Contacts of the helix formed by residues 396 - 425 (chain A) in PDB entry 2YPT
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 PHE 396 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A CYS* 3.3 54.7 - - + -
362A LEU* 3.6 32.1 - - + -
363A PHE 4.0 0.7 - - - -
366A LEU* 4.4 8.5 - - + -
391A ILE* 2.9 42.6 + - + +
392A PHE* 3.6 22.2 - + - +
394A PHE 3.4 0.2 - - - -
395A ILE* 1.3 78.5 - - + +
397A SER* 1.4 54.6 + - - +
398A PRO* 3.4 2.0 - - - -
399A TYR* 2.9 17.8 + + + +
400A ASN* 2.8 52.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 5.7 1.7 - - - +
26A PHE* 3.8 17.3 - - - -
27A SER* 5.1 7.1 + - - -
393A GLN 2.9 25.5 + - - -
394A PHE* 3.0 18.8 + - - +
395A ILE 3.3 0.2 - - - -
396A PHE* 1.4 73.7 - - - +
398A PRO* 1.4 66.5 - - - +
400A ASN* 3.3 10.9 + - - +
401A GLU* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 3.5 34.1 - - + -
394A PHE 4.4 1.8 - - - +
395A ILE 3.4 17.3 - - - +
396A PHE 3.5 0.4 - - - -
397A SER* 1.4 91.1 - - - +
399A TYR* 1.4 61.7 + - + +
401A GLU* 3.4 2.6 + - - +
402A VAL* 3.2 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ASN* 2.8 38.0 + - - -
358A LEU* 3.6 32.4 - - + +
359A CYS* 3.7 17.9 - - - -
362A LEU* 6.2 3.6 - - + -
396A PHE* 2.9 19.5 + + + +
398A PRO* 1.4 76.7 - - + +
400A ASN* 1.3 75.8 - - - +
402A VAL* 3.2 7.4 + - + +
403A LEU* 2.9 57.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ASN* 5.1 0.7 - - - +
359A CYS* 4.7 5.2 - - - -
392A PHE 3.0 27.5 + - - +
393A GLN* 4.8 3.0 + - - +
396A PHE* 2.8 31.5 + - - +
397A SER* 3.6 9.3 - - - +
399A TYR* 1.3 90.8 - - - +
401A GLU* 1.4 53.5 + - + +
403A LEU* 4.0 7.3 - - - +
404A SER* 2.8 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 4.3 15.9 - - + -
30A VAL* 3.8 27.8 - - + +
34A GLU* 4.0 10.2 - - - +
397A SER* 3.0 19.5 + - - +
398A PRO 3.7 5.2 - - - +
400A ASN* 1.4 74.0 - - + +
402A VAL* 1.4 63.3 + - + +
404A SER* 3.7 7.9 + - - -
405A PHE* 3.2 22.2 + - - +
455A TRP* 3.7 30.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 6.5 0.2 - - + -
398A PRO 3.2 18.3 + - - +
399A TYR* 3.2 8.0 + - + +
401A GLU* 1.4 73.8 - - + +
403A LEU* 1.4 59.5 - - - +
405A PHE* 3.1 8.9 + - + +
406A CYS* 2.9 46.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ILE* 5.3 7.2 - - + -
355A ASN* 3.4 35.4 - - + +
399A TYR* 2.9 47.4 + - + +
400A ASN* 4.0 7.0 - - - +
402A VAL* 1.4 77.1 - - - +
404A SER* 1.4 56.4 + - - +
406A CYS* 3.3 8.7 + - + +
407A LEU* 2.9 52.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ASN* 2.8 23.2 + - - +
401A GLU* 3.8 11.0 - - - -
402A VAL 3.3 0.2 - - - -
403A LEU* 1.4 74.0 - - - +
405A PHE* 1.4 55.9 - - - +
407A LEU* 3.5 8.4 + - - +
408A THR* 2.7 37.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A GLU 3.2 13.1 + - - +
402A VAL* 3.1 12.4 + - + +
404A SER* 1.4 71.7 - - - +
406A CYS* 1.3 67.4 + - - +
408A THR* 3.3 7.4 + - - -
409A VAL* 3.1 47.3 + - + +
454A MET* 3.3 45.3 - - + -
455A TRP* 3.5 52.0 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A VAL* 2.9 32.2 + - - +
