Contacts of the helix formed by residues 1290 - 1305 (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 THR1290 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1288B PRO* 5.0 0.7 - - + +
1289B VAL* 1.3 82.4 - - - +
1291B PHE* 1.3 60.1 + - - +
1292B THR* 3.4 11.1 + - - -
1293B ASP* 2.7 34.7 + - - +
1294B ILE 3.8 0.9 + - - -
1388B PHE* 5.4 0.7 - - - -
1479B PHE* 3.5 16.8 - - - -
1483B GLU* 3.8 14.1 - - - +
1484B GLY 3.8 14.4 - - - +
1486B ALA 2.8 28.0 + - - +
1487B GLY* 4.2 2.8 - - - -
1488B LYS* 4.0 27.7 + - + +
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Residues in contact with PHE1291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1267B LEU* 5.9 0.4 - - + -
1290B THR* 1.3 74.6 - - - +
1292B THR* 1.3 62.9 + - - +
1294B ILE* 2.9 25.5 + - + +
1295B PHE* 2.9 29.9 + - + -
1398B SER* 3.8 20.2 - - - -
1401B PHE* 3.4 51.8 - + + -
1466B HIS* 4.8 1.3 - + - -
1469B ILE* 4.3 10.8 - - + -
1470B MET* 3.1 37.5 - - + -
1479B PHE* 3.4 25.9 - + + -
1484B GLY 4.8 0.4 + - - -
1485B ARG* 3.7 27.1 - - + +
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Residues in contact with THR1292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1290B THR* 3.0 10.7 + - - -
1291B PHE* 1.3 79.5 - - - +
1293B ASP* 1.3 53.9 + - - +
1295B PHE* 3.7 1.2 - - - +
1296B GLY* 2.7 32.1 + - - -
1388B PHE* 4.4 6.1 - - + -
1391B GLY* 3.4 32.0 - - - +
1392B VAL* 3.5 20.9 - - + +
1395B SER* 3.8 1.6 - - - -
1398B SER* 2.9 16.3 + - - -
1485B ARG 2.5 23.8 + - - -
1486B ALA* 3.2 13.5 - - - -
1487B GLY* 3.4 3.5 + - - +
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Residues in contact with ASP1293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1279B LEU* 3.8 24.7 - - + +
1282B LYS* 2.6 36.1 + - - +
1288B PRO 4.2 1.0 - - - +
1289B VAL* 3.3 15.3 - - + -
1290B THR* 2.7 38.7 + - - +
1292B THR* 1.3 77.9 - - - +
1294B ILE* 1.3 58.0 + - - +
1296B GLY* 3.6 1.3 + - - -
1297B MET* 3.1 29.6 + - - +
1387B HIS* 4.8 3.5 - - - -
1388B PHE* 3.1 22.3 - - - +
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Residues in contact with ILE1294 (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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1267B LEU* 5.1 9.4 - - + -
1272B VAL* 5.5 6.7 - - + -
1275B TYR* 3.9 24.4 - - + -
1276B VAL* 5.0 5.4 - - + -
1279B LEU* 3.7 22.2 - - + -
1290B THR 4.5 0.4 - - - +
1291B PHE* 2.9 29.9 + - + +
1293B ASP* 1.3 75.6 - - - +
1295B PHE* 1.3 65.9 + - - +
1297B MET* 3.1 7.9 + - - +
1298B LEU* 2.9 20.5 + - + +
1469B ILE* 5.5 2.7 - - + -
1473B VAL* 3.8 28.7 - - + -
1478B LEU* 4.7 4.3 - - + -
1479B PHE* 3.9 24.7 - - + -
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Residues in contact with PHE1295 (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* 3.7 19.1 - + - -
1291B PHE* 2.9 21.5 + - + +
1292B THR 3.7 2.9 - - - +
1294B ILE* 1.3 77.4 - - - +
1296B GLY* 1.3 64.8 + - - +
1298B LEU* 3.1 15.4 + - + +
1299B ILE* 3.0 50.9 + - + +
1391B GLY* 4.0 18.4 - - - -
1394B GLY 3.3 23.3 - - - -
1397B PHE* 3.4 23.8 - + + -
1398B SER* 4.0 22.4 - - - -
1401B PHE* 3.9 27.1 - + - -
1683B PHE* 4.4 8.5 - + - -
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Residues in contact with GLY1296 (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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1292B THR 2.7 21.9 + - - -
1293B ASP 3.9 2.0 - - - -
1295B PHE* 1.3 74.8 - - - +
1297B MET* 1.3 55.7 + - - +
1299B ILE* 3.2 5.5 + - - +
1300B GLY 2.8 23.4 + - - -
1387B HIS* 3.2 32.7 - - - +
1388B PHE* 4.8 0.9 - - - -
1391B GLY* 3.6 12.6 - - - -
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Residues in contact with MET1297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1275B TYR* 3.1 65.2 + - + +
1278B SER* 4.5 13.9 - - - -
1279B LEU* 3.2 32.3 - - + -
1293B ASP 3.1 9.9 + - - +
1294B ILE* 3.1 9.6 + - - +
1296B GLY* 1.3 73.0 - - - +
1298B LEU* 1.3 60.8 + - - +
1301B GLU* 2.8 31.2 + - - +
1308B MET* 3.3 11.5 - - + +
