Contacts of the helix formed by residues 396 - 425 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B CYS* 3.3 55.2 - - + -
362B LEU* 3.6 32.3 - - + -
363B PHE 4.0 0.7 - - - -
366B LEU* 4.4 8.5 - - + -
391B ILE* 2.9 43.7 + - + +
392B PHE* 3.6 22.0 - + - +
394B PHE 3.4 0.8 - - - +
395B ILE* 1.4 75.8 - - + +
397B SER* 1.4 53.9 + - - +
398B PRO* 3.4 2.9 - - - -
399B TYR* 2.9 17.4 + + + +
400B ASN* 2.8 50.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B VAL* 5.6 1.9 - - - +
26B PHE* 3.7 17.7 - - - -
27B SER* 5.1 6.4 + - - -
393B GLN 3.0 19.9 + - - -
394B PHE* 2.9 24.6 + - - +
395B ILE 3.3 0.2 - - - -
396B PHE* 1.4 72.8 - - - +
398B PRO* 1.4 68.3 - - - +
400B ASN* 3.4 10.6 + - - +
401B GLU* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE* 3.5 33.6 - - + -
394B PHE 4.4 1.6 - - - +
395B ILE 3.4 16.6 - - - +
396B PHE* 3.5 0.9 - - - -
397B SER* 1.4 93.0 - - - +
399B TYR* 1.4 60.5 + - + +
401B GLU* 3.4 2.4 + - - +
402B VAL* 3.2 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B ASN* 2.8 37.8 + - - -
358B LEU* 3.6 30.6 - - + +
359B CYS* 3.7 17.7 - - - -
362B LEU* 6.2 3.6 - - + -
396B PHE* 2.9 19.6 + + + +
398B PRO* 1.4 76.2 - - + +
400B ASN* 1.3 73.8 + - - +
402B VAL* 3.2 7.5 + - + +
403B LEU* 2.9 56.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B ASN* 5.1 1.0 - - - +
359B CYS* 4.7 5.0 - - - -
392B PHE 3.1 27.1 + - - -
393B GLN* 4.9 7.3 + - - +
396B PHE* 2.8 30.5 + - - +
397B SER* 3.7 9.1 - - - +
399B TYR* 1.3 90.7 - - - +
401B GLU* 1.4 57.4 + - + +
403B LEU* 3.6 7.4 + - - +
404B SER* 2.9 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE* 4.3 15.9 - - + -
30B VAL* 3.8 27.9 - - + +
34B GLU* 4.0 10.4 - - - +
397B SER* 3.0 19.9 + - - +
398B PRO 3.7 5.2 - - - +
400B ASN* 1.4 75.0 - - + +
402B VAL* 1.4 64.1 - - + +
404B SER* 3.6 7.9 + - - -
405B PHE* 3.2 22.3 + - - +
455B TRP* 3.7 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B PRO* 3.2 19.1 + - + +
399B TYR* 3.2 6.7 + - + +
401B GLU* 1.4 73.6 - - + +
403B LEU* 1.4 58.6 + - - +
405B PHE* 3.1 9.9 + - + +
406B CYS* 2.9 45.0 + - - -
455B TRP* 6.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B ILE* 5.3 8.1 - - + -
355B ASN* 3.4 34.8 - - + +
399B TYR* 2.9 47.3 + - + +
400B ASN* 3.8 7.2 - - - +
402B VAL* 1.4 76.4 - - - +
404B SER* 1.4 58.2 + - - +
406B CYS* 3.3 8.9 + - + +
407B LEU* 2.9 52.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B ASN* 2.9 24.2 + - - +
401B GLU* 3.8 10.5 - - - -
402B VAL 3.3 0.2 - - - -
403B LEU* 1.4 74.3 - - - +
405B PHE* 1.4 56.3 + - - +
407B LEU* 3.5 8.4 + - - +
408B THR* 2.7 36.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B GLU 3.2 13.1 + - - +
402B VAL* 3.1 13.1 + - + +
404B SER* 1.4 72.6 - - - +
406B CYS* 1.3 68.8 + - - +
408B THR* 3.3 6.6 + - - -
409B VAL* 3.1 45.7 + - + +
412B ARG* 5.2 0.7 - - - -
454B MET* 3.3 30.3 - - + -
455B TRP* 3.5 52.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B VAL* 2.9 32.1 + - - +
403B LEU* 3.6 11.7 - - + +
405B PHE* 1.3 83.8 - - - +
407B LEU* 1.3 56.6 + - + +
409B VAL* 3.4 8.9 + - - +
410B LEU* 3.0 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ASN* 5.9 3.8 - - + +
