Contacts of the helix formed by residues 1291 - 1306 (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 ARG1291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1290A ASP* 3.9 28.9 - - - +
1292A GLU* 3.9 26.0 - - - +
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Residues in contact with GLU1292 (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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1291A ARG* 3.9 28.5 - - - +
1293A SER* 3.9 24.7 - - - +
1362A VAL* 4.3 24.0 - - - +
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Residues in contact with SER1293 (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* 3.9 25.1 - - - +
1294A TYR* 3.8 28.7 - - - +
1601A TYR* 4.2 21.5 - - - +
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Residues in contact with TYR1294 (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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1293A SER* 3.8 26.0 - - - +
1295A SER* 3.8 28.7 - - - +
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Residues in contact with SER1295 (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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1294A TYR* 3.8 28.9 - - - +
1296A LEU* 3.8 26.2 - - - +
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Residues in contact with LEU1296 (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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1295A SER* 3.8 28.5 - - - +
1297A ALA* 3.8 25.8 - - - +
1366A GLY* 4.1 25.4 - - - +
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Residues in contact with ALA1297 (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* 3.8 28.3 - - - +
1298A ALA* 3.8 26.0 - - - +
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Residues in contact with ALA1298 (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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1297A ALA* 3.8 27.1 - - - +
1299A GLY* 3.8 28.7 - - - +
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Residues in contact with GLY1299 (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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1298A ALA* 3.8 26.5 - - - +
1300A LEU* 3.8 28.5 - - - +
1366A GLY* 4.1 22.4 - - - +
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Residues in contact with LEU1300 (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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1299A GLY* 3.8 28.3 - - - +
1301A ALA* 3.8 26.7 - - - +
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Residues in contact with ALA1301 (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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1258A GLY* 4.0 27.4 - - - +
1300A LEU* 3.8 25.8 - - - +
1302A LEU* 3.8 28.7 - - - +
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Residues in contact with LEU1302 (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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1301A ALA* 3.8 25.4 - - - +
1303A GLY* 3.8 29.6 - - - +
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Residues in contact with GLY1303 (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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1302A LEU* 3.8 26.7 - - - +
1304A MET* 3.8 29.4 - - - +
1370A ALA* 4.1 25.4 - - - +
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Residues in contact with MET1304 (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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1303A GLY* 3.8 28.7 - - - +
1305A VAL* 3.8 25.8 - - - +
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Residues in contact with VAL1305 (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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1262A GLN* 4.2 20.2 - - - +
1304A MET* 3.8 28.5 - - - +
1306A CYS* 3.8 26.0 - - - +
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Residues in contact with CYS1306 (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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1265A ALA* 4.5 17.3 - - - +
1305A VAL* 3.8 28.7 - - - +
1307A LEU* 3.9 26.5 - - - +
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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