Contacts of the helix formed by residues 409 - 425 (chain A) in PDB entry 3QXY
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 LYS 409 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A LYS* 6.3 0.4 - - - +
377A PRO* 6.2 1.8 - - - +
407A LYS 3.9 0.2 + - - -
408A LEU* 1.3 76.8 - - - +
410A ALA* 1.3 65.9 + - - +
411A SER* 3.2 8.3 - - - +
412A TRP* 3.0 46.4 + - + +
413A ARG* 3.0 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A LEU 3.5 1.6 + - - -
409A LYS* 1.3 71.3 - - - +
411A SER* 1.3 56.9 + - - +
413A ARG* 3.3 27.0 + - - +
414A GLN* 2.8 30.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
375A CYS* 3.6 23.3 + - - +
409A LYS* 4.0 8.7 - - - +
410A ALA* 1.3 76.9 - - - +
412A TRP* 1.3 80.1 + - - +
414A GLN* 3.4 6.6 + - - +
415A LEU* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A THR* 4.0 19.1 - - + -
371A LEU* 3.8 37.4 + - + +
372A LYS* 3.3 40.8 + - + +
375A CYS* 3.7 21.2 - - + +
396A GLU* 4.4 13.7 - - - -
400A LEU* 5.5 0.4 - - + -
408A LEU* 4.2 32.3 - - + -
409A LYS* 3.0 40.5 + - + +
411A SER* 1.3 87.6 - - - +
413A ARG* 1.3 58.5 + - - +
415A LEU* 3.3 2.9 + - - +
416A LEU* 3.0 30.7 + - - +
477A EDO 4.6 10.8 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
405A ILE 3.5 25.1 - - - +
406A PRO* 3.5 20.8 + - - -
408A LEU* 3.0 25.5 + - + +
409A LYS 3.0 11.4 + - - +
410A ALA* 3.6 29.7 + - - +
412A TRP* 1.3 77.3 - - - +
414A GLN* 1.3 56.7 + - - +
416A LEU* 3.4 1.6 + - - -
417A GLN* 2.8 31.1 + - - +
471A LEU 4.2 8.9 + - - -
472A THR* 3.4 25.5 + - + +
473A SER* 4.2 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A ALA 2.8 17.0 + - - +
411A SER* 3.7 7.2 - - - +
413A ARG* 1.3 77.4 - - - +
415A LEU* 1.3 61.6 + - - +
417A GLN* 3.4 10.6 + - - +
418A ASN* 2.9 54.4 + - - +
472A THR 5.4 1.1 + - - -
473A SER* 5.9 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A VAL* 3.9 15.0 - - + +
321A ALA* 3.8 24.7 - - + +
322A ALA* 3.9 14.1 - - + +
371A LEU* 4.0 18.4 - - + -
374A LEU* 3.8 38.6 - - + -
375A CYS* 3.8 14.4 - - - -
411A SER 3.0 17.0 + - - +
412A TRP 3.7 4.0 - - - +
414A GLN* 1.3 77.8 - - - +
416A LEU* 1.3 60.6 + - - +
418A ASN* 3.4 4.3 + - + +
419A SER* 2.8 29.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
313A ILE* 4.5 11.4 - - + -
318A VAL* 5.8 2.9 - - + -
361A VAL* 6.3 0.4 - - + -
367A LEU* 4.3 30.5 - - + -
371A LEU* 4.0 23.7 - - + +
400A LEU* 5.9 1.1 - - + -
405A ILE* 4.7 11.9 - - + -
408A LEU* 4.9 7.2 - - + -
412A TRP 3.0 15.9 + - - +
413A ARG* 3.7 4.3 - - - +
415A LEU* 1.3 75.4 - - - +
417A GLN* 1.3 64.3 + - - +
419A SER* 3.2 8.5 + - - -
420A VAL* 3.0 27.4 + - - +
468A LEU* 4.4 28.9 - - + -
472A THR* 4.0 20.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
413A ARG 2.8 18.8 + - - +
414A GLN* 3.5 13.0 - - - +