403A LEU* 3.6 11.7 - - + +
405A PHE* 1.3 84.5 - - - +
407A LEU* 1.3 57.0 + - + +
409A VAL* 3.4 9.5 + - - +
410A LEU* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ASN* 4.8 10.8 - - - +
351A ILE* 3.8 39.5 - - + -
403A LEU* 2.9 49.4 + - + +
404A SER* 3.9 7.4 - - - +
405A PHE 3.3 0.2 - - - -
406A CYS* 1.3 73.1 - - + +
408A THR* 1.4 59.4 + - - +
410A LEU* 3.7 10.0 - - + +
411A SER* 2.9 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A SER* 2.7 22.9 + - - -
405A PHE* 3.3 9.7 + - - -
407A LEU* 1.4 72.4 - - - +
409A VAL* 1.4 63.3 + - - +
411A SER* 3.4 7.7 + - - -
412A ARG* 3.2 34.1 + - - +
454A MET 4.5 0.9 - - - +
455A TRP 3.9 13.5 + - - +
456A HIS 3.5 17.9 + - - +
457A TYR 3.4 23.6 - - - +
458A SER* 4.0 6.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A PHE* 3.1 43.5 + - + +
406A CYS* 3.6 10.5 - - - +
408A THR* 1.4 75.3 - - - +
410A LEU* 1.4 60.7 + - - +
412A ARG* 3.4 32.4 + - - +
413A ARG* 3.3 20.2 + - + +
454A MET* 4.6 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ASN* 6.0 1.6 - - - +
351A ILE* 5.9 6.1 - - + -
406A CYS 3.0 17.9 + - - +
407A LEU* 3.7 14.8 - - + +
409A VAL* 1.4 74.8 - - - +
411A SER* 1.4 53.3 + - - +
413A ARG* 3.2 9.5 + - - +
414A PHE* 2.8 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A LEU 2.9 18.3 + - - -
408A THR* 3.5 8.5 - - - -
409A VAL 3.4 0.2 - - - -
410A LEU* 1.4 76.0 - - - +
412A ARG* 1.4 54.9 + - - +
414A PHE* 3.4 8.6 + - - +
415A GLU* 3.0 32.9 + - - +
458A SER* 2.8 33.5 + - - -
459A HIS* 4.9 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A THR* 3.2 17.4 + - - +
409A VAL* 3.5 33.2 - - - +
410A LEU 3.3 0.2 - - - -
411A SER* 1.4 74.6 - - - +
413A ARG* 1.4 58.7 + - - +
415A GLU* 3.3 3.8 + - - +
416A PHE* 3.1 36.2 + - + -
453A SER 3.0 14.3 + - - -
454A MET* 2.8 49.2 + - - +
457A TYR* 2.7 35.8 + - - +
458A SER 3.2 18.1 + - - +
459A HIS 4.4 0.4 - - - -
460A PRO* 3.9 33.3 - - + +
461A PRO* 5.4 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A VAL* 3.3 10.5 + - + +
410A LEU* 3.2 10.9 + - - +
412A ARG* 1.4 78.5 - - - +
414A PHE* 1.4 56.1 + - - +
416A PHE* 3.5 10.8 + - - +
417A GLN* 3.2 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A HIS* 3.4 12.3 - - + -
344A HIS* 3.1 51.9 - - + -
348A ASN* 6.1 1.8 - - - +
410A LEU 2.8 17.1 + - - +
411A SER* 3.6 10.1 - - - +
413A ARG* 1.4 75.6 - - - +
415A GLU* 1.3 58.1 + - - +
418A ALA 3.2 11.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A HIS* 3.0 25.8 + - - -
339A HIS* 2.8 30.8 + - - -
411A SER* 3.0 22.2 + - - +
412A ARG 3.6 6.3 - - - +
413A ARG 3.3 0.2 - - - -
414A PHE* 1.3 74.7 - - - +
416A PHE* 1.4 59.3 + - - +
418A ALA* 3.3 4.0 + - - +
419A ASP* 3.0 36.5 + - - +
458A SER 4.5 1.1 - - - +
459A HIS* 3.2 45.2 + - + +
460A PRO* 3.8 15.7 - - + -
465A ARG* 3.7 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ARG* 3.1 26.7 + - + -
413A ARG* 3.7 11.2 - - - +
414A PHE 3.5 0.2 - - - -
415A GLU* 1.4 74.1 - - - +
417A GLN* 1.4 57.2 + - - +
419A ASP* 3.4 8.8 + - + +
420A ALA* 3.0 28.9 + - - +
