Contacts of the helix formed by residues 338 - 362 (chain A) in PDB entry 4MXP
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 GLN 338 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A VAL* 1.3 79.3 - - - +
339A ARG* 1.3 66.0 + - - +
340A VAL* 3.6 26.7 - - + +
341A THR* 3.2 15.3 + - - +
342A ARG* 3.1 19.0 + - - +
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Residues in contact with ARG 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A VAL 3.8 1.0 + - - -
338A GLN* 1.3 72.6 - - - +
340A VAL* 1.3 58.2 + - - +
342A ARG* 3.3 9.9 + - + +
343A ILE* 2.9 55.4 + - + +
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Residues in contact with VAL 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A GLN* 3.6 26.0 - - + +
339A ARG* 1.3 78.0 - - - +
341A THR* 1.3 63.5 + - - +
343A ILE* 3.4 11.4 + - + +
344A GLU* 2.9 57.2 + - + +
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Residues in contact with THR 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A VAL* 3.8 16.4 - - + -
338A GLN* 3.2 27.0 + - - +
340A VAL* 1.3 85.0 - - - +
342A ARG* 1.3 56.7 + - - +
344A GLU* 3.3 12.0 + - - +
345A ASN* 2.8 53.3 + - - +
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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
----------------------------------------------------------
337A VAL* 4.0 11.8 - - + +
338A GLN 3.1 12.3 + - - +
339A ARG* 3.6 12.8 - - - +
341A THR* 1.3 72.7 - - - +
343A ILE* 1.3 63.6 + - + +
345A ASN* 3.3 7.5 + - - +
346A LEU* 2.8 53.1 + - + +
384A LEU* 3.7 19.7 - - + +
388A ASP* 2.9 41.2 + - - +
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Residues in contact with ILE 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 ARG* 2.9 45.3 + - + +
340A VAL* 3.7 9.9 - - + +
342A ARG* 1.3 76.6 - - + +
344A GLU* 1.3 61.8 + - + +
346A LEU* 3.4 7.4 + - + +
347A GLU* 2.9 39.5 + - + +
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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
----------------------------------------------------------
340A VAL* 2.9 41.1 + - + +
341A THR* 3.7 12.8 + - - +
342A ARG 3.3 0.2 - - - -
343A ILE* 1.3 80.0 - - + +
345A ASN* 1.3 62.6 + - - +
347A GLU* 3.3 6.3 + - - +
348A ASN* 3.0 34.0 + - - +
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Residues in contact with ASN 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A VAL* 5.1 3.8 - - - +
341A THR* 2.8 39.3 + - - +
342A ARG* 3.7 6.7 - - - +
344A GLU* 1.3 78.4 - - - +
346A LEU* 1.3 56.9 + - - +
348A ASN* 3.3 3.0 + - - +
349A ALA* 2.9 24.8 + - - +
378A PHE* 3.4 16.4 - - - -
382A LYS* 3.5 45.9 + - + +
384A LEU* 3.9 18.9 - - + +
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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* 2.8 48.9 + - + +
343A ILE* 3.9 5.8 - - + +
345A ASN* 1.3 73.6 - - - +
347A GLU* 1.3 64.5 + - - +
349A ALA* 3.7 4.9 - - + +
350A LYS* 2.9 30.0 + - - +
384A LEU* 3.9 25.4 - - + -
388A ASP* 3.6 34.5 - - + +
389A LEU* 3.9 17.9 - - + +
392A GLU* 4.1 25.9 - - + +
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Residues in contact with GLU 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 ILE* 2.9 29.5 + - + +
344A GLU* 3.3 6.9 + - - +
346A LEU* 1.3 81.4 - - - +
348A ASN* 1.3 61.7 + - - +
