Contacts of the helix formed by residues 364 - 382 (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 ASN 364 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A MET* 3.0 40.9 + - - +
360A LEU* 5.6 0.2 - - - -
362A LYS* 3.2 1.9 - - + -
363A GLY* 1.3 73.9 - - - +
365A ILE* 1.3 58.1 + - - +
366A SER* 3.6 9.2 + - - -
367A GLY* 2.9 20.8 + - - -
368A TYR* 2.9 32.5 + - - +
646A ILE* 3.6 47.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A LEU* 5.6 3.1 - - + -
363A GLY* 3.2 16.0 + - - +
364A ASN* 1.3 73.6 + - - +
366A SER* 1.3 62.3 + - - +
368A TYR* 3.3 6.9 + - + +
369A LEU* 3.0 36.7 + - + +
405A ILE* 3.7 21.5 - - + -
409A LEU* 4.3 16.2 - - + -
466A LYS* 4.6 5.4 - - + +
467A ILE* 3.5 42.4 - - + +
470A GLY* 3.7 28.9 - - - -
646A ILE* 5.2 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ASN* 3.5 6.8 + - - -
365A ILE* 1.3 78.8 - - - +
367A GLY* 1.3 59.5 + - - +
369A LEU* 3.4 2.1 + - - +
370A LYS* 3.0 29.2 + - - +
470A GLY* 3.8 19.3 + - - -
473A GLN* 3.8 27.2 + - - +
474A PHE* 4.0 13.8 - - - -
477A ASP* 4.2 13.9 + - - +
646A ILE* 5.5 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A MET* 3.7 19.5 - - - +
364A ASN* 2.9 24.9 + - - -
366A SER* 1.3 76.5 + - - +
368A TYR* 1.3 63.2 + - - +
370A LYS* 3.4 9.1 + - - +
371A ALA* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ALA* 3.4 22.7 - - + -
359A MET* 3.5 14.6 - - + +
360A LEU* 3.9 20.9 - - + +
364A ASN 2.9 19.2 + - - +
365A ILE* 3.6 7.4 - - + +
367A GLY* 1.3 75.7 - - - +
369A LEU* 1.3 67.6 + - + +
371A ALA* 3.2 4.0 + - - +
372A ALA* 2.7 39.1 + - + +
406A LEU* 3.2 18.1 - - + +
409A LEU* 3.6 18.4 - - + -
440A SER* 2.7 39.7 + - - -
443A PHE* 3.4 34.9 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ILE* 3.0 36.3 + - + +
366A SER 3.9 0.9 - - - +
368A TYR* 1.3 96.8 - - + +
370A LYS* 1.3 59.3 + - - +
372A ALA* 4.3 1.6 - - - -
373A ASN* 2.9 31.9 + - - +
409A LEU* 4.1 6.3 - - + -
436A VAL* 3.7 36.1 - - + +
439A MET* 3.5 18.9 - - + +
440A SER* 4.8 0.4 - - - -
470A GLY 4.4 0.2 - - - +
471A ILE* 4.2 11.2 - - + -
474A PHE* 3.5 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A SER 3.0 18.2 + - - +
367A GLY* 3.6 9.0 - - - +
369A LEU* 1.3 75.2 - - - +
371A ALA* 1.3 62.1 + - - +
373A ASN* 3.6 3.9 - - - +
374A GLU* 3.2 22.3 + - - +
474A PHE* 3.9 13.5 - - + -
477A ASP* 5.5 15.9 - - + +
478A VAL* 6.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A LEU* 4.5 4.7 - - - +
355A ASN* 4.1 11.9 - - + +
356A ALA* 3.5 35.0 - - - +
359A MET* 4.9 2.0 - - + -
367A GLY 3.0 16.7 + - - +
368A TYR 3.5 0.9 - - - +
370A LYS* 1.3 75.6 - - - +
372A ALA* 1.3 59.6 + - - +
374A GLU* 3.3 5.7 + - - +
375A LEU* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ALA* 4.1 4.9 - - - +
368A TYR* 2.7 41.5 + - + +
369A LEU* 3.8 5.4 - - - +
371A ALA* 1.3 73.8 - - - +
373A ASN* 1.3 63.3 + - - +
375A LEU* 3.5 9.4 + - - +
376A HIS* 3.1 24.9 + - - +
439A MET* 4.0 30.1 - - + +
442A PHE* 5.5 0.2 - - - -