460A PRO* 3.5 30.7 - - + -
464A GLU* 3.7 37.5 - - + -
465A ARG* 4.1 9.2 - - + -
468A ALA* 4.1 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU* 3.4 21.4 - - + +
344A HIS* 3.6 24.9 - - + +
413A ARG 3.2 17.1 + - - +
415A GLU 3.3 0.4 - - - -
416A PHE* 1.4 74.8 - - - +
418A ALA* 1.4 56.2 + - - +
420A ALA* 3.4 7.8 + - - +
421A PHE* 3.0 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A HIS* 3.4 51.6 - - + +
338A GLY* 4.7 0.7 - - - -
339A HIS* 3.6 27.4 - - + +
342A LEU* 4.1 5.1 - - - +
344A HIS* 4.7 0.4 - - + -
414A PHE 3.2 3.5 + - - +
415A GLU 3.5 3.4 - - - +
417A GLN* 1.4 76.6 - - - +
419A ASP* 1.4 58.3 + - - +
420A ALA 3.4 0.2 - - - -
421A PHE* 3.5 8.2 + - - +
422A ALA* 3.2 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A HIS* 2.8 25.3 + - - +
415A GLU 3.0 23.9 + - - +
416A PHE* 3.6 11.0 - - + +
417A GLN 3.3 0.2 - - - -
418A ALA* 1.4 72.8 - - - +
420A ALA* 1.4 60.1 + - - +
422A ALA* 3.3 8.6 + - - +
423A LYS* 3.2 21.3 + - - +
431A LEU* 5.9 2.1 - - - +
435A LEU* 4.8 6.2 - - - +
465A ARG* 3.1 42.9 + - - +
468A ALA* 6.1 3.1 - - + -
469A LEU* 3.8 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A PHE 3.0 17.3 + - - +
417A GLN* 3.5 9.6 - - - +
419A ASP* 1.4 74.1 - - - +
421A PHE* 1.4 57.9 + - - +
423A LYS* 3.4 8.6 + - - +
424A LYS* 3.0 26.2 + - - +
472A MET* 6.0 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ILE* 5.4 10.1 - - + -
334A GLY 3.4 17.5 - - - -
337A LEU* 4.4 7.2 - - + -
338A GLY* 3.5 17.7 - - - -
341A LYS* 3.7 25.8 - - + -
342A LEU* 4.0 23.3 - - + -
417A GLN 3.0 14.1 + - - +
418A ALA 3.5 9.4 - - - +
419A ASP 3.3 0.2 - - - -
420A ALA* 1.4 74.6 - - - +
422A ALA* 1.4 59.5 + - - +
424A LYS* 3.3 11.9 + - + +
425A LEU* 3.1 50.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ALA 4.2 10.1 - - - +
334A GLY* 4.3 2.2 - - - -
335A HIS* 4.1 19.1 - - + +
418A ALA 3.2 13.5 + - - +
419A ASP* 3.3 12.8 + - - +
421A PHE* 1.4 74.8 - - - +
423A LYS* 1.4 60.4 + - - +
425A LEU* 3.3 18.8 + - - +
427A LYS* 3.2 28.2 + - + +
428A ALA 4.5 2.0 - - - -
431A LEU* 4.8 13.7 - - + -
469A LEU* 5.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A ASP 3.2 12.6 + - - +
420A ALA* 3.6 11.2 - - - +
421A PHE 3.3 0.2 - - - -
422A ALA* 1.4 74.5 - - - +
424A LYS* 1.4 58.1 + - - +
425A LEU 3.2 0.4 - - - -
426A GLY* 3.1 18.2 + - - -
428A ALA* 3.8 25.6 - - + +
469A LEU* 4.4 4.7 - - + -
472A MET* 3.8 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A ALA 3.0 15.4 + - - +
421A PHE* 3.4 19.5 - - + +
423A LYS* 1.4 76.5 - - - +
425A LEU* 1.4 59.5 + - + +
426A GLY 3.3 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A SER* 5.7 6.1 - - - +
245A ILE* 5.4 10.3 - - + -
334A GLY* 3.7 29.4 - - - +
337A LEU* 5.7 2.9 - - + -
421A PHE* 3.1 47.2 + - + +
422A ALA* 3.5 9.6 - - - +
423A LYS 3.2 0.6 - - - -
424A LYS* 1.4 77.0 - - + +
426A GLY* 1.3 58.2 + - - +
427A LYS* 3.4 12.9 + - + +
----------------------------------------------------------
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