350A LYS* 3.4 26.9 + - - +
351A LYS* 3.1 35.3 + - - +
392A GLU* 3.9 19.1 - - - +
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Residues in contact with ASN 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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344A GLU* 3.0 25.4 + - - +
345A ASN* 3.8 5.3 + - - +
347A GLU* 1.3 73.9 - - - +
349A ALA* 1.3 61.2 + - - +
351A LYS* 3.2 25.4 + - - +
352A LEU* 3.0 34.4 + - + +
378A PHE* 4.0 21.8 - - + -
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Residues in contact with ALA 349 (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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345A ASN 2.9 17.6 + - - +
346A LEU* 3.7 7.9 - - - +
348A ASN* 1.3 78.1 - - - +
350A LYS* 1.3 55.7 + - - +
352A LEU* 3.2 5.3 + - - -
353A TRP* 2.8 26.5 + - - +
375A LEU* 3.4 10.0 - - - +
378A PHE* 3.9 13.6 - - + -
379A MET* 3.6 32.5 - - + -
384A LEU* 4.8 0.7 - - + -
389A LEU* 4.1 11.4 - - + -
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Residues in contact with LYS 350 (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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346A LEU 2.9 18.4 + - - +
347A GLU* 3.5 29.0 + - - +
348A ASN 3.2 0.2 - - - -
349A ALA* 1.3 76.1 - - - +
351A LYS* 1.3 58.9 + - + +
353A TRP* 3.3 7.0 + - - +
354A ASP* 2.8 28.3 + - + +
389A LEU* 3.8 12.0 - - + +
392A GLU* 2.8 25.6 + - + +
393A LEU* 3.8 12.3 - - + -
395A ASP* 2.8 31.1 + - - -
396A LYS* 3.4 29.6 - - + +
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Residues in contact with LYS 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A GLU* 3.1 22.7 + - - +
348A ASN* 3.5 24.8 + - - +
350A LYS* 1.3 77.2 - - + +
352A LEU* 1.3 59.0 - - + +
354A ASP* 3.3 7.9 + - - +
355A ASN* 2.9 38.7 + - - +
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Residues in contact with LEU 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ASN* 3.0 18.7 + - + +
349A ALA* 3.2 7.6 + - - +
351A LYS* 1.3 74.5 - - + +
353A TRP* 1.3 64.8 + - - +
355A ASN* 3.3 19.8 + - + +
356A ALA* 3.1 21.7 + - - +
371A ALA* 4.5 6.5 - - - +
374A GLU* 3.9 30.7 - - + +
375A LEU* 3.9 17.0 - - + +
378A PHE* 3.6 44.4 - - + -
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Residues in contact with TRP 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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349A ALA 2.8 19.1 + - - +
350A LYS* 3.5 6.3 - - - +
352A LEU* 1.3 72.0 - - - +
354A ASP* 1.3 64.6 + - + +
356A ALA* 3.2 5.2 + - - +
357A ASN* 2.9 57.6 + - + -
375A LEU* 3.7 23.0 - - + +
389A LEU* 4.2 6.5 - - + -
393A LEU* 3.7 27.0 - - + +
396A LYS* 3.6 32.3 - - + -
397A THR 4.5 3.6 - - - -
398A ILE* 3.6 27.1 - - + -
443A PHE* 3.0 43.9 + + - -
446A CYS* 3.8 12.3 - - + +
447A LYS* 3.7 16.1 - - + +
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Residues in contact with ASP 354 (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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350A LYS 2.8 16.8 + - - +
351A LYS* 3.5 9.0 - - - +
352A LEU 3.2 0.2 - - - -
353A TRP* 1.3 83.3 - - + +
355A ASN* 1.3 62.7 + - - +
357A ASN* 3.3 5.2 + - - +
358A SER* 2.8 35.7 + - - -
396A LYS* 3.1 38.0 + - - +
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Residues in contact with ASN 355 (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 LYS* 2.9 22.2 + - - +
