Contacts of the helix formed by residues 369 - 384 (chain H) in PDB entry 6MZL
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 PRO 369 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315H ARG* 5.9 4.0 - - - -
316H GLN* 3.8 10.8 - - - +
367H LYS 3.7 9.2 - - - +
368H THR* 1.3 87.9 - - - +
370H TRP* 1.3 65.8 + - + +
371H THR* 3.3 19.5 - - + -
372H THR* 2.3 42.4 + - + +
373H ARG* 2.9 12.4 + - - +
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Residues in contact with TRP 370 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316H GLN* 3.1 11.3 - - - +
368H THR 5.2 2.6 + - - -
369H PRO* 1.3 76.8 - - + +
371H THR* 1.3 55.1 + - - +
373H ARG* 3.2 41.5 - - + +
374H TYR* 2.6 42.5 + - + +
402H ARG* 5.1 1.6 - - + -
403H ILE* 4.1 14.1 - - + -
406H VAL* 3.6 31.6 - - + +
415H ILE* 5.5 1.1 - - + +
416H ASP* 3.1 49.2 + - + +
419H GLY* 4.7 13.9 - - - -
420H ALA* 3.9 21.3 - - + -
423H VAL* 4.1 20.9 - - + -
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Residues in contact with THR 371 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312H ILE 4.3 3.6 - - - +
313H VAL 2.4 28.9 + - - +
314H SER 2.8 24.0 + - - +
315H ARG* 4.3 3.8 - - - -
316H GLN* 3.4 29.5 - - + +
327H TRP* 3.2 31.0 - - - -
369H PRO* 3.7 15.3 - - + -
370H TRP* 1.3 77.5 - - - +
372H THR* 1.3 68.0 + - + +
374H TYR* 3.8 3.7 - - - +
375H GLY* 2.9 27.4 + - - -
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Residues in contact with THR 372 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312H ILE 4.8 6.4 - - - +
313H VAL* 4.0 17.0 - - + +
315H ARG* 6.2 0.4 - - - -
362H SER* 4.9 9.1 - - - -
368H THR* 3.4 8.2 - - - -
369H PRO* 2.3 55.1 + - + +
371H THR* 1.3 86.2 - - + +
373H ARG* 1.3 62.8 + - - +
375H GLY 3.9 0.2 - - - -
376H SER* 2.9 32.7 + - - -
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Residues in contact with ARG 373 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362H SER 4.7 7.4 - - - +
363H TRP* 5.0 5.6 + - + +
368H THR* 3.3 40.4 + - - +
369H PRO 2.9 11.1 + - - +
370H TRP* 3.2 46.1 - - + +
372H THR* 1.3 81.3 + - - +
374H TYR* 1.3 58.0 + - - +
376H SER* 2.6 22.3 + - - -
377H ILE* 2.9 31.3 + - + +
399H GLU* 3.3 44.1 + - - +
402H ARG* 3.2 37.6 - - - +
403H ILE* 5.1 3.4 - - - +
423H VAL* 5.7 0.9 - - + -
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Residues in contact with TYR 374 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327H TRP* 3.9 17.9 - + + -
328H ALA* 3.3 32.8 - - - +
331H ASP* 3.2 26.8 + - - -
370H TRP* 2.6 23.3 + - + +
371H THR* 3.8 4.3 - - - +
373H ARG* 1.3 78.7 - - - +
375H GLY* 1.3 60.4 + - - +
377H ILE* 3.3 4.2 + - - +
378H ALA* 2.9 26.3 + - - +
419H GLY* 4.4 2.2 - - - -
422H HIS* 3.0 49.0 + + - +
423H VAL* 3.5 28.4 - - + +
426H LEU* 3.5 28.4 - - + +
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Residues in contact with GLY 375 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312H ILE* 3.5 33.3 - - - +
327H TRP* 6.5 0.4 - - - -
331H ASP* 4.5 2.9 - - - -
359H PHE* 4.6 0.3 - - - -
371H THR 2.9 16.9 + - - -
374H TYR* 1.3 80.2 - - - +
376H SER* 1.3 60.5 + - - +
378H ALA* 3.2 8.7 + - - +
379H GLY* 2.9 23.9 + - - -
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Residues in contact with SER 376 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312H ILE 5.1 0.8 + - - -
359H PHE* 4.0 25.2 - - - -
362H SER* 3.8 26.6 - - - -
363H TRP* 4.2 9.2 - - - -
372H THR 2.9 16.0 + - - -
373H ARG* 2.6 26.9 + - - -
375H GLY* 1.3 74.5 - - - +
377H ILE* 1.3 69.4 + - - +
379H GLY* 3.2 1.6 + - - -
380H LEU* 3.0 31.2 + - - +
