Contacts of the helix formed by residues 1385 - 1394 (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 PRO1385 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1282B LYS* 6.2 0.7 - - + -
1308B MET 4.0 8.3 - - - +
1309B ASN* 4.6 10.1 - - + +
1310B THR 3.5 10.5 - - - +
1311B THR* 4.5 4.3 - - + -
1383B GLU 3.9 4.9 - - - +
1384B ASN* 1.3 97.2 - - + +
1386B LEU* 1.3 67.7 + - - +
1387B HIS* 3.4 41.3 - - + +
1388B PHE* 3.0 20.2 + - + +
1389B LEU* 3.6 4.7 + - - +
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Residues in contact with LEU1386 (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* 3.9 36.6 - - - +
1239B SER* 4.4 3.8 - - - -
1304B ILE* 5.0 6.5 - - + -
1310B THR* 2.7 44.3 + - + +
1311B THR* 3.9 5.9 - - - +
1312B LEU* 4.2 26.0 - - + +
1315B LEU* 4.5 11.0 - - + -
1329B PHE* 5.6 0.4 - - + -
1384B ASN 3.9 0.6 + - - -
1385B PRO* 1.3 71.4 - - - +
1387B HIS* 1.3 58.4 + - - +
1389B LEU* 3.0 10.5 + - + +
1390B MET* 2.9 30.9 + - + +
1393B TRP* 3.8 27.6 - - + -
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Residues in contact with HIS1387 (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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1279B LEU* 5.7 3.6 - - - +
1293B ASP 4.8 2.4 + - - -
1296B GLY* 3.2 25.0 - - - +
1297B MET* 3.4 36.8 - - + +
1300B GLY* 3.9 15.9 - - - -
1304B ILE* 4.5 7.4 - - + +
1308B MET* 3.1 42.2 + - + +
1309B ASN* 5.0 4.0 - - - -
1385B PRO* 3.4 24.2 - - + +
1386B LEU* 1.3 78.6 - - - +
1388B PHE* 1.3 82.1 + - + +
1390B MET* 3.4 12.2 + - - +
1391B GLY 3.0 16.8 + - - -
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Residues in contact with PHE1388 (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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1282B LYS* 3.5 9.0 - - - +
1288B PRO 5.9 0.2 - - - -
1290B THR* 5.4 0.7 - - - -
1292B THR* 4.4 8.7 - - + -
1293B ASP* 3.1 45.1 - - - +
1296B GLY* 4.8 2.9 - - - -
1368B PHE* 4.4 11.2 - + - -
1384B ASN* 3.3 39.5 - - + +
1385B PRO* 3.0 15.3 + - + +
1387B HIS* 1.3 90.0 - - + +
1389B LEU* 1.3 69.4 + - + +
1391B GLY* 3.1 3.3 + - - -
1392B VAL* 2.9 49.6 + - + +
1487B GLY* 5.2 5.6 - - - -
1488B LYS 4.8 15.0 - - - -
1489B VAL* 5.3 5.2 - - + -
1547B VAL* 5.9 1.3 - - + -
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Residues in contact with LEU1389 (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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1312B LEU* 4.0 33.9 - - + +
1349B PHE* 4.2 10.5 - - + -
1354B ILE* 5.2 2.2 - - + -
1368B PHE* 3.9 33.7 - - + -
1383B GLU* 5.8 0.4 - - - +
1384B ASN* 5.0 7.6 - - + +
1385B PRO 3.6 8.7 + - - +
1386B LEU* 3.0 12.2 + - + +
1388B PHE* 1.3 86.5 - - + +
1390B MET* 1.3 53.6 + - - +
1392B VAL* 2.8 10.3 + - + +
1393B TRP* 2.6 71.2 + - + -
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Residues in contact with MET1390 (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* 2.9 50.1 + - + +
1235B SER* 3.6 29.2 - - - +
1236B THR* 4.5 3.1 - - - +
1296B GLY* 4.9 0.2 - - - -
1299B ILE* 3.4 30.7 - - + +
1300B GLY* 5.1 0.2 - - - -
1303B LEU* 3.8 21.5 - - + -
1304B ILE* 4.1 19.5 - - + -
1386B LEU* 2.9 16.3 + - - +
1387B HIS* 3.6 23.1 - - - +
1389B LEU* 1.3 74.9 - - - +
1391B GLY* 1.3 62.2 + - - +
1393B TRP* 3.6 12.4 + - + -
1394B GLY* 3.1 11.8 + - - -
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Residues in contact with GLY1391 (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* 3.4 14.4 - - - +
1295B PHE* 4.0 10.4 - - - -
1296B GLY* 3.6 25.5 - - - -
1387B HIS 3.0 10.7 + - - -
1388B PHE 3.4 4.5 - - - -
1389B LEU 3.0 0.4 - - - -
1390B MET* 1.3 78.5 - - - +
1392B VAL* 1.3 55.7 + - - +
1394B GLY 3.4 1.9 - - - -
1395B SER* 3.0 28.4 + - - -
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Residues in contact with VAL1392 (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* 3.8 9.6 - - + -
1331B CYS* 4.3 15.9 - - + -
1349B PHE* 5.3 3.6 - - + -
1368B PHE* 5.6 2.7 - - + -
1388B PHE* 2.9 51.6 + - + +
1389B LEU* 2.8 14.3 + - + +
1391B GLY* 1.3 74.7 - - - +
1393B TRP* 1.3 67.6 + - + +
1395B SER* 2.8 24.8 + - - -
1487B GLY* 4.5 5.6 - - - -
1547B VAL* 3.9 35.4 - - + +
1548B VAL 4.2 0.3 - - - -
1549B ASP 3.9 4.2 + - - -
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Residues in contact with TRP1393 (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 SER* 3.3 13.0 + - - +
1231B THR* 3.0 47.3 - - + +
1235B SER* 3.5 18.2 - - - -
1312B LEU* 4.9 2.0 - - + -
1329B PHE* 3.4 41.4 - + + +
1330B THR 3.2 28.8 - - - +
1331B CYS* 4.1 9.9 - - + -
1349B PHE* 3.5 32.9 - + + -
1386B LEU* 3.8 17.0 - - + -
1389B LEU* 2.6 56.1 + - + +
1390B MET* 3.8 6.3 - - - +
1392B VAL* 1.3 73.4 - - + +
1394B GLY* 1.3 56.2 + - - +
1395B SER 3.5 0.4 - - - -
1549B ASP* 3.2 22.1 - - - +
1550B SER 4.6 1.2 + - - -
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Residues in contact with GLY1394 (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 SER* 4.1 7.2 - - - -
1232B TRP* 3.9 19.9 - - - +
1295B PHE* 3.3 10.6 - - - -
1390B MET 3.1 9.1 + - - -
1391B GLY 3.4 4.7 - - - -
1392B VAL 3.1 0.8 - - - -
1393B TRP* 1.3 77.6 - - - +
1395B SER* 1.3 56.6 + - - +
1396B ALA 3.0 11.6 + - - -
1397B PHE* 3.1 21.1 + - - -
1549B ASP* 3.0 8.3 - - - -
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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