351B ILE* 3.8 31.4 - - + -
403B LEU* 2.9 47.3 + - + +
404B SER* 3.5 7.8 + - - +
405B PHE 3.3 0.2 - - - -
406B CYS* 1.3 74.5 - - + +
408B THR* 1.4 59.7 + - - +
410B LEU* 3.6 24.6 - - + +
411B SER* 2.9 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B SER* 2.7 22.5 + - - -
405B PHE* 3.3 8.6 + - - -
407B LEU* 1.4 71.7 - - - +
409B VAL* 1.4 64.6 + - - +
411B SER* 3.4 7.8 + - - -
412B ARG* 3.2 33.3 + - - +
454B MET 4.6 1.1 - - - +
455B TRP 3.9 13.7 + - - +
456B HIS 3.5 17.9 + - - +
457B TYR 3.4 24.2 - - - +
458B SER* 4.0 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B PHE* 3.1 43.1 + - + +
406B CYS* 3.4 10.5 + - - +
408B THR* 1.4 75.9 - - - +
410B LEU* 1.4 59.7 + - - +
412B ARG* 3.4 32.8 + - - +
413B ARG* 3.3 20.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 410 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ASN* 5.9 2.2 - - + -
351B ILE* 3.8 26.2 - - + -
406B CYS 3.0 16.8 + - - +
407B LEU* 3.6 18.6 - - + +
408B THR 3.3 0.2 - - - -
409B VAL* 1.4 74.0 - - - +
411B SER* 1.4 54.6 + - - +
413B ARG* 3.2 9.6 + - + +
414B PHE* 2.8 76.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 411 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B LEU 2.9 19.4 + - - -
408B THR* 3.5 8.1 - - - -
409B VAL 3.4 0.2 - - - -
410B LEU* 1.4 76.6 - - - +
412B ARG* 1.4 54.8 + - - +
414B PHE* 3.4 10.5 + - - +
415B GLU* 3.0 33.6 + - - +
458B SER* 2.8 33.0 + - - -
459B HIS* 4.9 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B PHE* 4.9 0.4 - - - -
408B THR* 3.2 18.0 + - - +
409B VAL* 3.5 34.0 + - - +
410B LEU 3.3 0.2 - - - -
411B SER* 1.4 74.5 - - - +
413B ARG* 1.4 57.4 + - - +
415B GLU* 3.3 4.2 + - - +
416B PHE* 3.2 36.7 + - + -
453B SER* 3.0 14.3 + - - -
454B MET* 2.8 40.2 + - - +
457B TYR* 2.7 37.3 + - - +
458B SER 3.2 19.0 + - - +
459B HIS 4.5 0.2 - - - -
460B PRO* 3.9 31.5 - - + +
461B PRO* 5.4 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B VAL* 3.3 9.7 + - + +
410B LEU* 3.2 13.3 + - + +
412B ARG* 1.4 78.1 - - - +
414B PHE* 1.4 60.0 + - + +
416B PHE* 3.5 10.3 + - - +
417B GLN* 3.2 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 414 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B HIS* 3.4 12.2 - - + -
344B HIS* 3.1 82.0 - + + -
347B LYS* 4.0 19.5 - - + -
348B ASN* 4.9 4.9 - - + -
351B ILE* 5.4 0.7 - - + -
410B LEU* 2.8 57.5 + - + +
411B SER* 3.6 9.9 - - - +
412B ARG 3.3 0.2 - - - -
413B ARG* 1.4 76.6 - - + +
415B GLU* 1.3 59.1 + - - +
417B GLN* 3.9 10.5 - - - -
418B ALA 3.2 10.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B HIS* 3.0 24.3 + - - -
339B HIS* 2.8 29.5 + - - -
411B SER* 3.0 21.8 + - - +
412B ARG 3.6 5.8 - - - +
413B ARG 3.3 0.2 - - - -
414B PHE* 1.3 75.5 - - + +
416B PHE* 1.4 58.2 + - - +
418B ALA* 3.2 3.8 + - - +
419B ASP* 3.0 36.7 + - - +
458B SER 4.5 1.1 - - - +
459B HIS* 3.2 44.9 + - + +
460B PRO* 3.8 15.9 - - + -
465B ARG* 3.5 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B ARG* 3.2 27.1 + - + -
413B ARG* 3.7 10.8 - - - +
414B PHE 3.5 0.2 - - - -
415B GLU* 1.4 74.4 - - - +
417B GLN* 1.4 57.8 + - + +