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Residues in contact with ILE 377 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363H TRP* 3.4 33.2 - - + +
373H ARG* 2.9 27.7 + - + +
374H TYR* 3.5 4.5 - - - +
376H SER* 1.3 80.3 + - - +
378H ALA* 1.3 58.2 + - - +
380H LEU* 3.5 8.1 + - - +
381H ALA* 2.8 31.8 + - + +
388H ILE* 5.3 0.9 - - - +
392H ILE* 5.4 7.5 - - + +
399H GLU* 4.3 6.7 - - - +
423H VAL* 4.3 22.2 - - + -
426H LEU* 3.7 23.1 - - + -
427H LEU* 4.2 25.1 - - + +
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Residues in contact with ALA 378 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312H ILE* 5.6 0.2 - - + -
331H ASP* 3.5 40.4 - - + +
334H ALA* 4.2 6.1 - - + -
374H TYR 2.9 14.7 + - - +
375H GLY* 3.3 9.2 - - - +
376H SER 3.1 0.2 - - - -
377H ILE* 1.3 78.3 - - - +
379H GLY* 1.3 57.5 + - - +
381H ALA* 3.1 8.5 + - - +
382H GLU* 2.9 31.9 + - - +
426H LEU* 4.5 8.5 - - + -
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Residues in contact with GLY 379 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312H ILE* 5.8 0.2 - - - -
334H ALA* 4.1 15.8 - - - +
337H VAL* 5.3 4.4 - - - +
359H PHE* 3.5 28.8 - - - -
375H GLY 2.9 12.4 + - - -
376H SER 3.2 0.4 + - - -
378H ALA* 1.3 73.2 - - - +
380H LEU* 1.3 59.6 + - - +
382H GLU* 3.3 4.8 + - - +
383H LEU* 3.0 30.3 + - - +
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Residues in contact with LEU 380 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356H THR* 4.7 10.5 - - + +
359H PHE* 3.6 41.7 - - + +
360H THR* 5.7 1.1 - - - +
363H TRP* 4.7 9.9 - - + -
376H SER 3.0 20.8 + - - +
377H ILE* 3.8 5.4 - - - +
379H GLY* 1.3 75.2 - - - +
381H ALA* 1.3 62.3 + - - +
383H LEU* 3.1 21.1 + - + +
384H GLY 3.3 8.5 + - - -
387H VAL* 3.4 29.9 - - + +
388H ILE* 3.6 5.1 - - + +
391H LEU* 4.9 8.1 - - + -
392H ILE* 3.8 28.7 - - + -
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Residues in contact with ALA 381 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377H ILE* 2.8 22.1 + - + +
378H ALA* 3.3 10.3 - - - +
380H LEU* 1.3 76.8 - - - +
382H GLU* 1.3 61.9 - - + +
384H GLY* 3.2 12.0 + - - -
388H ILE* 3.8 7.4 - - + +
426H LEU* 6.3 3.4 - - + -
430H HIS* 2.7 54.5 + - + +
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Residues in contact with GLU 382 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331H ASP* 4.1 7.6 - - + +
332H PHE* 5.8 0.2 - - - -
334H ALA* 3.5 19.1 - - + +
335H ARG* 3.3 48.5 - - - +
337H VAL* 5.6 0.2 - - + -
338H ALA* 3.3 23.1 - - + +
378H ALA* 2.9 19.4 + - + +
379H GLY 3.8 4.0 - - - +
380H LEU 3.3 0.2 - - - -
381H ALA* 1.3 75.0 - - + +
383H LEU* 1.3 64.7 + - - +
384H GLY* 3.4 1.6 + - - -
430H HIS* 5.1 8.0 - - - -
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Residues in contact with LEU 383 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337H VAL* 5.3 6.1 - - + -
338H ALA* 4.7 15.9 - - + +
341H CYS* 5.0 12.1 - - + -
352H GLN* 4.8 20.9 - - + +
355H ILE* 5.1 6.3 - - + -
356H THR* 3.8 28.9 - - + -
359H PHE* 4.4 9.9 - - + -
379H GLY 3.0 17.4 + - - +
380H LEU* 3.1 22.8 + - + +
382H GLU* 1.3 77.2 - - - +
384H GLY* 1.3 58.9 + - - +
385H HIS 4.0 0.7 + - - -
387H VAL* 3.7 18.5 - - + +
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Residues in contact with GLY 384 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380H LEU 3.3 1.6 + - - -
381H ALA 3.2 13.3 + - - -
382H GLU 3.2 4.6 - - - -
383H LEU* 1.3 80.8 - - - +
385H HIS* 1.3 65.2 + - - +
386H ASP 3.7 0.4 - - - -
387H VAL* 3.3 6.2 - - - +
388H ILE* 3.2 27.2 + - - +
430H HIS* 5.2 1.8 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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