Contacts of the helix formed by residues 338 - 349 (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 338 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A GLU* 3.0 28.6 + - - -
336A HIS 4.2 0.4 + - - -
337A ILE* 1.3 78.6 - - - +
339A CYS* 1.3 62.3 + - - +
340A ALA* 3.0 9.4 + - - +
341A ALA* 2.7 23.6 + - - +
342A LYS* 3.1 24.1 + - - +
367A TRP* 3.8 2.8 - - - -
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Residues in contact with CYS 339 (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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338A SER* 1.3 71.1 + - - +
340A ALA* 1.3 56.5 + - - +
341A ALA 2.8 4.5 + - - -
342A LYS* 3.0 9.2 + - - +
343A ASP* 2.7 37.4 + - + +
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Residues in contact with ALA 340 (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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338A SER* 3.0 6.1 + - - +
339A CYS* 1.3 77.6 - - - +
341A ALA* 1.3 63.9 + - - +
343A ASP* 3.9 8.3 - - - -
344A LEU* 3.2 6.8 + - - +
365A HIS* 3.1 25.1 + - - +
366A PRO* 5.2 4.9 - - + -
367A TRP* 3.5 28.9 - - + +
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Residues in contact with ALA 341 (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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179A GLU* 3.7 11.4 - - - +
285A LEU* 5.6 1.7 - - - +
289A LEU* 4.3 10.8 - - + -
337A ILE* 3.7 20.0 - - + -
338A SER* 2.7 27.1 + - - +
339A CYS 2.8 0.6 + - - -
340A ALA* 1.3 69.7 - - - +
342A LYS* 1.3 68.3 + - - +
344A LEU* 2.8 18.3 + - - +
345A ILE* 3.2 15.5 + - - +
367A TRP* 3.5 17.0 - - + +
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Residues in contact with LYS 342 (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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329A PHE* 3.7 35.7 - - + -
334A TRP* 2.6 68.6 + - + -
335A ALA 3.9 5.9 + - - -
337A ILE* 3.1 15.5 + - + +
338A SER 3.1 16.8 - - - +
339A CYS* 3.0 11.7 + - - +
341A ALA* 1.3 78.8 - - - +
343A ASP* 1.3 62.1 + - - +
345A ILE* 3.3 8.6 + - - +
346A SER* 2.9 27.3 + - - -
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Residues in contact with ASP 343 (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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339A CYS* 2.7 21.9 + - + +
340A ALA* 3.6 10.1 - - - +
342A LYS* 1.3 69.9 - - - +
344A LEU* 1.3 64.4 + - - +
346A SER* 2.6 22.6 + - - -
347A LYS* 2.6 41.5 + - - +
365A HIS* 2.7 28.5 - - - -
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Residues in contact with LEU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A VAL* 4.8 5.6 - - + -
285A LEU* 3.7 23.8 - - + -
340A ALA 3.2 3.9 + - - +
341A ALA* 2.8 13.9 + - - +
343A ASP* 1.3 72.2 + - - +
345A ILE* 1.3 70.9 + - - +
347A LYS* 2.5 20.0 + - - +
348A LEU* 3.2 24.4 + - + +
357A LEU* 3.5 27.8 - - + -
362A VAL* 4.5 9.2 - - + -
365A HIS* 3.5 32.1 - - + +
367A TRP* 3.9 21.5 - - + -
368A VAL* 4.3 14.8 - - + -
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Residues in contact with ILE 345 (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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282A GLY* 4.4 5.2 - - - +
285A LEU* 4.0 22.7 - - + -
286A TYR* 3.7 26.5 - - + +
289A LEU* 4.3 5.8 - - + -
327A TYR* 4.6 2.0 - - + -
329A PHE* 4.2 14.1 - - + -
334A TRP* 3.6 36.8 - - + -
341A ALA 3.2 10.6 + - - +
342A LYS* 3.6 7.6 - - - +
344A LEU* 1.3 75.7 - - - +
346A SER* 1.3 53.8 + - - +
348A LEU* 2.7 31.0 + - - +
349A LEU* 2.8 41.9 + - + +
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Residues in contact with SER 346 (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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327A TYR* 2.7 31.9 + - - -
329A PHE* 5.2 4.0 - - - -
342A LYS 2.9 13.8 + - - -
343A ASP* 2.6 25.8 + - - -
344A LEU 2.9 1.0 + - - -
345A ILE* 1.3 73.2 - - - +
347A LYS* 1.3 58.7 + - - +
348A LEU 3.3 0.2 - - - -
349A LEU 3.7 1.5 - - - +
350A VAL* 2.9 19.2 - - - +
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Residues in contact with LYS 347 (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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343A ASP* 2.6 48.3 + - - +
344A LEU 2.5 15.9 + - - +
346A SER* 1.3 73.8 + - - +
348A LEU* 1.3 56.4 + - - -
350A VAL* 3.2 10.4 - - - +
356A ARG* 3.0 16.6 - - - -
357A LEU* 2.9 51.3 - - + +
365A HIS* 4.8 4.7 - - - +
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Residues in contact with LEU 348 (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* 5.8 0.7 - - + -
278A LEU* 3.3 38.8 - - + +
279A TRP* 3.9 5.7 - - - -
281A LEU* 4.7 9.2 - - + -
282A GLY* 3.9 26.5 - - - +
285A LEU* 5.1 3.8 - - + -
344A LEU* 3.2 33.1 + - + +
345A ILE* 2.7 8.9 + - - +
347A LYS* 1.3 77.7 - - - +
349A LEU* 1.3 55.9 + - - +
350A VAL 2.6 16.7 + - - -
356A ARG* 2.9 25.5 + - + +
357A LEU* 4.0 17.3 - - + +
362A VAL* 4.1 19.5 - - + -
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Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A TRP* 3.7 37.7 - - + +
282A GLY 4.2 7.9 - - - +
283A VAL* 3.6 28.9 - - + +
286A TYR* 4.8 1.1 - - + -
294A PRO* 3.9 32.1 - - + -
295A PHE* 4.3 2.5 - - + -
327A TYR* 3.4 45.1 + - + -
345A ILE* 2.8 33.0 + - + +
346A SER 3.7 2.6 - - - +
348A LEU* 1.3 70.5 - - - +
350A VAL* 1.3 59.7 + - - +
351A ARG* 4.3 1.6 + - - +
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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