Contacts of the helix formed by residues 427 - 448 (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 THR 427 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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425A GLU* 2.8 9.6 + - - -
426A SER* 1.3 83.4 + - - +
428A VAL* 1.3 70.1 + - + +
430A PRO* 3.8 0.9 - - - -
431A GLY* 3.1 26.0 + - - -
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Residues in contact with VAL 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A GLU* 2.8 21.9 + - + +
427A THR* 1.3 81.4 - - + +
429A GLU* 1.3 66.0 + - - +
431A GLY* 3.3 1.0 + - - -
432A LEU* 3.0 42.5 + - + +
483A SER* 6.5 0.7 - - - -
484A LYS 3.9 15.0 - - - +
485A ILE* 3.6 23.3 - - + -
486A TRP 5.7 0.9 - - - +
490A THR* 4.8 2.5 - - - +
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Residues in contact with GLU 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A TYR* 2.7 30.5 + - + +
420A ALA* 3.8 14.7 - - + +
425A GLU* 3.1 3.3 + - - +
428A VAL* 1.3 77.8 - - - +
430A PRO* 1.3 67.1 - - + +
432A LEU* 3.4 7.4 + - - +
433A VAL* 3.1 28.9 + - + +
475A ILE* 5.2 3.6 - - + -
485A ILE* 4.0 21.6 - - + +
493A LEU* 4.5 0.4 - - - +
494A MET* 3.5 6.2 - - + +
497A LYS* 2.8 33.3 + - - -
522A LYS* 2.7 43.8 + - - +
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Residues in contact with PRO 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A SER* 3.6 26.1 - - - +
420A ALA* 3.5 20.6 - - + +
421A ALA* 3.7 13.0 - - + -
425A GLU* 3.7 9.0 - - - +
426A SER 3.5 26.9 - - - +
427A THR 4.6 0.2 - - - +
428A VAL 3.6 2.0 - - - -
429A GLU* 1.3 93.5 - - + +
431A GLY* 1.3 56.7 + - - +
434A SER* 2.8 37.5 + - - +
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Residues in contact with GLY 431 (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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427A THR 3.1 20.6 + - - -
428A VAL 3.7 0.7 - - - -
430A PRO* 1.3 77.6 - - - +
432A LEU* 1.3 61.4 + - - +
434A SER* 3.5 5.1 + - - -
435A ALA* 3.1 22.7 + - - +
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Residues in contact with LEU 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A VAL* 3.0 40.6 + - + +
429A GLU* 3.6 7.9 - - - +
431A GLY* 1.3 75.7 - - - +
433A VAL* 1.3 63.0 + - - +
435A ALA* 3.3 18.7 + - - +
436A VAL* 3.5 10.6 + - - +
474A PHE* 4.9 5.9 - - + -
475A ILE* 3.8 38.6 - - + -
478A VAL* 4.3 23.8 - - + -
479A ALA* 6.0 3.8 - - + -
485A ILE* 4.6 6.5 - - + -
490A THR* 4.7 4.3 - - + -
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Residues in contact with VAL 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ALA* 3.3 40.6 - - + +
416A TYR* 3.6 44.0 - - + -
417A SER* 3.7 15.7 - - - +
429A GLU* 3.1 17.6 + - + +
432A LEU* 1.3 75.3 - - - +
434A SER* 1.3 64.1 + - - +
436A VAL* 3.0 23.0 + - - +
437A ASN* 3.5 4.0 + - - +
471A ILE* 4.3 6.3 - - + -
475A ILE* 4.0 12.8 - - + -
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Residues in contact with SER 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A SER* 3.5 17.5 + - - -
430A PRO* 2.8 26.3 + - - +
431A GLY* 3.8 5.6 - - - -
433A VAL* 1.3 74.7 - - - +
435A ALA* 1.3 60.6 + - - +
437A ASN* 3.1 20.3 + - - +
438A LYS* 3.2 12.7 + - - +
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Residues in contact with ALA 435 (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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431A GLY 3.1 13.8 + - - +
