Contacts of the helix formed by residues 431 - 459 (chain A) in PDB entry 1GWX
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 LEU 431 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LEU* 4.4 21.5 - - + +
379A LEU* 4.0 13.9 - - + -
421A LEU* 4.2 17.7 - - + -
425A HIS* 3.7 43.3 - - + +
428A ALA* 3.8 7.2 - - + -
429A GLN* 2.5 30.2 + - - +
430A TYR* 1.3 68.9 - - - +
432A PHE* 1.3 72.8 + - - +
434A LYS* 2.8 6.5 + - + +
435A LEU* 2.7 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A LEU* 3.3 41.5 - - + -
417A LEU* 3.8 18.2 - - + -
418A GLU* 3.3 48.2 - - + +
421A LEU* 3.5 15.6 - - + +
431A LEU* 1.3 74.3 - - - +
433A PRO* 1.3 75.7 - - + +
435A LEU* 2.6 28.9 + - - +
436A LEU* 3.1 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A TYR* 3.6 25.4 - - + +
431A LEU 3.8 1.1 - - - +
432A PHE* 1.3 103.3 - - + +
434A LYS* 1.3 62.8 + - - +
435A LEU 3.2 0.2 - - - -
436A LEU* 3.2 15.9 + - + +
437A GLN* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LEU* 5.0 15.7 - - + -
429A GLN* 3.1 51.5 - - - +
430A TYR* 2.8 36.0 + - + +
431A LEU* 2.8 10.4 + - - +
432A PHE 2.8 0.4 + - - -
433A PRO* 1.3 76.7 - - - +
435A LEU* 1.3 61.5 + - - +
436A LEU 3.1 0.4 + - - -
437A GLN* 3.3 7.8 + - + +
438A LYS* 3.2 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A PHE* 3.9 7.4 - - + -
377A LEU* 3.5 23.1 - - + -
379A LEU* 3.7 29.4 - - + -
383A ASP* 5.6 0.7 - - + -
387A PHE* 3.1 39.2 - - + -
417A LEU* 4.2 15.5 - - + -
421A LEU* 4.2 16.6 - - + -
431A LEU* 2.7 26.2 + - + +
432A PHE* 2.6 15.9 + - - +
434A LYS* 1.3 70.5 - - - +
436A LEU* 1.3 61.5 + - + +
438A LYS* 3.6 2.2 - - + +
439A MET* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A LEU* 3.8 33.7 - - + -
417A LEU* 6.0 0.9 - - + -
432A PHE* 3.1 43.0 + - + +
433A PRO* 3.3 14.8 - - + +
434A LYS 3.1 0.4 - - - -
435A LEU* 1.3 77.9 - - + +
437A GLN* 1.3 65.1 + - - +
438A LYS 3.1 1.6 - - - -
439A MET* 3.1 31.7 + - - +
440A ALA* 3.3 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A PRO 3.1 9.2 + - - +
434A LYS* 3.3 10.1 + - + +
436A LEU* 1.3 78.8 - - - +
438A LYS* 1.3 58.8 + - + +
440A ALA* 3.1 16.4 + - - +
441A ASP* 2.8 55.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A PHE* 4.0 11.4 - - + -
373A LYS* 4.2 14.1 + - - +
374A PHE* 3.3 37.5 - - + +
377A LEU* 3.8 33.7 - - + +
387A PHE* 4.0 11.0 - - + -
434A LYS* 3.2 24.7 + - + +
435A LEU* 3.6 12.3 - - - +
436A LEU 3.1 0.4 - - - -
437A GLN* 1.3 77.2 - - + +
439A MET* 1.3 51.3 + - - +
441A ASP* 3.0 18.5 + - - +
442A LEU* 2.5 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A PHE* 3.8 15.9 - - + -
390A ALA* 4.0 10.1 - - + +
391A ILE* 3.6 43.5 - - + +
394A CYS* 6.3 0.2 - - + -
410A GLN* 5.0 7.6 - - - +
414A LEU* 4.6 11.4 - - - -
435A LEU* 2.9 25.1 - - - +
436A LEU* 3.2 28.3 - - - +
438A LYS* 1.3 77.2 - - - +
440A ALA* 1.3 57.3 + - - +
442A LEU* 3.2 13.1 + - - +
443A ARG* 2.8 51.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A LEU 3.3 5.4 + - - +
437A GLN* 3.1 27.2 + - - +
439A MET* 1.3 75.3 - - - +
441A ASP* 1.3 66.8 + - - +