416A LEU* 1.3 76.0 - - - +
418A ASN* 1.3 72.6 + - - +
420A VAL* 3.3 6.7 + - - +
421A LEU* 3.1 37.7 + - + +
469A LEU* 3.1 34.5 - - - +
472A THR* 2.9 28.8 + - - +
473A SER 3.5 21.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ALA* 4.0 20.6 + - + -
324A GLN* 4.5 16.0 + - - +
414A GLN* 2.9 42.1 + - - +
415A LEU* 4.0 5.1 - - + +
417A GLN* 1.3 82.1 - - - +
419A SER* 1.3 61.5 + - - +
421A LEU* 3.5 14.7 + - - +
422A LEU* 3.2 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ILE* 4.3 11.2 - - - -
317A THR* 3.6 7.5 - - - +
318A VAL* 3.5 35.5 - - - +
321A ALA* 3.3 18.2 - - - +
415A LEU 2.8 18.8 + - - -
416A LEU* 3.6 8.0 - - - -
418A ASN* 1.3 76.2 - - - +
420A VAL* 1.3 58.6 + - - +
422A LEU* 3.4 3.5 + - - +
423A THR* 2.9 31.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ILE* 3.8 22.2 - - + -
416A LEU* 3.0 21.0 + - + +
417A GLN* 3.7 5.6 - - - +
419A SER* 1.3 74.3 - - - +
421A LEU* 1.3 59.8 + - - +
423A THR* 3.1 7.4 + - - -
424A LEU* 2.8 37.2 + - + +
465A LEU* 3.4 33.4 - - + +
468A LEU* 3.8 25.6 - - + +
469A LEU* 3.4 20.2 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
417A GLN* 3.1 33.5 + - - +
418A ASN* 3.7 20.0 - - - +
420A VAL* 1.3 75.8 - - - +
422A LEU* 1.3 62.2 + - + +
424A LEU* 3.4 7.6 + - + +
425A GLN* 3.2 38.8 + - - +
469A LEU* 3.8 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A THR* 3.7 17.0 - - + +
320A GLU* 3.8 33.0 - - + +
321A ALA* 4.0 25.4 - - + +
324A GLN* 3.9 22.9 - - - +
418A ASN 3.2 15.9 + - - +
419A SER 3.6 7.0 - - - +
421A LEU* 1.3 74.8 - - + +
423A THR* 1.3 67.6 + - - +
425A GLN* 3.2 35.3 + - - +
426A THR* 3.6 11.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ASP 3.5 24.2 - - - +
313A ILE* 3.6 20.8 - - - +
314A GLN* 4.8 1.5 + - + +
317A THR* 3.9 7.5 + - - +
419A SER 2.9 15.8 + - - -
420A VAL* 3.1 9.6 + - - -
422A LEU* 1.3 75.6 - - - +
424A LEU* 1.3 61.8 + - - +
426A THR* 2.7 36.9 + - + +
427A TYR* 3.7 6.5 - - + +
465A LEU* 3.9 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A VAL* 2.8 30.8 + - + +
421A LEU* 3.8 8.1 - - + +
422A LEU 3.4 0.2 - - - -
423A THR* 1.3 72.4 - - - +
425A GLN* 1.3 61.2 + - + +
426A THR 3.3 0.9 + - - -
427A TYR* 3.4 16.8 + - + +
429A THR 4.8 0.5 - - - +
430A ASP* 6.5 0.7 - - - -
431A LEU 5.9 0.7 - - - +
462A LYS* 4.1 19.7 - - + -
465A LEU* 3.8 28.3 - - + -
466A HIS* 3.6 40.8 - - + +
469A LEU* 3.9 22.7 - - + -
476A EDO 3.3 17.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A GLN* 5.3 0.5 + - - -
421A LEU* 3.2 29.9 + - - +
422A LEU* 3.5 28.1 - - - +
423A THR 3.1 1.2 + - - -
424A LEU* 1.3 77.0 - - + +
426A THR* 1.3 61.0 + - - +
427A TYR 3.2 7.6 + - - +
476A EDO 3.9 18.5 - - - +
----------------------------------------------------------
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