432A LEU* 3.4 12.6 - - - +
434A SER* 1.3 77.0 - - - +
436A VAL* 1.3 56.1 + - - +
438A LYS* 3.3 9.9 + - + +
439A MET* 2.9 46.0 + - + +
474A PHE* 5.8 1.1 - - + -
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Residues in contact with VAL 436 (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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369A LEU* 3.7 30.1 - - + -
409A LEU* 4.3 13.2 - - + -
413A ALA* 4.1 17.0 - - + -
432A LEU 3.8 11.9 - - - +
433A VAL* 3.1 11.9 - - - +
435A ALA* 1.3 76.9 - - - +
437A ASN* 1.3 62.0 + - - +
439A MET* 3.3 8.4 - - - +
440A SER* 3.0 27.7 + - - -
471A ILE* 4.4 17.0 - - + -
474A PHE* 3.8 30.5 - - + -
475A ILE* 5.7 0.2 - - + -
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Residues in contact with ASN 437 (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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409A LEU* 4.2 0.9 - - - +
410A TRP* 2.9 55.5 - - + +
413A ALA* 3.6 11.1 + - - +
414A SER* 3.2 40.2 + - - +
417A SER* 5.2 1.8 + - - -
433A VAL 3.5 2.4 + - - -
434A SER* 3.1 13.2 + - - +
436A VAL* 1.3 78.8 - - - +
438A LYS* 1.3 62.8 + - - +
440A SER* 4.0 2.7 - - - -
441A ALA* 3.0 27.2 + - - +
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Residues in contact with LYS 438 (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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376A HIS* 3.8 29.4 + - + -
380A LYS* 5.4 4.5 - - - +
434A SER 3.2 13.3 + - - +
435A ALA* 3.3 11.9 + - - +
437A ASN* 1.3 76.4 - - - +
439A MET* 1.3 62.2 + - - +
441A ALA* 3.6 5.3 + - - +
442A PHE* 3.1 21.8 + - - +
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Residues in contact with MET 439 (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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369A LEU* 3.5 37.5 - - + +
372A ALA* 4.0 23.8 - - + +
373A ASN* 3.7 23.8 - - - +
376A HIS* 4.2 17.5 + - - +
435A ALA* 2.9 33.7 + - + +
436A VAL* 3.3 13.0 - - - +
438A LYS* 1.3 76.5 - - - +
440A SER* 1.3 62.4 + - - +
442A PHE* 3.3 4.3 + - - +
443A PHE* 3.0 26.7 + - - +
474A PHE* 3.7 26.9 - - + -
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Residues in contact with SER 440 (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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368A TYR* 2.7 35.3 + - - -
369A LEU* 4.8 1.1 - - - -
372A ALA* 4.9 0.2 - - - -
406A LEU* 3.4 14.3 + - - +
409A LEU* 3.5 17.9 - - - +
410A TRP* 5.7 4.0 - - - -
436A VAL 3.0 18.9 + - - -
437A ASN* 4.0 5.2 - - - -
439A MET* 1.3 75.6 - - - +
441A ALA* 1.3 65.2 - - - +
443A PHE* 3.3 4.7 + - - +
444A MET* 3.1 22.3 + - - +
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Residues in contact with ALA 441 (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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410A TRP* 4.0 20.7 - - + -
437A ASN 3.0 18.7 + - - +
438A LYS* 3.7 6.1 - - - +
440A SER* 1.3 77.2 - - - +
442A PHE* 1.3 56.1 + - - +
444A MET* 3.3 7.3 + - - +
445A ASP* 2.9 43.6 + - - +
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Residues in contact with PHE 442 (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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372A ALA 5.5 0.2 - - - -
375A LEU* 4.3 7.4 - - + -
376A HIS* 3.4 53.2 - + + +
379A MET* 3.8 37.2 - - + -
380A LYS* 5.7 2.5 - - + -