443A ARG* 3.0 22.8 + - - +
444A GLN* 3.0 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A PHE* 3.8 19.4 - - + -
437A GLN* 2.8 50.0 + - - +
438A LYS* 3.1 29.5 + - - +
440A ALA* 1.3 75.3 - - - +
442A LEU* 1.3 58.2 + - - +
444A GLN* 3.0 6.7 + - - +
445A LEU* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A GLU* 3.2 46.4 - - + +
327A PHE* 4.0 11.2 - - + -
328A ALA* 3.8 15.9 - - + +
370A PHE* 3.6 27.4 - - + -
387A PHE* 3.4 37.9 - - + -
391A ILE* 4.8 7.2 - - + -
438A LYS 2.5 26.0 + - - +
439A MET* 3.3 10.5 - - - +
441A ASP* 1.3 74.9 - - - +
443A ARG* 1.3 58.8 + - - +
445A LEU* 4.1 4.7 - - + +
446A VAL* 3.2 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A GLU* 3.1 38.8 + - - +
391A ILE 5.0 0.4 + - - -
394A CYS* 4.2 16.2 - - - +
396A ASP* 5.8 2.9 - - - -
397A ARG* 3.6 19.8 - - - +
439A MET* 2.8 45.8 + - - +
440A ALA* 3.0 14.2 + - - +
442A LEU* 1.3 78.4 - - - +
444A GLN* 1.3 66.7 + - - +
446A VAL* 4.2 3.5 + - - +
447A THR* 3.9 17.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ALA 3.0 10.7 + - - +
441A ASP* 3.0 8.3 + - - +
443A ARG* 1.3 86.5 + - - +
445A LEU* 1.3 61.3 + - - +
446A VAL 3.1 1.3 - - - -
447A THR* 2.8 41.8 + - + +
448A GLU* 3.1 13.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A PHE* 3.3 37.7 - - + -
366A PRO* 3.6 33.2 - - + +
367A LYS* 3.6 19.3 - - + +
370A PHE* 3.9 23.8 - - + -
441A ASP 3.0 15.6 + - - +
442A LEU* 4.5 5.2 - - + +
444A GLN* 1.3 76.7 - - - +
446A VAL* 1.3 60.3 + - + +
448A GLU* 2.9 36.0 - - - +
449A HIS* 3.1 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A TYR 5.0 5.6 - - - +
323A HIS* 4.1 15.0 - - + -
324A GLU* 3.5 29.6 - - + +
327A PHE* 3.3 29.6 - - + -
442A LEU 3.2 19.2 + - - +
443A ARG* 4.3 4.5 - - - +
444A GLN 3.1 0.8 - - - -
445A LEU* 1.3 77.0 - - - +
447A THR* 1.3 57.1 + - - +
449A HIS* 3.9 6.9 - - - +
450A ALA* 3.2 23.9 + - - +
473A TYR* 5.1 2.7 - - + +
476A MET* 4.5 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ARG 3.9 10.2 + - - -
444A GLN* 2.8 34.8 + - + +
446A VAL* 1.3 79.8 - - - +
448A GLU* 1.3 62.6 + - + +
449A HIS 3.2 0.4 - - - -
450A ALA* 3.5 6.3 + - - +
451A GLN* 3.0 48.6 + - - +
476A MET* 6.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A PRO* 3.3 28.9 - - - +
367A LYS* 3.5 13.2 + - - -
444A GLN 3.1 5.5 + - - +
445A LEU* 2.9 39.4 - - - +
447A THR* 1.3 76.9 - - + +
449A HIS* 1.3 59.3 + - - +
450A ALA 3.3 0.2 - - - -
451A GLN* 3.3 18.4 + - - +
452A MET* 2.9 51.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A 433 2.4 63.0 + + - -
327A PHE* 3.7 15.7 - + + -
363A ILE* 3.9 6.8 + - - +
367A LYS* 2.9 34.2 + - - +
445A LEU 3.1 18.3 + - - +
446A VAL* 3.9 7.4 - - - +
448A GLU* 1.3 77.4 - - - +
450A ALA* 1.3 60.2 + - - +
451A GLN 3.1 0.2 - - - -
452A MET* 3.2 6.4 + - - +
453A MET* 2.8 50.5 + - + +
473A TYR* 3.1 15.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A VAL 3.2 16.3 + - - +
447A THR* 3.6 6.7 - - - +
448A GLU 3.3 0.2 - - - -
449A HIS* 1.3 81.4 - - - +
451A GLN* 1.3 56.5 + - + +
453A MET* 3.4 4.4 + - - +
454A GLN* 2.8 29.5 + - - +