419B ASP* 3.3 12.6 + - + +
420B ALA* 3.0 28.4 + - - +
460B PRO* 3.6 30.3 - - + +
464B GLU* 3.7 36.6 - - + -
465B ARG* 4.3 4.9 - - - -
468B ALA* 4.1 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B LEU* 3.4 27.0 - - + +
344B HIS* 2.8 37.5 + - + -
413B ARG* 3.2 30.4 + - - +
414B PHE* 4.5 9.4 - - - -
416B PHE* 1.4 75.4 - - + +
418B ALA* 1.3 57.2 + - - +
420B ALA* 3.4 8.4 + - - +
421B PHE 3.0 21.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B HIS* 3.4 55.4 - - + +
338B GLY* 4.7 0.2 - - - -
339B HIS* 3.5 28.3 - - + +
342B LEU* 4.1 7.8 - - - +
344B HIS* 4.6 0.9 - - + -
414B PHE 3.2 3.0 + - - +
415B GLU 3.2 2.7 + - - +
417B GLN* 1.3 75.4 - - - +
419B ASP* 1.3 61.7 + - - +
421B PHE* 3.7 4.2 + - - +
422B ALA 3.3 14.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B HIS* 2.9 22.3 + - - +
415B GLU 3.0 23.7 + - - +
416B PHE* 3.6 12.6 - - + +
417B GLN 3.3 0.2 - - - -
418B ALA* 1.3 72.6 - - - +
420B ALA* 1.4 60.1 + - - +
421B PHE 3.3 0.2 - - - -
422B ALA* 3.3 8.2 + - - +
423B LYS* 3.2 21.1 + - - +
431B LEU* 5.9 2.4 - - - +
465B ARG* 3.1 43.5 + - - +
468B ALA* 6.0 3.1 - - + -
469B LEU* 3.7 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B PHE 3.0 17.1 + - - +
417B GLN* 3.4 9.8 + - - +
419B ASP* 1.4 73.6 - - - +
421B PHE* 1.4 57.3 + - - +
423B LYS* 3.4 8.8 + - - +
424B LYS* 3.0 26.4 + - - +
472B MET* 5.9 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ILE* 5.5 10.1 - - + -
334B GLY 3.5 17.0 - - - -
337B LEU* 4.4 7.2 - - + -
338B GLY* 3.5 17.9 - - - -
341B LYS* 3.7 26.2 - - + -
342B LEU* 4.0 22.4 - - + -
417B GLN 3.0 16.2 + - - +
418B ALA 3.7 6.3 - - - +
419B ASP 3.3 0.4 - - - -
420B ALA* 1.4 75.0 - - - +
422B ALA* 1.4 58.5 + - - +
424B LYS* 3.3 12.4 + - + +
425B LEU* 3.1 49.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B ALA 4.2 10.1 - - - +
334B GLY* 4.3 1.6 - - - -
335B HIS* 4.1 19.5 - - + +
418B ALA 3.3 13.0 + - - +
419B ASP* 3.3 12.7 + - - +
421B PHE* 1.4 77.1 - - - +
423B LYS* 1.4 59.4 + - - +
425B LEU* 3.3 19.3 + - - +
427B LYS* 3.2 27.9 + - + +
428B ALA 4.5 2.0 - - - -
431B LEU* 4.8 13.9 - - + -
469B LEU* 5.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B ASP 3.2 12.4 + - - +
420B ALA* 3.6 11.0 - - - +
421B PHE 3.3 0.2 - - - -
422B ALA* 1.4 73.4 - - - +
424B LYS* 1.4 59.7 + - - +
425B LEU 3.2 0.7 - - - -
426B GLY* 3.2 17.7 + - - -
428B ALA* 3.7 25.3 - - + +
469B LEU* 4.4 5.4 - - + -
472B MET* 3.7 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 424 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B ALA 3.0 14.8 + - - +
421B PHE* 3.4 18.8 - - + +
423B LYS* 1.4 75.0 - - - +
425B LEU* 1.4 59.8 + - - +
426B GLY* 3.3 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B MET* 5.5 17.3 - - + -
244B SER* 5.7 5.4 - - - +
245B ILE* 5.5 10.3 - - + +
334B GLY* 3.7 29.4 - - - +
337B LEU* 5.6 2.0 - - + -
421B PHE* 3.1 46.6 + - + +
422B ALA* 3.5 9.0 - - - +
423B LYS 3.2 0.6 - - - -
424B LYS* 1.4 76.0 - - + +
426B GLY* 1.3 59.1 + - - +
427B LYS* 3.4 7.2 + - + +
----------------------------------------------------------
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