1387B HIS* 3.4 32.1 - - + +
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Residues in contact with LEU1298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1263B PRO* 3.9 25.6 - - + +
1264B LEU* 4.3 14.1 - - + -
1266B LEU* 4.1 14.4 - - + -
1267B LEU* 4.1 18.2 - - + -
1275B TYR* 3.6 20.6 + - + +
1294B ILE* 2.9 11.7 + - + +
1295B PHE* 3.3 19.3 - - + +
1297B MET* 1.3 78.1 - - - +
1299B ILE* 1.3 57.0 + - + +
1301B GLU* 3.5 1.4 + - - +
1302B THR* 2.7 40.9 + - + +
1401B PHE* 4.1 30.3 - - + -
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Residues in contact with ILE1299 (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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1199B PHE* 4.5 8.7 - - + -
1232B TRP* 4.2 26.2 - - + +
1295B PHE* 3.0 52.5 + - + +
1296B GLY* 3.4 9.4 - - - +
1298B LEU* 1.3 79.9 - - + +
1300B GLY* 1.3 63.6 + - - +
1302B THR* 3.3 6.6 + - + -
1303B LEU* 3.0 32.4 + - + +
1390B MET* 3.4 38.6 - - + +
1683B PHE* 4.3 10.1 - - + -
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Residues in contact with GLY1300 (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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1296B GLY 2.8 14.3 + - - -
1297B MET 3.6 3.1 - - - -
1299B ILE* 1.3 78.6 - - - +
1301B GLU* 1.3 59.4 + - - +
1304B ILE* 2.7 45.5 + - - -
1305B HIS 3.2 4.3 + - - -
1308B MET* 3.6 15.3 - - - -
1387B HIS* 3.9 8.3 - - - +
1390B MET* 5.1 1.1 - - - -
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Residues in contact with GLU1301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1266B LEU* 3.7 24.0 - - + +
1271B LYS* 3.0 33.4 + - - +
1275B TYR* 2.4 35.5 + - + +
1297B MET 2.8 19.2 + - - +
1298B LEU 3.9 3.1 - - - +
1299B ILE 3.4 0.2 - - - -
1300B GLY* 1.3 72.3 - - - +
1302B THR* 1.3 57.7 + - - +
1305B HIS* 3.0 36.4 + - + +
1308B MET* 3.3 14.5 - - + +
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Residues in contact with THR1302 (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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1199B PHE* 4.2 12.5 - - + -
1258B ASN* 3.2 39.3 + - - +
1259B VAL* 5.3 0.5 - - - +
1263B PRO* 4.0 26.3 - - + +
1266B LEU* 3.9 19.7 - - + -
1298B LEU* 2.7 25.1 - - + +
1299B ILE* 3.7 5.0 + - + +
1300B GLY 3.2 0.4 - - - -
1301B GLU* 1.3 78.0 - - - +
1303B LEU* 1.3 74.5 + - - +
1305B HIS* 3.9 2.5 + - - -
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Residues in contact with LEU1303 (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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1199B PHE* 4.6 6.1 - - + -
1202B MET* 3.6 30.1 - - + -
1232B TRP* 3.9 6.5 - - + -
1236B THR* 3.7 24.2 - - - +
1255B LEU* 3.4 31.9 - - + +
1258B ASN* 4.0 11.9 - - + +
1259B VAL* 4.4 7.4 - - + -
1299B ILE* 3.0 36.0 + - + +
1302B THR* 1.3 94.5 + - - +
1304B ILE* 1.3 66.4 + - + +
1305B HIS* 3.8 3.8 + - - -
1306B ASN* 5.3 1.0 - - - +
1307B ARG* 4.5 3.1 + - - -
1390B MET* 3.8 13.7 - - + -
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Residues in contact with ILE1304 (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 5.0 0.4 - - - +
1236B THR* 4.1 15.9 - - - +
1239B SER* 3.9 9.0 - - - +
1300B GLY* 2.7 32.0 + - - +
1303B LEU* 1.3 80.6 - - + +
1305B HIS* 1.3 63.5 + - - +
1306B ASN* 3.1 6.7 - - - -
1307B ARG* 3.0 58.2 + - + +
1308B MET* 3.1 14.4 + - - +
1310B THR* 5.2 4.5 - - - +
1386B LEU* 5.0 9.2 - - + -
1387B HIS* 4.5 13.2 - - + +
1390B MET* 4.1 22.9 - - - -
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Residues in contact with HIS1305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1258B ASN* 3.3 38.2 + - - -
1300B GLY 3.2 4.1 + - - -
1301B GLU* 3.0 31.7 + - + +
1302B THR 3.9 6.0 + - - -
1303B LEU 5.1 1.1 - - - -
1304B ILE* 1.3 76.0 + - - +
1306B ASN* 1.3 77.6 + - + +
1307B ARG 3.3 2.8 + - - -
1308B MET* 4.1 18.2 + - - +
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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