Contacts of the helix formed by residues 358 - 365 (chain A) in PDB entry 6CJH
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 SER 358 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275A ARG* 3.7 26.6 - - - +
356A ARG 3.6 2.2 + - - -
357A LEU* 1.3 74.8 - - - +
359A ALA* 1.3 66.1 + - - +
360A ALA* 3.7 9.7 + - - +
361A GLN* 3.0 42.2 + - - +
362A VAL* 2.8 21.0 + - - +
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Residues in contact with ALA 359 (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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190A ALA* 4.3 5.9 - - - +
193A LEU* 4.2 2.2 - - + -
194A ASP* 3.6 36.6 - - + +
197A HIS* 3.7 18.8 + - + +
275A ARG* 5.3 0.2 - - - +
278A LEU* 3.6 25.1 - - + +
358A SER* 1.3 68.9 - - - +
360A ALA* 1.3 66.9 + - - +
362A VAL* 2.8 22.1 + - - +
363A LEU* 3.5 7.5 + - - +
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Residues in contact with ALA 360 (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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194A ASP* 3.5 22.8 + - - +
358A SER* 3.7 8.0 + - - +
359A ALA* 1.3 76.9 - - - +
361A GLN* 1.3 65.7 + - + +
362A VAL 2.7 2.1 + - - -
363A LEU* 2.8 20.4 + - - +
364A GLN* 3.2 21.3 - - - +
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Residues in contact with GLN 361 (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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275A ARG* 3.9 10.7 + - - -
355A GLN 4.8 3.2 + - - -
356A ARG 4.7 0.4 + - - -
357A LEU* 3.2 24.9 - - + +
358A SER* 3.0 43.9 + - - +
360A ALA* 1.3 78.2 - - + +
362A VAL* 1.3 62.1 - - - +
364A GLN* 3.4 22.2 + - - +
365A HIS* 3.7 7.8 + - - +
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Residues in contact with VAL 362 (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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186A VAL* 4.3 19.7 - - + -
190A ALA* 4.1 17.9 - - + -
278A LEU* 3.7 21.3 - - + -
281A LEU* 4.5 4.7 - - + -
344A LEU* 4.5 9.9 - - + -
348A LEU* 4.1 10.8 - - + -
357A LEU* 3.9 22.2 - - + -
358A SER 2.8 17.6 + - - +
359A ALA* 2.8 14.5 + - - +
360A ALA 2.7 4.9 + - - -
361A GLN* 1.3 69.3 - - - +
363A LEU* 1.3 63.0 + - - +
364A GLN 3.1 1.0 + - - -
365A HIS* 3.3 19.5 + - - +
368A VAL* 3.6 12.2 - - + +
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Residues in contact with LEU 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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187A GLN* 3.4 42.4 - - + +
190A ALA* 3.6 13.7 - - + -
191A SER* 3.4 26.5 - - - +
194A ASP* 4.3 11.2 - - + +
359A ALA 4.2 5.4 - - - +
360A ALA* 2.8 26.1 + - - +
362A VAL* 1.3 72.9 - - - +
364A GLN* 1.3 69.3 + - - +
365A HIS 3.5 0.2 + - - -
368A VAL* 3.5 14.5 - - + +
369A GLN* 3.4 23.2 + - - +
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Residues in contact with GLN 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 ALA* 3.2 22.6 - - - +
361A GLN* 3.5 18.4 - - - +
362A VAL 3.1 0.4 - - - -
363A LEU* 1.3 81.3 - - - +
365A HIS* 1.3 69.8 + - - +
366A PRO* 3.1 7.5 - - - +
369A GLN* 3.1 24.3 + - - +
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Residues in contact with HIS 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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340A ALA* 3.1 28.9 + - - +
343A ASP* 2.7 33.0 + - - -
344A LEU* 3.5 30.2 - - + +
347A LYS* 4.8 4.2 + - - +
357A LEU* 5.1 4.8 - - + +
361A GLN 3.7 5.9 + - - +
362A VAL* 3.3 16.1 + - - +
364A GLN* 1.3 78.9 - - - +
366A PRO* 1.3 80.7 - - + +
367A TRP* 2.7 39.1 + - + +
368A VAL* 3.0 17.3 + - + +
369A GLN* 3.2 6.6 + - - +
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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