Contacts of the helix formed by residues 351 - 365 (chain A) in PDB entry 2Q8J
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 GLY 351 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349A ALA 3.6 1.8 + - - -
350A VAL* 1.3 76.7 - - - +
352A PRO* 1.3 74.6 - - - +
353A GLU 3.4 2.1 + - - -
354A GLU 3.5 0.2 + - - -
355A GLN 3.1 15.2 + - - -
373A THR* 3.7 11.0 - - - +
374A ALA 2.8 19.1 + - - -
375A SER* 4.8 1.8 - - - -
518A ASN* 4.3 15.9 - - - -
519A SER* 5.9 0.9 - - - -
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Residues in contact with PRO 352 (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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351A GLY* 1.3 81.9 - - - +
353A GLU* 1.3 69.7 + - + +
355A GLN* 3.3 14.4 + - + +
356A LYS* 3.0 23.4 + - - +
373A THR* 4.7 1.5 - - + -
518A ASN* 4.6 0.2 - - - +
519A SER* 5.9 0.7 - - - +
520A LYS* 3.3 44.4 - - + +
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Residues in contact with GLU 353 (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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351A GLY 3.4 0.8 + - - -
352A PRO* 1.3 82.2 - - + +
354A GLU* 1.3 58.4 - - - +
356A LYS* 3.2 11.7 + - - +
357A LYS 3.1 20.3 + - - -
519A SER* 2.5 47.7 + - - +
520A LYS* 5.6 3.4 - - + -
637A LYS* 3.0 31.5 + - - -
639A LEU* 3.9 22.6 - - + +
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Residues in contact with GLU 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A CYS 4.4 1.0 - - - +
349A ALA* 3.6 9.8 - - + +
350A VAL* 2.7 54.9 + - - +
351A GLY 3.5 1.2 + - - -
352A PRO 3.3 0.2 - - - -
353A GLU* 1.3 76.1 - - - +
355A GLN* 1.3 61.5 + - - +
357A LYS* 3.2 3.0 + - - +
358A CYS* 2.7 30.3 + - - +
519A SER* 5.0 2.7 + - - +
638A ASN 4.4 3.3 - - - +
639A LEU* 4.0 22.8 - - + +
640A LEU* 3.0 45.7 + - + +
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Residues in contact with GLN 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ALA* 3.4 10.1 - - + +
351A GLY 3.1 15.1 + - - +
352A PRO* 3.6 14.2 - - + +
354A GLU* 1.3 76.2 - - - +
356A LYS* 1.3 56.4 + - - +
358A CYS* 3.0 1.9 + - - -
359A GLN* 2.8 60.7 + - + +
371A CYS* 5.0 9.8 - - + +
373A THR* 3.0 33.3 + - + +
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Residues in contact with LYS 356 (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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352A PRO 3.0 16.2 + - - +
353A GLU* 3.7 9.4 - - - +
354A GLU 3.2 0.4 - - - -
355A GLN* 1.3 75.9 - - - +
357A LYS* 1.3 65.7 + - + +
359A GLN* 3.5 20.6 + - - +
360A GLN* 3.5 34.6 + - - +
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Residues in contact with LYS 357 (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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353A GLU 3.1 13.2 + - - +
354A GLU* 3.8 7.0 - - - +
356A LYS* 1.3 81.9 - - + +
358A CYS* 1.3 63.8 + - - +
360A GLN* 3.4 9.3 + - - +
361A TRP* 3.3 17.7 + - - +
629A PHE* 4.4 16.8 - - + -
630A CYS 4.3 4.0 - - - -
631A LEU* 2.8 31.6 + - - +
632A PHE 4.4 1.0 - - - -
633A LYS 2.9 30.9 + - - +
634A SER* 3.8 7.4 + - - -
639A LEU* 3.0 45.4 + - + +
640A LEU* 4.1 13.7 - - + -
641A PHE 4.9 1.6 + - - +
643A ASP* 5.0 0.2 + - - -
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Residues in contact with CYS 358 (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 TRP* 3.9 26.7 - - - -
