Contacts of the helix formed by residues 1312 - 1319 (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 LEU1312 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1311B THR* 1.3 74.8 - - - +
1313B SER* 1.3 63.7 + - - +
1315B LEU* 3.0 40.3 + - + +
1329B PHE* 4.1 16.4 - - + -
1349B PHE* 4.2 13.5 - - + -
1350B SER 3.3 35.4 - - - +
1351B PRO* 3.9 7.2 - - + +
1354B ILE* 4.2 20.4 - - + -
1365B PRO* 4.3 6.5 - - + -
1383B GLU* 3.0 8.2 + - - +
1384B ASN 4.9 0.8 + - - -
1386B LEU* 4.2 15.1 - - + +
1389B LEU* 4.0 29.6 - - + +
1393B TRP* 4.9 0.9 - - + -
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Residues in contact with SER1313 (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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1311B THR* 3.2 2.4 - - - -
1312B LEU* 1.3 78.1 - - - +
1314B SER* 1.3 61.4 + - - +
1315B LEU 3.0 1.6 + - - -
1316B LYS* 3.1 45.0 + - - +
1351B PRO 4.3 4.3 - - - -
1365B PRO* 3.3 18.0 - - - +
1366B ASP* 3.7 9.5 + - - +
1383B GLU* 2.7 29.6 + - - -
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Residues in contact with SER1314 (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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1310B THR* 3.3 12.7 - - - +
1311B THR* 2.7 42.2 + - - -
1313B SER* 1.3 75.7 - - - +
1315B LEU* 1.3 63.5 + - - +
1316B LYS 3.0 2.3 + - - -
1317B GLU* 2.9 46.4 + - - +
1318B LYS* 4.5 1.6 + - - +
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Residues in contact with LEU1315 (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* 5.6 1.1 - - - -
1238B TYR* 3.6 45.1 - - + +
1239B SER* 4.1 14.4 - - - -
1310B THR* 4.4 2.0 - - + -
1311B THR 3.8 12.1 - - - +
1312B LEU* 3.0 34.7 + - + +
1314B SER* 1.3 80.0 + - - +
1316B LYS* 1.3 64.6 + - - +
1317B GLU 3.0 0.9 - - - -
1318B LYS* 2.9 22.5 + - + +
1319B VAL* 3.7 6.6 + - - +
1327B PRO* 4.7 3.4 - - + -
1329B PHE* 4.6 14.6 - - + -
1351B PRO* 3.9 17.9 - - + +
1386B LEU* 4.5 12.1 - - + -
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Residues in contact with LYS1316 (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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1153B GLN* 3.5 30.1 - - - +
1313B SER* 3.1 40.4 + - - +
1314B SER 3.0 1.2 - - - -
1315B LEU* 1.3 78.0 - - - +
1317B GLU* 1.3 54.8 + - + +
1319B VAL* 2.9 11.7 + - - -
1320B ASN* 2.8 38.4 + - + +
1351B PRO* 3.2 31.1 + - - +
1352B TYR* 3.8 17.7 - - + +
1364B ALA* 6.1 0.2 - - - +
1365B PRO* 4.4 8.1 - - - +
1366B ASP* 5.9 0.8 + - - -
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Residues in contact with GLU1317 (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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1314B SER* 2.9 38.4 - - - +
1315B LEU 3.0 0.2 - - - -
1316B LYS* 1.3 79.0 - - + +
1318B LYS* 1.3 73.4 + - + +
1319B VAL 3.2 0.7 - - - -
1320B ASN* 3.0 22.8 - - - +
1323B GLN* 3.4 4.5 - - - +
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Residues in contact with LYS1318 (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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1238B TYR* 3.0 41.2 + - + +
1239B SER* 4.3 4.8 + - - +
1240B HIS 2.8 33.3 + - - -
1241B PRO* 4.1 10.7 + - - +
1243B PHE* 2.8 34.5 - - + +
1244B PRO* 4.4 1.3 - - + -
1314B SER 5.2 0.4 + - - +
1315B LEU* 2.9 16.5 + - + +
1317B GLU* 1.3 93.8 + - + +
1319B VAL* 1.3 61.0 + - + +
1323B GLN* 3.4 13.4 - - - +
1324B CYS* 3.5 25.0 - - - +
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Residues in contact with VAL1319 (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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1157B PHE* 3.0 40.5 - - + -
1238B TYR* 5.7 0.9 - - + -
1315B LEU 4.1 3.6 - - - +
1316B LYS* 2.9 18.6 + - - +
1318B LYS* 1.3 83.8 - - + +
1320B ASN* 1.3 63.9 + - - +
1321B THR 3.2 3.4 - - - -
1322B ALA* 3.1 12.0 + - - -
1323B GLN* 4.0 4.0 - - - +
1324B CYS* 3.7 13.9 - - + +
1325B PRO 4.4 4.7 - - - +
1326B LEU* 4.1 15.0 - - + -
1327B PRO* 4.9 4.3 - - + -
1351B PRO* 4.8 4.5 - - + -
1352B TYR* 3.1 32.6 + - + +
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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