Contacts of the helix formed by residues 408 - 426 (chain A) in PDB entry 6V3O
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 SER 408 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A PHE* 3.6 1.1 - - - +
407A THR* 1.3 83.5 + - - +
409A ILE* 1.3 63.1 + - - +
410A GLU* 3.0 26.0 + - - +
411A GLU* 3.1 22.3 + - - +
412A PHE* 3.4 13.7 + - - +
448A LEU* 3.4 15.6 - - - +
527A ASP* 5.6 8.3 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
284A ARG* 5.3 9.6 - - - +
408A SER* 1.3 73.5 - - - +
410A GLU* 1.3 75.7 + - + +
411A GLU 3.3 0.2 - - - -
412A PHE* 3.2 5.5 + - - +
413A LEU* 2.8 41.9 + - + +
443A VAL* 4.7 16.8 - - + +
444A PHE* 6.0 6.7 - - + -
447A GLY* 4.0 12.6 - - - -
448A LEU* 3.8 38.1 - - + +
527A ASP* 4.5 21.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A SER* 3.0 21.3 + - - +
409A ILE* 1.3 94.1 + - + +
411A GLU* 1.3 59.8 + - - +
413A LEU* 3.2 18.6 + - + +
414A GLU* 3.2 21.3 + - - +
527A ASP* 5.0 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A LYS* 2.9 27.0 + - - +
402A ALA 5.0 0.7 - - - +
403A GLU* 4.4 3.8 - - - +
405A SER 3.2 13.5 - - - +
406A PHE* 3.6 14.4 - - + -
407A THR* 3.2 33.3 + - - +
408A SER* 3.1 16.3 + - - +
409A ILE 3.3 0.2 - - - -
410A GLU* 1.3 78.2 - - - +
412A PHE* 1.3 60.5 + - - +
414A GLU* 3.8 7.4 + - - +
415A PRO* 3.4 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A TYR* 3.9 41.3 - + + -
323A ILE* 5.0 4.5 - - + -
378A VAL* 3.8 24.5 - - + -
382A LEU* 4.4 6.7 - - + -
406A PHE* 3.8 35.8 - + + -
408A SER 3.4 10.5 + - - +
409A ILE* 3.2 9.9 + - - +
411A GLU* 1.3 78.0 - - - +
413A LEU* 1.3 60.1 + - - +
415A PRO* 3.3 11.3 - - - +
416A LEU* 3.6 24.2 - - + +
439A LEU* 5.3 0.7 - - + -
443A VAL* 3.6 36.1 - - + -
447A GLY 5.8 0.2 - - - -
448A LEU* 3.9 18.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
409A ILE* 2.8 30.6 + - + +
410A GLU* 3.2 10.0 + - + +
412A PHE* 1.3 76.2 - - - +
414A GLU* 1.3 59.9 + - - +
416A LEU* 3.2 6.9 + - + +
417A GLU* 2.8 45.9 + - + +
440A LEU* 3.8 22.7 - - + -
443A VAL* 3.7 27.8 - - + -
444A PHE* 3.4 47.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ARG* 5.2 12.7 + - - +
410A GLU 3.2 17.2 + - - +
411A GLU* 4.1 6.7 - - - +
413A LEU* 1.3 76.4 - - - +
415A PRO* 1.3 69.8 - - + +
417A GLU* 3.9 7.2 - - - +
418A LEU* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ARG* 5.3 6.5 - - - +
374A ILE* 4.0 13.8 - - + +
375A LEU* 6.0 0.4 - - - -
377A HIS* 6.1 4.0 - - + -
378A VAL* 3.7 30.3 - - + -
406A PHE* 4.8 9.0 - - + -
411A GLU 3.4 13.5 - - - +
412A PHE 3.3 15.0 - - - +
414A GLU* 1.3 91.8 - - + +
416A LEU* 1.3 60.6 + - - +
418A LEU* 3.3 10.6 + - + +
419A CYS* 3.2 27.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ILE* 4.1 14.1 - - + -
375A LEU* 4.1 15.7 - - + -
378A VAL* 4.8 4.9 - - + -
412A PHE* 3.6 33.0 - - + +
413A LEU* 3.2 9.3 + - + +
415A PRO* 1.3 77.3 - - + +
417A GLU* 1.3 58.3 + - - +
419A CYS* 3.2 9.2 + - - +
420A TYR* 3.0 24.4 + - - +
436A LEU* 4.3 11.8 - - + +
439A LEU* 3.9 26.7 - - + -
440A LEU* 3.8 23.1 - - + -
443A VAL* 4.0 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A TYR* 2.4 44.8 + - + +
413A LEU* 2.8 40.1 + - + +
414A GLU* 4.1 6.4 + - - +
416A LEU* 1.3 70.4 - - - +
418A LEU* 1.3 64.8 + - - +
