Contacts of the helix formed by residues 1364 - 1368 (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 ALA1364 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1143B ASP 5.2 0.6 + - - -
1316B LYS* 6.1 0.2 - - - +
1352B TYR 3.9 5.2 - - - +
1353B GLU* 4.9 0.7 - - - -
1363B MET* 1.3 86.8 - - - +
1365B PRO* 1.3 76.9 - - + +
1366B ASP* 3.2 13.2 - - - +
1367B LEU* 3.1 32.7 + - + +
1368B PHE 3.9 0.7 + - - -
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Residues in contact with PRO1365 (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* 4.3 17.3 - - + -
1313B SER* 3.3 22.0 - - - +
1316B LYS* 4.4 5.4 - - - +
1350B SER 3.7 11.4 - - - +
1351B PRO 3.6 22.4 - - - +
1352B TYR* 3.1 24.2 - - - +
1353B GLU* 3.8 4.3 - - - +
1354B ILE* 3.8 11.9 - - + +
1363B MET 3.8 0.2 - - - -
1364B ALA* 1.3 86.2 - - + +
1366B ASP* 1.3 61.0 + - - +
1367B LEU 3.1 1.0 + - - -
1368B PHE* 3.1 18.5 + - - +
1383B GLU* 4.1 11.6 - - - +
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Residues in contact with ASP1366 (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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1313B SER* 3.7 6.8 + - - +
1316B LYS* 5.9 0.9 + - - -
1364B ALA* 4.0 12.0 - - - +
1365B PRO* 1.3 78.6 - - - +
1367B LEU* 1.3 89.6 + - - +
1368B PHE 3.4 2.2 + - - +
1370B SER* 3.9 6.8 + - - -
1380B LYS* 3.6 22.8 + - - +
1381B TYR 4.1 11.8 - - - +
1383B GLU* 3.7 32.9 + - + +
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Residues in contact with LEU1367 (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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1143B ASP* 5.1 11.9 - - + +
1363B MET* 3.9 7.9 - - + -
1364B ALA* 3.1 35.6 + - + +
1366B ASP* 1.3 103.2 + - - +
1368B PHE* 1.3 60.1 + - - +
1369B GLY 2.8 11.1 + - - -
1370B SER* 2.8 20.1 + - - +
1372B PHE* 3.7 31.0 - - + -
1377B VAL* 4.1 17.9 - - + -
1380B LYS* 3.7 31.4 - - + +
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Residues in contact with PHE1368 (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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1287B GLN* 5.0 0.3 + - - -
1347B VAL* 5.2 3.4 - - + -
1349B PHE* 4.2 14.6 - + - -
1354B ILE* 3.5 46.7 - - + -
1363B MET* 3.8 18.1 - - + -
1364B ALA 3.9 0.2 + - - -
1365B PRO 3.1 10.0 + - - +
1366B ASP 3.4 2.5 - - - +
1367B LEU* 1.3 74.9 - - - +
1369B GLY* 1.3 57.9 + - - +
1370B SER 3.6 0.2 - - - -
1383B GLU* 5.8 0.5 - - - +
1384B ASN* 3.5 23.0 + - + +
1388B PHE* 4.4 13.7 - + - -
1389B LEU* 3.9 31.6 - - + -
1392B VAL* 5.6 2.5 - - + -
1489B VAL* 4.2 28.0 - - + -
1492B PHE* 4.8 11.2 - + - -
1547B VAL* 4.7 19.5 - - + -
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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