9 18.0 + - - -
1232B TRP 3.8 2.7 - - - -
1234B MET* 1.3 76.4 - - - +
1236B THR* 1.3 60.4 + - - +
1238B TYR* 5.1 2.0 - - - -
1239B SER* 2.8 34.2 + - - +
1304B ILE* 5.1 1.8 - - - -
1315B LEU* 5.5 0.8 - - - +
1329B PHE* 3.9 5.9 - - - -
1386B LEU* 3.9 18.0 - - - +
1390B MET* 3.6 28.9 - - - +
1393B TRP* 3.5 22.9 - - - -
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Residues in contact with THR1236 (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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1232B TRP 2.8 19.2 + - - -
1233B TYR* 3.2 9.8 + - + -
1235B SER* 1.3 77.4 - - - +
1237B LEU* 1.3 62.3 + - - +
1239B SER* 4.0 3.8 - - - -
1240B HIS* 3.5 6.6 + - - +
1251B ILE* 4.5 12.5 - - + +
1255B LEU* 4.4 20.5 - - + +
1303B LEU* 3.7 40.7 - - - +
1304B ILE* 4.1 6.3 - - - +
1307B ARG* 3.0 29.6 + - - +
1390B MET* 4.5 0.9 - - - +
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Residues in contact with LEU1237 (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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1209B MET* 4.2 19.7 - - + -
1233B TYR* 2.9 52.9 + - + +
1234B MET* 3.7 4.5 - - + +
1236B THR* 1.3 73.8 - - - +
1238B TYR* 1.3 71.9 + - + +
1239B SER 3.1 3.2 + - - -
1240B HIS* 3.2 12.5 + - - +
1243B PHE* 3.4 47.9 - - + +
1248B PRO* 4.2 12.8 - - + -
1251B ILE* 3.4 36.5 - - + +
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Residues in contact with TYR1238 (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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1209B MET* 5.4 4.3 - - + +
1224B VAL* 4.2 13.7 - - + +
1234B MET* 2.7 34.4 + - + +
1237B LEU* 1.3 86.1 - - + +
1239B SER* 1.3 55.4 + - - +
1240B HIS 3.4 0.4 - - - -
1243B PHE* 3.9 23.8 - + - -
1315B LEU* 3.6 26.3 - - + +
1318B LYS* 3.0 43.4 - - + +
1319B VAL* 5.6 1.6 - - + -
1324B CYS* 3.9 14.8 - - + -
1325B PRO* 2.4 49.9 + - + +
1327B PRO* 3.5 35.0 - - + +
1329B PHE* 5.9 0.2 - - + -
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Residues in contact with SER1239 (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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1235B SER 2.8 23.3 + - - -
1236B THR 3.6 2.4 + - - -
1238B TYR* 1.3 75.7 - - - +
1240B HIS* 1.3 66.3 + - - +
1241B PRO* 3.4 2.8 - - - +
1304B ILE* 3.9 7.0 - - - +
1307B ARG* 2.8 32.5 + - - -
1310B THR* 3.8 29.6 + - - +
1315B LEU* 4.1 9.2 - - - -
1318B LYS* 4.3 6.2 + - - +
1386B LEU* 4.4 5.0 - - - +
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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