420A TYR* 4.1 7.0 - - - -
421A LYS* 3.1 32.9 + - + +
440A LEU* 4.3 8.5 - - + -
444A PHE* 5.0 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ASN* 4.6 4.5 - - - +
338A GLU* 3.5 37.7 - - + +
339A LEU* 3.8 39.3 - - + +
342A ARG* 3.7 39.5 - - + +
374A ILE* 5.0 2.9 - - + -
414A GLU 3.0 18.3 + - - +
415A PRO* 3.4 8.7 - - + +
417A GLU* 1.3 78.8 - - - +
419A CYS* 1.3 57.2 + - - +
421A LYS* 4.2 2.7 - - + +
422A SER* 3.1 29.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU* 5.2 3.1 - - + -
339A LEU* 4.2 14.6 - - - -
371A TYR* 3.9 25.5 - - + -
374A ILE* 4.1 22.7 - - - -
375A LEU* 4.7 16.6 - - + -
415A PRO 3.2 15.2 + - - -
416A LEU* 3.2 8.6 + - - +
418A LEU* 1.3 78.0 - - - +
420A TYR* 1.3 65.7 + - - +
422A SER* 3.9 0.5 - - - -
423A LEU* 2.9 28.2 + - - +
436A LEU* 4.0 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A TYR* 4.2 22.1 - + - +
416A LEU 3.0 12.9 + - - +
417A GLU* 3.3 12.3 + - - +
419A CYS* 1.3 77.8 - - - +
421A LYS* 1.3 74.8 + - + +
423A LEU* 3.4 4.0 + - - +
424A CYS* 3.1 49.6 + - - -
429A LYS* 3.9 13.6 + - - -
432A ALA* 3.6 23.1 - - + +
433A ASP* 2.6 30.0 + - - -
436A LEU* 3.6 15.0 - - + +
437A LEU* 4.7 11.8 - - + +
440A LEU* 3.8 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A TYR* 4.5 13.2 + - - -
336A ASN* 4.2 4.0 - - - +
417A GLU* 3.1 19.6 + - + +
418A LEU* 4.4 3.1 - - + +
420A TYR* 1.3 91.2 - - + +
422A SER* 1.3 56.0 + - - +
424A CYS* 3.6 6.0 - - + +
425A ASP* 2.7 48.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A CYS* 3.2 6.1 - - - +
336A ASN* 3.1 43.3 + - - +
339A LEU* 3.4 14.4 - - - +
371A TYR* 2.9 16.7 + - - -
418A LEU 3.1 20.5 + - - -
419A CYS 3.9 0.9 - - - -
421A LYS* 1.3 76.6 - - - +
423A LEU* 1.3 63.3 + - - +
425A ASP* 3.1 1.7 + - - +
426A CYS* 3.1 27.4 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
330A LEU* 4.4 12.8 - - + -
332A MET* 3.8 22.4 - - + -
334A ARG 5.6 0.2 - - - +
371A TYR* 3.6 28.3 - - + +
419A CYS 2.9 21.2 + - - +
420A TYR 3.6 4.3 - - - +
422A SER* 1.3 77.5 + - - +
424A CYS* 1.3 54.3 + - - +
426A CYS* 3.6 4.4 + - - -
428A ASP* 2.7 58.0 + - + +
431A ILE* 4.2 9.4 - - + -
432A ALA* 3.7 32.5 - - + +
436A LEU* 3.9 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A TYR* 3.1 52.8 + - - +
421A LYS* 3.8 9.0 - - + +
423A LEU* 1.3 74.4 - - - +
425A ASP* 1.3 68.7 + - - +
426A CYS 3.1 0.4 - - - -
427A GLY* 3.1 12.8 + - - -
429A LYS* 3.7 42.6 - - + +
432A ALA* 4.1 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ASN* 3.2 30.8 + - + +
421A LYS* 2.7 32.7 + - - +
422A SER* 3.1 8.7 + - - +
424A CYS* 1.3 74.3 - - - +
426A CYS* 1.3 59.2 + - - +
427A GLY 3.4 2.3 + - - -
929B PHE* 3.9 10.7 - - - -
931B ASP* 5.5 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ARG* 4.3 18.6 - - + +
335A CYS* 3.5 40.4 - - - -
336A ASN* 3.7 5.2 - - - -
371A TYR* 4.9 0.4 - - - +
422A SER 3.1 16.1 + - - +
423A LEU* 3.6 3.3 + - - +
424A CYS 3.1 0.6 - - - -
425A ASP* 1.3 76.9 - - - +
427A GLY* 1.3 60.7 + - - +
428A ASP* 3.3 11.9 + - - +
226B ARG* 3.3 21.7 + - - -
928B GLU* 4.7 0.5 - - - +
929B PHE* 3.8 20.4 - - + -
931B ASP* 5.1 9.0 - - - -
----------------------------------------------------------
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