Contacts of the helix formed by residues 1454 - 1475 (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 LEU1454 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1453A ASN* 3.8 28.9 - - - +
1455A GLU* 3.8 26.0 - - - +
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Residues in contact with GLU1455 (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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1454A LEU* 3.8 29.2 - - - +
1456A THR* 3.8 25.8 - - - +
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Residues in contact with THR1456 (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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1455A GLU* 3.8 25.8 - - - +
1457A LEU* 3.8 28.7 - - - +
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Residues in contact with LEU1457 (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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1456A THR* 3.8 28.7 - - - +
1458A SER* 3.8 27.6 - - - +
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Residues in contact with SER1458 (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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1457A LEU* 3.8 26.7 - - - +
1459A GLN* 3.8 29.6 - - - +
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Residues in contact with GLN1459 (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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1458A SER* 3.8 29.4 - - - +
1460A ALA* 3.8 26.9 - - - +
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Residues in contact with ALA1460 (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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1459A GLN* 3.8 28.9 - - - +
1461A HIS* 3.8 26.0 - - - +
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Residues in contact with HIS1461 (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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1460A ALA* 3.8 26.5 - - - +
1462A VAL* 3.8 28.9 - - - +
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Residues in contact with VAL1462 (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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1461A HIS* 3.8 28.9 - - - +
1463A TYR* 3.9 25.4 - - - +
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Residues in contact with TYR1463 (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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1462A VAL* 3.9 26.0 - - - +
1464A ILE* 3.8 29.2 - - - +
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Residues in contact with ILE1464 (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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1463A TYR* 3.8 28.9 - - - +
1465A ILE* 3.8 25.6 - - - +
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Residues in contact with ILE1465 (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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1464A ILE* 3.8 25.6 - - - +
1466A ALA* 3.8 28.9 - - - +
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Residues in contact with ALA1466 (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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1465A ILE* 3.8 28.9 - - - +
1467A GLY* 3.8 26.2 - - - +
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Residues in contact with GLY1467 (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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1405A LEU* 4.1 24.9 - - - +
1409A LEU* 4.6 17.7 - - - +
1466A ALA* 3.8 28.9 - - - +
1468A ALA* 3.8 25.1 - - - +
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Residues in contact with ALA1468 (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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1467A GLY* 3.8 27.4 - - - +
1469A CYS* 3.8 28.9 - - - +
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Residues in contact with CYS1469 (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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1468A ALA* 3.8 28.9 - - - +
1470A LEU* 3.9 24.9 - - - +
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Residues in contact with LEU1470 (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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1469A CYS* 3.9 25.1 - - - +
1471A SER* 3.7 29.4 - - - +
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Residues in contact with SER1471 (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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1409A LEU* 4.6 20.6 - - - +
1470A LEU* 3.7 30.3 - - - +
1472A LEU* 3.8 25.4 - - - +
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Residues in contact with LEU1472 (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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1471A SER* 3.8 28.5 - - - +
1473A GLY* 3.8 24.9 - - - +
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Residues in contact with GLY1473 (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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1472A LEU* 3.8 26.0 - - - +
1474A PHE* 3.8 28.5 - - - +
1522A SER* 3.9 27.6 - - - +
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Residues in contact with PHE1474 (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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1473A GLY* 3.8 24.9 - - - +
1475A ARG* 3.8 29.6 - - - +
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Residues in contact with ARG1475 (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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1474A PHE* 3.8 26.5 - - - +
1476A PHE* 3.7 30.3 - - - +
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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