352A LEU* 3.3 22.5 + - + +
354A ASP* 1.3 77.6 - - - +
356A ALA* 1.3 61.6 + - - +
358A SER* 3.4 6.9 + - - -
359A MET* 3.2 28.3 + - + +
371A ALA* 4.1 10.5 - - + -
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Residues in contact with ALA 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 LEU 3.1 11.7 + - - +
353A TRP* 3.2 8.3 + - - +
355A ASN* 1.3 74.1 - - - +
357A ASN* 1.3 65.9 + - - +
359A MET* 3.2 3.3 + - - +
360A LEU 2.9 18.7 + - - -
368A TYR* 3.4 21.2 - - + -
371A ALA* 3.5 23.7 - - + +
372A ALA* 4.1 9.4 - - - +
375A LEU* 5.4 0.9 - - + -
443A PHE* 3.6 21.3 - - + -
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Residues in contact with ASN 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 TRP* 2.9 42.9 + - + +
354A ASP* 3.8 7.3 + - - +
356A ALA* 1.3 76.5 - - - +
358A SER* 1.3 58.6 + - - +
360A LEU* 3.3 9.3 + - - +
361A GLU* 2.8 38.7 + - - +
396A LYS* 5.5 1.0 - - - +
397A THR 2.9 28.8 + - - +
398A ILE* 4.0 10.6 - - - +
399A SER 5.0 1.0 + - - -
402A GLY* 5.9 0.5 - - - -
443A PHE* 3.6 17.1 - - + -
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Residues in contact with SER 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A ASP* 2.8 22.2 + - - -
355A ASN* 3.6 8.5 - - - -
357A ASN* 1.3 77.5 - - - +
359A MET* 1.3 63.0 + - - +
361A GLU* 3.4 6.7 + - - +
362A LYS* 3.2 40.0 + - - +
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Residues in contact with MET 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 ASN* 3.2 14.4 + - + +
356A ALA 3.6 6.5 - - - +
358A SER* 1.3 77.5 - - - +
360A LEU* 1.3 65.0 + - - +
362A LYS* 3.2 11.5 + - + +
363A GLY 3.1 3.6 + - - -
364A ASN* 3.0 60.6 + - - +
367A GLY* 3.7 21.3 - - - +
368A TYR* 3.5 18.8 - - - +
371A ALA* 4.9 2.0 - - + -
646A ILE 5.4 0.4 - - - +
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Residues in contact with LEU 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 ALA 2.9 16.2 + - - +
357A ASN* 3.5 13.2 - - - +
359A MET* 1.3 74.4 - - - +
361A GLU* 1.3 58.9 + - - +
363A GLY* 2.9 21.1 + - - -
364A ASN 5.0 1.1 - - - +
365A ILE* 5.6 1.8 - - + -
368A TYR* 3.9 21.7 - - + +
398A ILE* 4.5 2.0 - - + -
402A GLY* 3.9 19.1 - - - +
405A ILE* 3.5 49.8 - - + +
406A LEU* 3.8 29.4 - - + -
443A PHE* 3.7 28.0 - - + -
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Residues in contact with GLU 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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357A ASN* 2.8 23.0 + - - +
358A SER* 3.6 8.5 - - - +
359A MET 3.3 0.2 - - - -
360A LEU* 1.3 77.3 - - - +
362A LYS* 1.3 54.0 + - + +
363A GLY 3.2 0.4 - - - -
397A THR 5.6 0.5 - - - +
399A SER* 2.6 38.5 + - - -
401A LYS* 2.7 43.1 + - - +
402A GLY* 4.4 3.4 + - - -
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Residues in contact with LYS 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A SER* 3.2 26.1 + - - +
359A MET* 3.2 16.5 + - - +
360A LEU 3.2 0.8 - - - -
361A GLU* 1.3 78.2 - - + +
363A GLY* 1.3 61.1 + - - +
364A ASN* 3.4 2.1 + - + +
401A LYS* 4.3 5.3 + - - +
645A LYS 4.0 5.6 - - - +
646A ILE* 3.7 40.9 + - - +
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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