Contacts of the helix formed by residues 1360 - 1374 (chain A) in PDB entry 5KHR
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 VAL1360 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1359A ASN* 3.7 29.4 - - - +
1361A ASP* 3.7 26.9 - - - +
1364A CYS* 4.7 19.3 - - - +
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Residues in contact with ASP1361 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1360A VAL* 3.7 29.8 - - - +
1362A VAL* 3.8 25.4 - - - +
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Residues in contact with VAL1362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1292A GLU* 4.3 24.7 - - - +
1361A ASP* 3.8 28.0 - - - +
1363A THR* 3.9 26.7 - - - +
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Residues in contact with THR1363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1362A VAL* 3.9 28.7 - - - +
1364A CYS* 3.8 29.2 - - - +
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Residues in contact with CYS1364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1329A MET* 3.9 27.6 - - - +
1360A VAL* 4.7 15.0 - - - +
1363A THR* 3.8 28.9 - - - +
1365A PRO* 3.9 27.1 - - - -
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Residues in contact with PRO1365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1364A CYS* 3.9 25.6 - - - -
1366A GLY* 3.8 28.5 - - - -
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Residues in contact with GLY1366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1296A LEU* 4.1 26.0 - - - +
1299A GLY* 4.1 18.4 - - - +
1365A PRO* 3.8 25.6 - - - -
1367A ALA* 3.8 28.7 - - - +
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Residues in contact with ALA1367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1366A GLY* 3.8 29.2 - - - +
1368A THR* 3.9 26.0 - - - +
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Residues in contact with THR1368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1367A ALA* 3.9 25.1 - - - +
1369A LEU* 3.8 28.9 - - - +
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Residues in contact with LEU1369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1368A THR* 3.8 29.2 - - - +
1370A ALA* 3.8 26.5 - - - +
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Residues in contact with ALA1370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1303A GLY* 4.1 26.5 - - - +
1369A LEU* 3.8 28.9 - - - +
1371A LEU* 3.8 26.2 - - - +
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Residues in contact with LEU1371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1370A ALA* 3.8 28.3 - - - +
1372A ALA* 3.9 25.6 - - - +
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Residues in contact with ALA1372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1371A LEU* 3.9 25.6 - - - +
1373A MET* 3.8 28.5 - - - +
1410A ALA* 4.7 20.4 - - - +
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Residues in contact with MET1373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1372A ALA* 3.8 28.5 - - - +
1374A ILE* 3.9 26.9 - - - +
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Residues in contact with ILE1374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1307A LEU* 4.7 7.4 - - - +
1308A GLY* 4.1 16.2 - - - +
1373A MET* 3.9 25.8 - - - +
1375A TYR* 3.8 28.7 - - - +
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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