Contacts of the helix formed by residues 362 - 369 (chain A) in PDB entry 5KJY
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 CYS 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A ILE* 4.0 24.2 - - + -
256A LEU* 4.3 4.3 - - - -
258A SER* 4.8 4.5 - - - +
259A LEU* 4.0 26.9 - - + -
359A LEU* 3.0 31.4 + - - -
361A PRO* 1.3 77.4 - - - +
363A SER* 1.3 65.7 + - - +
364A ASP 3.2 2.7 - - - -
365A ILE* 3.1 18.9 + - + +
366A LEU* 3.0 28.7 + - - +
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Residues in contact with SER 363 (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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330A LEU* 4.0 21.2 - - - +
355A PHE* 5.8 2.7 - - - -
359A LEU* 2.9 11.5 + - - -
360A GLY* 3.1 20.7 + - - -
362A CYS* 1.3 77.0 - - - +
364A ASP* 1.3 67.0 + - - +
366A LEU* 3.5 11.3 + - - +
367A LYS* 3.0 32.6 + - - +
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Residues in contact with ASP 364 (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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360A GLY 4.7 0.2 + - - -
361A PRO 5.3 1.1 + - - +
362A CYS* 3.2 1.2 - - - +
363A SER* 1.3 88.3 + - - +
365A ILE* 1.3 60.0 + - + +
367A LYS* 3.4 17.7 + - - +
368A ARG* 3.0 32.7 + - - +
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Residues in contact with ILE 365 (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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255A ILE* 3.9 25.4 - - + -
258A SER* 4.6 13.9 - - - +
361A PRO 5.0 3.4 - - - +
362A CYS* 3.1 24.8 + - + +
364A ASP* 1.3 77.0 - - + +
366A LEU* 1.3 66.4 + - - +
368A ARG* 3.4 9.6 + - + +
369A ASN* 3.2 28.2 + - - +
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Residues in contact with LEU 366 (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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255A ILE* 3.7 20.9 - - + -
256A LEU* 4.3 5.6 - - + -
292A PHE* 5.1 4.0 - - + -
323A TYR* 3.5 40.9 + - + +
326A GLU* 4.7 6.8 - - + +
330A LEU* 3.7 12.5 - - + +
355A PHE* 4.3 18.2 - - + -
359A LEU* 4.2 22.4 - - + -
362A CYS* 3.0 29.0 + - - +
363A SER* 3.6 12.8 - - - +
365A ILE* 1.3 77.6 - - - +
367A LYS* 1.3 62.2 + - - +
369A ASN* 3.4 11.3 + - - +
370A ILE* 3.5 14.2 + - - +
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Residues in contact with LYS 367 (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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330A LEU* 3.8 42.1 - - + +
331A MET* 5.2 6.3 - - + -
363A SER* 3.0 22.0 + - - +
364A ASP* 3.7 18.8 - - - +
365A ILE 3.2 0.2 - - - -
366A LEU* 1.3 75.0 - - - +
368A ARG* 1.3 65.3 + - - +
370A ILE* 3.1 27.7 + - + +
371A GLN* 4.3 5.5 + - - -
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Residues in contact with ARG 368 (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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364A ASP 3.0 19.2 + - - +
365A ILE* 3.7 10.5 - - + +
366A LEU 3.4 0.2 - - - -
367A LYS* 1.3 75.3 - - - +
369A ASN* 1.3 64.0 + - - +
370A ILE 3.3 1.0 + - - -
371A GLN* 3.3 23.6 + - - +
372A GLN* 4.5 3.6 + - - +
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Residues in contact with ASN 369 (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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254A SER* 5.4 3.8 + - - -
255A ILE* 3.7 23.3 - - + +
323A TYR* 4.4 8.9 + - - +
326A GLU* 5.6 0.7 - - - +
365A ILE* 3.2 25.2 + - - +
366A LEU 3.7 5.8 - - - +
367A LYS 3.2 0.8 - - - -
368A ARG* 1.3 73.7 - - - +
370A ILE* 1.3 65.7 + - - +
371A GLN 3.1 2.5 - - - -
372A GLN* 3.0 45.3 + - - +
373A TYR* 4.0 8.7 + - - -
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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