443A PHE* 4.6 4.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A LEU 2.9 17.6 + - - +
370A LYS* 3.6 6.7 - - - +
372A ALA* 1.3 78.8 - - - +
374A GLU* 1.3 56.5 + - - +
376A HIS* 3.4 4.3 + - - +
377A LYS* 3.0 32.3 + - - +
439A MET* 3.7 28.9 - - + +
474A PHE* 4.1 16.2 - - + -
478A VAL* 4.4 9.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A LEU* 4.1 22.7 - - + +
370A LYS 3.2 14.1 + - - +
371A ALA* 3.8 5.8 - - - +
373A ASN* 1.3 77.5 - - - +
375A LEU* 1.3 64.8 + - - +
377A LYS* 4.3 16.4 + - - +
378A PHE* 3.0 42.1 + - - +
381A GLU* 4.8 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ALA* 3.4 28.3 - - - +
352A LEU* 3.9 18.0 - - + +
353A TRP* 3.7 38.4 - - + +
356A ALA* 5.4 0.4 - - + -
371A ALA 3.0 16.9 + - - +
372A ALA* 3.6 7.6 - - - +
374A GLU* 1.3 74.7 - - - +
376A HIS* 1.3 58.2 + - - +
378A PHE* 3.8 0.7 - - - +
379A MET* 2.9 48.2 + - + +
389A LEU* 4.2 6.5 - - + -
442A PHE* 4.3 8.3 - - + -
443A PHE* 4.2 23.8 - - + -
446A CYS* 4.4 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A ALA 3.1 14.6 + - - +
373A ASN* 3.6 6.7 + - - +
375A LEU* 1.3 81.9 - - - +
377A LYS* 1.3 62.1 + - - +
379A MET* 3.8 1.0 - - - +
380A LYS* 3.0 58.7 + - + +
438A LYS* 3.8 43.8 + - + +
439A MET* 4.2 16.0 - - + +
442A PHE* 3.4 49.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ASN* 3.0 20.3 + - - +
374A GLU* 3.9 19.2 + - - +
376A HIS* 1.3 77.2 - - - +
378A PHE* 1.3 59.3 + - - +
380A LYS* 3.2 16.3 + - - +
381A GLU* 2.8 57.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ASN* 3.4 31.6 - - + -
348A ASN* 4.0 18.8 - - + -
349A ALA* 3.9 17.0 - - + -
352A LEU* 3.6 24.2 - - + -
374A GLU* 3.0 28.1 + - - +
375A LEU 3.8 0.4 - - - +
377A LYS* 1.3 74.3 - - - +
379A MET* 1.3 69.4 + - + +
381A GLU* 3.1 20.4 + - - +
382A LYS* 3.0 59.8 + - + +
384A LEU* 4.9 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU* 5.3 0.4 - - + -
349A ALA* 3.6 27.8 - - + -
375A LEU* 2.9 31.7 + - + +
376A HIS 3.8 3.4 - - - +
378A PHE* 1.3 76.5 - - + +
380A LYS* 1.3 62.5 + - - +
382A LYS* 3.1 2.6 + - - -
383A ASN 3.0 4.2 + - - -
384A LEU* 2.9 55.1 + - + +
385A LYS 3.1 35.0 - - - +
386A GLU 4.3 0.2 - - - +
389A LEU* 3.8 22.9 - - + +
442A PHE* 3.8 24.2 - - + -
446A CYS* 4.4 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A HIS* 3.0 56.8 + - + +
377A LYS* 3.5 17.3 - - - +
379A MET* 1.3 76.0 - - + +
381A GLU* 1.3 62.2 + - + +
383A ASN* 3.2 14.5 + - - +
384A LEU 4.8 2.5 - - - +
438A LYS* 5.4 5.0 - - - +
442A PHE* 5.7 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A GLU* 4.8 4.3 - - - +
377A LYS* 2.8 48.7 + - + +
378A PHE* 3.1 26.0 + - - +
380A LYS* 1.3 72.2 - - - +
382A LYS* 1.3 69.0 + - + +
383A ASN* 3.3 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ASN* 3.5 35.2 + - - +
378A PHE* 3.0 52.2 + - + +
379A MET 3.1 0.9 + - - +
381A GLU* 1.3 84.7 - - + +
383A ASN* 1.3 70.7 + - - +
384A LEU* 3.2 26.9 + - + +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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