473A TYR* 3.6 32.6 - - + -
476A MET* 4.7 4.5 - - + +
477A TYR 4.2 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A THR* 3.0 33.8 + - + +
448A GLU* 3.5 18.7 - - - +
449A HIS 3.1 0.4 - - - -
450A ALA* 1.3 73.9 - - + +
452A MET* 1.3 58.9 + - - +
453A MET 3.1 1.3 - - - -
454A GLN* 2.8 27.2 + - - +
455A ARG* 2.9 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 452 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ASP* 3.2 36.8 - - + +
363A ILE* 3.5 33.0 - - + +
366A PRO* 4.2 6.1 - - + -
367A LYS* 4.8 0.9 - - - -
448A GLU* 2.9 44.6 + - + +
449A HIS* 3.6 12.8 - - - +
451A GLN* 1.3 74.7 - - - +
453A MET* 1.3 66.2 + - + +
455A ARG* 3.2 9.8 + - - +
456A ILE* 2.9 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 453 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A 433 3.5 30.3 - - + +
282A PHE* 4.0 11.7 - - + -
363A ILE* 3.9 33.2 - - + -
449A HIS* 2.8 59.5 + - + +
450A ALA* 3.4 7.6 - - - +
452A MET* 1.3 78.7 - - + +
454A GLN* 1.3 63.1 + - - +
456A ILE* 3.1 10.0 - - + +
457A LYS* 3.0 24.0 + - - +
465A LEU* 5.7 4.7 - - + -
473A TYR* 4.1 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 454 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A ALA 2.8 15.3 + - - +
451A GLN* 2.8 18.1 + - - +
453A MET* 1.3 78.5 - - - +
455A ARG* 1.3 61.1 + - + +
457A LYS* 3.3 31.3 + - - +
458A LYS* 3.3 13.7 + - - +
473A TYR* 5.0 12.5 - - - +
476A MET 5.5 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 455 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A GLN* 2.9 15.8 + - + +
452A MET* 3.2 9.2 + - - +
454A GLN* 1.3 76.4 - - - +
456A ILE* 1.3 53.6 + - - +
458A LYS* 3.1 36.6 + - - +
459A THR* 2.7 57.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 456 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PHE* 3.3 40.6 - - + -
359A PRO* 5.5 7.2 - - + -
360A PHE* 3.6 22.0 - - + -
363A ILE* 5.7 3.8 - - + -
452A MET 2.9 21.0 + - - +
453A MET* 3.1 29.2 - - + +
455A ARG* 1.3 75.2 - - - +
457A LYS* 1.3 58.4 + - - +
459A THR* 3.6 9.4 - - + -
460A GLU* 2.9 41.6 + - + +
463A THR* 4.3 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 457 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A MET 3.0 12.6 + - - +
454A GLN* 3.6 26.7 - - - +
455A ARG 3.1 0.2 - - - -
456A ILE* 1.3 77.8 - - - +
458A LYS* 1.3 59.8 + - - +
460A GLU 4.6 1.8 - - - -
461A THR* 4.9 9.4 - - - -
465A LEU* 5.9 7.0 - - + -
470A GLN* 3.2 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 458 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A GLN 3.3 8.4 + - - +
455A ARG* 3.1 33.1 + - - +
457A LYS* 1.3 81.7 - - - +
459A THR* 1.3 60.1 + - - +
461A THR* 4.7 9.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 459 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A PRO* 5.5 5.2 - - + -
455A ARG* 2.7 55.6 + - + +
456A ILE* 3.6 5.4 - - - -
458A LYS* 1.3 74.3 - - - +
460A GLU* 1.3 78.9 + - - +
461A THR* 3.5 8.8 + - - +
----------------------------------------------------------
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