Contacts of the helix formed by residues 403 - 425 (chain A) in PDB entry 1NYX
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 VAL 403 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A GLY* 3.8 21.8 - - - +
396A ASP* 5.8 0.4 - - - +
400A LEU* 3.8 27.8 - - + +
401A LEU 3.7 2.8 + - - +
402A ASN* 1.3 74.5 - - - +
404A LYS* 1.3 56.5 + - - +
405A PRO* 3.0 3.7 - - - +
406A ILE* 2.6 30.9 + - - +
407A GLU* 2.7 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A VAL* 1.3 76.3 - - - +
405A PRO* 1.3 68.7 - - + +
407A GLU* 3.7 13.0 - - + +
408A ASP* 2.8 69.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LEU* 4.2 22.4 - - + -
402A ASN* 3.6 31.2 - - + +
403A VAL 3.0 7.0 - - - +
404A LYS* 1.3 103.3 - - + +
406A ILE* 1.3 66.1 + - - +
408A ASP* 3.3 8.9 + - + +
409A ILE* 3.2 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LEU* 3.4 24.2 - - + +
313A ASP* 3.7 23.1 - - + +
317A LEU* 3.8 22.9 - - + -
393A LEU* 4.2 17.2 - - + +
394A SER 4.0 4.7 - - - +
395A GLY* 3.7 26.7 - - - +
400A LEU* 3.9 23.1 - - + -
402A ASN 3.7 11.2 - - - +
403A VAL* 2.6 14.0 + - - +
405A PRO* 1.3 71.0 - - + +
407A GLU* 1.3 64.9 + - - +
409A ILE* 3.5 3.6 + - - +
410A GLN* 3.3 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A SER 4.1 7.5 - - - +
395A GLY* 4.0 12.0 - - - -
396A ASP* 4.0 16.3 + - - +
403A VAL* 2.7 46.4 + - + +
404A LYS* 3.6 12.0 - - + +
406A ILE* 1.3 74.1 - - - +
408A ASP* 1.3 56.4 + - - +
410A GLN* 3.2 7.2 + - - +
411A ASP* 2.4 44.5 + - - +
434B LYS* 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A LYS* 2.8 57.5 + - - +
405A PRO* 3.5 7.3 - - + +
407A GLU* 1.3 71.7 - - - +
409A ILE* 1.3 67.2 + - - +
410A GLN 3.4 0.2 + - - -
411A ASP* 3.3 20.0 + - - +
412A ASN* 3.5 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ILE* 5.2 1.3 - - + -
304A PRO 3.8 17.0 - - - +
305A GLY* 3.5 35.2 - - - +
306A PHE 3.8 0.2 - - - +
309A LEU* 4.1 16.8 - - + -
393A LEU* 3.3 40.2 - - + -
405A PRO 3.2 13.8 + - - +
406A ILE 3.8 2.2 - - - +
407A GLU 3.3 0.2 - - - -
408A ASP* 1.3 78.1 - - + +
410A GLN* 1.3 59.6 + - - +
412A ASN* 2.9 27.4 + - - +
413A LEU* 3.1 17.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A VAL* 3.4 21.7 - - + +
393A LEU* 2.3 36.7 - - + +
394A SER* 3.0 23.2 + - - +
406A ILE 3.3 5.6 + - - +
407A GLU* 3.2 8.1 + - - +
409A ILE* 1.3 78.2 - - - +
411A ASP* 1.3 59.6 + - - +
412A ASN 2.7 5.9 + - - -
413A LEU* 2.8 7.1 + - - +
414A LEU* 2.7 59.1 + - + +
437B GLN* 3.3 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A GLU* 2.4 37.1 + - - +
408A ASP* 3.3 16.5 - - - +