349A ALA* 4.2 12.1 - - + -
354A GLU 2.7 22.3 + - - +
355A GLN 3.0 3.8 + - - +
357A LYS* 1.3 74.0 - - - +
359A GLN* 1.3 50.9 + - - +
360A GLN 3.1 0.3 + - - -
361A TRP* 3.1 12.1 + - - +
362A SER 2.8 31.4 + - - -
369A VAL* 4.9 1.3 - - - -
370A THR 4.5 0.2 - - - -
371A CYS* 2.1 52.0 - - + -
640A LEU* 4.2 11.0 - - + +
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Residues in contact with GLN 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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355A GLN* 2.8 58.8 + - + +
356A LYS* 3.9 12.7 - - - +
357A LYS 3.3 0.4 - - - -
358A CYS* 1.3 70.5 - - - +
360A GLN* 1.3 59.1 + - + +
362A SER* 3.3 8.9 + - - -
363A GLN* 2.9 34.6 + - - +
371A CYS* 3.7 6.9 - - + -
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Residues in contact with GLN 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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356A LYS* 3.5 35.5 + - - +
357A LYS* 3.4 10.9 + - - +
358A CYS 3.2 0.4 - - - -
359A GLN* 1.3 75.6 - - + +
361A TRP* 1.3 66.0 + - - +
362A SER 3.1 0.9 - - - -
363A GLN* 3.2 17.9 - - - +
364A GLN* 3.1 30.4 + - + +
629A PHE* 4.3 19.5 - - + -
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Residues in contact with TRP 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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347A TRP* 3.9 46.9 - + - -
357A LYS 3.3 6.1 + - - +
358A CYS* 3.1 11.8 + - - +
360A GLN* 1.3 77.7 - - - +
362A SER* 1.3 63.3 + - - +
364A GLN* 4.9 0.9 - - - -
365A SER* 3.0 23.3 + - - -
369A VAL* 4.0 29.6 - - + -
611A LEU* 4.4 6.1 - - + -
614A GLN* 2.8 39.7 + - + +
618A PHE* 4.0 11.0 - + - -
629A PHE* 3.7 33.6 - + + -
631A LEU* 3.4 32.7 - - + +
640A LEU* 3.9 20.2 - - + -
641A PHE* 4.7 3.8 - + - -
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Residues in contact with SER 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A CYS 2.8 13.9 + - - -
359A GLN* 3.5 10.5 - - - -
360A GLN 3.1 0.4 - - - -
361A TRP* 1.3 76.1 - - - +
363A GLN* 1.4 62.2 + - - +
365A SER* 2.9 16.5 + - - -
367A GLN* 3.2 35.1 + - - +
369A VAL* 3.0 28.6 + - - +
370A THR* 4.2 4.5 + - - -
371A CYS* 4.1 12.1 - - - -
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Residues in contact with GLN 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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359A GLN* 2.9 21.1 + - - +
360A GLN* 3.2 22.6 - - - +
362A SER* 1.4 68.7 + - - +
364A GLN* 1.3 67.8 + - - +
366A GLY* 3.0 22.0 + - - -
367A GLN* 4.4 5.7 + - - +
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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 GLN* 3.1 18.7 + - + +
361A TRP 4.3 2.2 - - - +
363A GLN* 1.3 85.3 - - - +
365A SER* 1.3 58.9 + - - +
366A GLY 3.3 1.7 + - - -
618A PHE* 3.6 26.7 - - + -
624A ASN* 5.8 0.3 + - - -
628A LYS* 3.2 50.5 + - - +
629A PHE* 3.6 24.0 - - + -
701A NAG 3.7 10.2 - - - +
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Residues in contact with SER 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A TRP* 3.0 16.3 + - - -
362A SER* 2.9 16.8 + - - -
364A GLN* 1.3 79.5 - - - +
366A GLY* 1.3 60.3 + - - +
368A ASN* 3.2 34.8 + - - -
369A VAL* 3.5 9.3 + - - +
614A GLN* 3.6 31.9 - - - -
618A PHE* 4.4 3.4 - - - -
701A NAG 3.5 14.4 + - - -
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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