Contacts of the helix formed by residues 336 - 351 (chain A) in PDB entry 1JQO
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 ASN 336 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A CYS* 1.3 78.5 - - - +
337A ASP* 1.3 82.1 + - - +
338A GLU* 3.5 22.4 - - - +
339A LEU* 3.7 9.4 + - + +
340A ARG* 3.0 22.7 + - - +
418A LEU* 4.8 2.3 - - - +
421A LYS* 3.9 17.6 + - - +
422A SER* 3.2 35.2 + - - +
425A ASP* 3.9 26.6 + - - +
426A CYS* 4.0 7.0 - - - -
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Residues in contact with ASP 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A CYS 3.7 1.4 + - - +
336A ASN* 1.3 85.8 + - - +
338A GLU* 1.3 61.1 + - - +
340A ARG* 3.5 12.8 - - - +
341A VAL* 3.3 18.9 - - - +
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Residues in contact with GLU 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ASN* 3.0 17.2 - - - +
337A ASP* 1.3 79.6 - - - +
339A LEU* 1.3 64.1 + - - +
341A VAL* 3.4 16.3 + - - +
342A ARG* 3.4 12.9 + - + +
418A LEU* 3.7 22.3 - - + +
421A LYS* 3.7 21.1 + - - +
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Residues in contact with LEU 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A CYS* 3.4 9.4 - - + -
336A ASN* 3.3 18.2 + - + +
338A GLU* 1.3 75.7 - - - +
340A ARG* 1.3 60.5 + - - +
342A ARG* 3.3 6.3 + - - +
343A ALA* 2.8 29.6 + - + +
370A PRO* 3.2 35.2 - - + -
371A TYR* 3.7 21.1 - - + -
374A ILE* 3.3 28.7 - - + -
418A LEU* 4.3 11.4 - - + +
419A CYS* 4.3 8.3 - - - -
422A SER* 3.5 26.7 - - - +
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Residues in contact with ARG 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A TRP* 3.0 32.5 + - - -
334A ARG* 4.8 0.8 - - - +
335A CYS* 3.2 30.7 - - - +
336A ASN 3.0 12.0 + - - +
337A ASP* 3.5 14.8 - - - +
339A LEU* 1.3 78.7 - - - +
341A VAL* 1.3 65.6 + - + +
343A ALA* 3.6 3.9 - - - +
344A GLU* 3.1 40.4 + - + +
370A PRO* 4.1 5.8 - - - +
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Residues in contact with VAL 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ASP 3.3 18.4 - - - +
338A GLU* 3.6 9.0 - - - +
339A LEU 3.2 0.2 - - - -
340A ARG* 1.3 72.4 - - + +
342A ARG* 1.3 68.2 + - - +
343A ALA 2.8 1.6 + - - -
344A GLU* 2.8 20.0 + - - +
345A GLU* 2.9 43.5 + - + +
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Residues in contact with ARG 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A GLU* 3.4 11.0 + - + +
339A LEU 3.6 6.5 - - - +
341A VAL* 1.3 79.6 - - - +
343A ALA* 1.3 60.9 + - - +
345A GLU* 3.7 19.6 + - - +
346A LEU* 3.2 59.5 + - - +
374A ILE* 4.6 10.3 - - + +
377A HIS* 4.6 10.7 + - - -
414A GLU* 3.1 38.5 + - - -
415A PRO* 4.5 16.4 - - - +
418A LEU* 3.7 25.7 - - + +
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Residues in contact with ALA 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 LEU* 2.8 26.0 + - + +
340A ARG* 3.6 5.8 - - - +
341A VAL 2.8 0.8 + - - -
342A ARG* 1.3 75.1 - - - +
344A GLU* 1.3 65.8 + - + +
346A LEU* 3.0 15.1 + - - +
347A HIS* 3.1 10.0 + - - +
367A PRO* 5.5 6.1 - - + +
370A PRO* 4.1 25.1 - - + +
373A VAL* 3.7 19.5 - - + +
374A ILE* 4.5 6.4 - - + +
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Residues in contact with GLU 344 (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 ARG* 3.1 35.3 + - + +
341A VAL* 2.8 13.9 + - - +
343A ALA* 1.3 74.9 - - + +
345A GLU* 1.3 62.4 + - + +
347A HIS* 3.0 24.0 + - - +
348A SER* 3.3 9.4 + - - -
367A PRO* 5.1 13.0 - - + +
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Residues in contact with GLU 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A VAL* 2.9 42.0 + - + +
342A ARG* 3.8 21.3 + - - +
344A GLU* 1.3 75.7 - - + +
346A LEU* 1.3 61.0 + - + +
348A SER* 3.3 7.9 + - - -
349A SER* 3.1 29.7 + - - -
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Residues in contact with LEU 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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342A ARG* 3.2 42.0 - - - +
343A ALA 3.0 6.1 + - - +
345A GLU* 1.3 80.5 - - + +
347A HIS* 1.3 61.5 + - - +
349A SER* 3.8 9.3 - - - +
350A SER* 3.1 26.2 + - - -
373A VAL* 4.2 10.8 - - + -
374A ILE* 4.1 24.7 - - + -
377A HIS* 3.9 42.6 - - + +
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Residues in contact with HIS 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ALA 3.1 9.8 + - - +
344A GLU* 3.0 17.1 + - - +
346A LEU* 1.3 78.5 - - - +
348A SER* 1.3 62.6 + - - +
350A SER* 3.0 18.8 + - - -
351A GLY* 3.6 2.6 + - - -
364A GLN* 3.0 28.7 + - + -
365A ILE 3.4 21.0 + - - -
366A PRO* 4.0 3.4 - - + -
367A PRO* 3.2 43.5 - - + +
373A VAL* 4.8 5.7 - - + +
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Residues in contact with SER 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A GLU 3.3 7.2 + - - -
345A GLU* 3.3 12.1 + - - -
347A HIS* 1.3 80.4 - - - +
349A SER* 1.3 65.9 + - - +
350A SER 4.3 0.2 - - - -
351A GLY* 4.1 8.2 + - - +
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Residues in contact with SER 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A GLU 3.1 19.9 + - - -
346A LEU* 3.9 12.6 - - - +
348A SER* 1.3 77.6 + - - +
350A SER* 1.3 66.7 + - - +
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Residues in contact with SER 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU 3.1 14.8 + - - -
347A HIS* 3.0 6.4 + - - -
349A SER* 1.3 80.6 - - - +
351A GLY* 1.3 50.5 + - - -
352A SER* 2.7 32.7 + - - -
364A GLN* 2.6 35.6 + - - +
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Residues in contact with GLY 351 (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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347A HIS 3.6 4.2 + - - -
348A SER* 4.1 6.3 + - - -
349A SER 3.7 0.4 - - - -
350A SER* 1.3 81.7 + - - +
352A SER* 1.3 55.3 + - - -
353A LYS* 3.7 10.2 + - - +
364A GLN* 3.0 22.4 - - - +
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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