409A ILE 3.4 0.4 - - - -
410A GLN* 1.3 77.4 + - - +
412A ASN* 1.3 56.8 + - - +
414A LEU* 4.0 15.5 - - - +
415A GLN* 3.3 27.6 + - - +
429B SER* 4.0 16.9 + - - +
430B GLN* 4.0 5.9 - - + +
434B LYS* 2.8 42.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 3.9 10.7 - - - +
214A LEU* 3.5 23.2 - - - +
304A PRO* 6.0 2.6 - - - +
408A ASP 3.5 8.6 + - - +
409A ILE* 2.9 17.7 + - - +
410A GLN 2.7 0.4 - - - -
411A ASP* 1.3 79.5 - - - +
413A LEU* 1.3 63.6 + - - +
414A LEU 3.1 1.1 - - - -
415A GLN* 2.9 21.4 + - - +
416A ALA* 2.9 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LEU* 4.5 11.4 - - + -
218A LEU* 3.9 28.3 - - + -
303A ILE* 4.2 11.9 - - + -
304A PRO* 5.6 1.6 - - + +
386A ILE* 3.4 7.3 - - - +
389A ALA* 3.5 39.3 - - + +
390A VAL* 3.6 16.2 - - + +
393A LEU* 3.7 27.8 - - + -
409A ILE* 3.1 16.8 + - + +
410A GLN* 2.8 7.5 + - - +
412A ASN* 1.3 77.2 - - - +
414A LEU* 1.3 58.5 + - - +
416A ALA* 3.0 9.5 + - - +
417A LEU 2.9 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A VAL* 3.2 37.9 - - + -
410A GLN* 2.7 44.4 + - - +
411A ASP* 4.0 12.1 - - - +
413A LEU* 1.3 70.2 - - - +
415A GLN* 1.3 66.7 - - - +
417A LEU* 3.2 4.1 + - - +
418A GLU* 2.8 25.8 + - - +
432A PHE* 3.7 5.4 - - + -
436A LEU* 4.4 15.9 - - + -
430B GLN* 3.6 20.4 - - + -
433B ALA* 3.6 24.0 - - + -
434B LYS* 4.6 6.1 - - + -
437B GLN* 4.6 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A GLU* 4.7 15.8 + - - +
211A LEU* 3.4 26.7 - - + +
411A ASP 3.3 13.4 + - - +
412A ASN* 2.9 24.7 + - - +
414A LEU* 1.3 79.4 - - - +
416A ALA* 1.3 66.2 + - - +
418A GLU* 3.5 5.3 + - - +
419A LEU* 3.3 18.5 + - - +
429B SER* 4.8 9.5 + - - -
430B GLN* 2.9 27.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 3.7 20.8 - - + +
214A LEU* 4.0 24.0 - - + -
215A ALA* 4.9 3.7 - - + +
218A LEU* 5.0 0.9 - - + -
386A ILE* 3.8 19.7 - - + -
412A ASN 2.9 11.5 + - - +
413A LEU* 3.1 11.2 - - - +
415A GLN* 1.3 74.6 - - - +
417A LEU* 1.3 59.7 + - - +
419A LEU* 2.9 7.8 + - - +
420A GLN* 2.8 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ASP 3.8 14.6 - - - +
386A ILE* 3.4 32.6 - - + +
387A PHE* 3.9 35.2 - - + +
390A VAL* 4.4 9.2 - - + -
413A LEU 2.9 8.4 + - - +
414A LEU* 3.5 8.3 - - - +
416A ALA* 1.3 75.6 - - - +
418A GLU* 1.3 55.6 - - - +
419A LEU 2.7 12.1 + - - -
420A GLN* 2.8 12.6 + - + -
421A LEU* 3.0 37.3 + - + +
432A PHE* 3.9 17.9 - - + -
435A LEU* 4.2 9.4 - - + -
436A LEU* 4.8 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A LEU 2.8 15.7 + - - +
415A GLN* 3.9 5.5 - - - +
417A LEU* 1.3 71.4 - - - +
419A LEU* 1.3 56.6 + - - +
421A LEU* 4.2 2.4 - - - +