384A LEU 4.6 2.7 - - - -
385A LYS* 5.0 2.0 - - - -
386A GLU* 3.5 36.0 - - + +
438A LYS 3.1 15.4 + - - +
439A MET 3.5 9.0 - - - +
440A SER 3.2 0.2 - - - -
441A ALA* 1.3 74.1 - - - +
443A PHE* 1.3 67.3 + - - +
445A ASP* 3.3 5.6 + - - +
446A CYS* 3.0 46.0 + - - -
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Residues in contact with PHE 443 (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* 3.0 75.9 + + - -
356A ALA* 3.6 20.6 - - + -
357A ASN* 3.6 27.4 - - - -
360A LEU* 3.7 22.9 - - + -
368A TYR* 3.4 24.7 - + + +
372A ALA* 4.6 4.5 - - + -
375A LEU* 4.2 16.6 - - + +
398A ILE* 3.7 16.2 - - + -
406A LEU* 4.2 6.1 - - + -
439A MET 3.0 12.2 + - - +
440A SER 3.4 6.7 - - - +
442A PHE* 1.3 77.2 - - - +
444A MET* 1.3 67.1 + - - +
446A CYS* 3.4 4.5 + - - +
447A LYS* 3.9 0.7 + - - +
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Residues in contact with MET 444 (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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398A ILE* 4.2 4.0 - - + -
403A TYR* 3.8 33.2 - - + -
406A LEU* 3.9 27.6 - - + -
440A SER 3.1 10.4 + - - +
441A ALA* 3.8 9.6 - - - +
442A PHE 3.2 0.2 - - - -
443A PHE* 1.3 85.1 - - - +
445A ASP* 1.3 70.4 + - - +
447A LYS* 3.1 7.6 + - - +
448A LEU* 2.9 45.1 + - + +
454A ALA* 4.6 8.1 - - + -
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Residues in contact with ASP 445 (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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386A GLU* 3.5 25.9 - - + +
390A ARG* 2.8 32.6 + - - +
441A ALA* 2.9 28.5 + - - +
442A PHE* 3.9 0.4 - - - +
444A MET* 1.3 86.8 - - - +
446A CYS* 1.3 60.0 + - - +
447A LYS 3.2 0.2 - - - -
448A LEU* 3.2 15.5 - - - +
450A PRO* 6.1 1.5 - - - +
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Residues in contact with CYS 446 (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* 3.8 14.1 - - + -
375A LEU* 4.4 5.6 - - - -
379A MET* 4.4 1.3 - - - -
386A GLU* 4.0 18.2 - - - -
389A LEU* 3.9 24.2 - - + -
390A ARG* 3.0 32.4 - - - +
393A LEU* 3.5 5.1 - - + +
442A PHE* 3.0 51.3 + - - -
443A PHE 3.5 10.3 - - - +
444A MET 3.2 0.4 - - - -
445A ASP* 1.3 78.2 - - - +
447A LYS* 1.3 56.5 + - - +
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Residues in contact with LYS 447 (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* 3.7 24.7 - - + +
390A ARG* 3.4 17.4 + - - +
393A LEU* 2.9 41.7 + - + +
394A SER* 4.1 8.7 + - - +
396A LYS 2.9 20.9 + - - +
397A THR* 4.7 4.0 - - - +
398A ILE* 3.8 23.8 - - + +
403A TYR* 4.2 8.3 - - - +
443A PHE 3.9 0.2 + - - -
444A MET 3.1 8.7 + - - +
446A CYS* 1.3 80.8 - - - +
448A LEU* 1.3 61.3 + - + +
449A SER 4.0 0.3 + - - -
452A GLU* 4.3 3.6 - - - +
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Residues in contact with LEU 448 (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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390A ARG* 3.4 4.0 + - - -
403A TYR* 3.3 26.5 - - + +
444A MET* 2.9 37.1 + - + +
445A ASP* 3.2 25.4 - - - +
447A LYS* 1.3 80.0 - - + +
449A SER* 1.3 65.8 + - - +
450A PRO* 4.8 0.2 - - - +
452A GLU* 3.7 36.6 - - + +
453A ARG 4.1 10.1 - - - +
454A ALA* 3.6 28.9 - - - +
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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
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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