422A LYS* 3.3 30.3 + - + +
432A PHE* 3.4 45.8 - - + +
418B GLU* 3.1 25.1 - - - +
422B LYS* 4.7 10.2 + - - -
430B GLN* 3.3 24.6 + - - +
432B PHE* 4.9 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A SER* 3.9 32.3 - - - +
211A LEU* 3.9 17.3 - - + -
212A ARG* 3.5 27.1 - - - +
415A GLN 3.3 8.7 + - - +
416A ALA 2.9 8.5 + - - +
417A LEU 2.7 4.8 + - - -
418A GLU* 1.3 74.7 - - - +
420A GLN* 1.3 56.1 + - - +
421A LEU 2.9 4.9 - - - -
422A LYS* 3.2 10.4 + - + +
423A LEU* 2.9 58.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ARG* 3.4 31.9 + - - +
215A ALA* 4.8 7.6 + - + +
219A TYR* 5.8 0.2 - - - +
382A SER* 2.5 51.8 + - - +
383A ASP* 3.1 18.7 - - - +
386A ILE* 3.2 29.4 - - + +
416A ALA 2.8 6.9 + - - +
417A LEU* 3.6 4.7 - - + +
419A LEU* 1.3 74.4 - - - +
421A LEU* 1.3 58.4 + - + +
423A LEU* 5.1 0.2 - - - +
424A ASN* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A LEU* 4.4 4.7 - - + -
383A ASP* 3.7 33.0 - - + +
417A LEU* 3.0 32.5 + - + +
418A GLU 4.3 2.5 - - - +
419A LEU 2.9 0.4 - - - -
420A GLN* 1.3 76.9 - - - +
422A LYS* 1.3 56.5 + - - +
423A LEU 2.7 14.9 + - - -
424A ASN* 4.2 0.4 - - - +
425A HIS* 2.8 32.6 + - - +
428A SER 6.1 0.4 - - - -
431A LEU* 4.1 30.3 - - + +
432A PHE* 3.6 47.1 - - + +
435A LEU* 4.3 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ASP* 5.2 12.6 - - - +
418A GLU* 3.3 22.4 + - + +
419A LEU* 3.2 12.0 + - + +
421A LEU* 1.3 77.3 - - - +
423A LEU* 1.3 65.8 + - + +
425A HIS 5.1 2.7 - - - -
426A PRO* 4.0 18.1 - - - +
422B LYS* 6.0 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ASP* 5.6 10.3 - - - +
212A ARG* 3.0 45.8 - - - +
419A LEU* 2.9 33.7 + - + +
420A GLN* 4.5 0.7 - - - +
421A LEU 2.7 1.8 + - - -
422A LYS* 1.3 86.7 - - + +
424A ASN* 1.3 58.5 + - - +
425A HIS 3.4 2.0 - - - -
426A PRO* 3.4 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ASP* 2.4 32.6 + - - +
382A SER* 3.8 6.4 + - - -
383A ASP* 3.2 9.4 + - - +
420A GLN* 3.0 25.8 + - - +
421A LEU 3.1 2.0 + - - -
423A LEU* 1.3 76.6 - - - +
425A HIS* 1.3 87.2 + - - +
426A PRO* 3.3 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LEU 4.7 3.1 - - - -
378A GLU* 2.8 31.1 + - + -
379A LEU* 4.2 1.2 - - - -
380A ASP* 3.9 4.8 + - + +
383A ASP* 2.8 28.0 + - - -
420A GLN 4.9 0.4 + - - -
421A LEU* 2.8 16.1 + - - +
422A LYS* 5.1 1.4 - - - -
424A ASN* 1.3 115.2 + - - +
426A PRO* 1.3 67.3 - - - +
427A GLU* 3.2 16.2 - - - +
428A SER* 2.8 33.9 + - - +
431A LEU* 3.8 21.4 - - + +
----------------------------------------------------------
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