Contacts of the helix formed by residues 417 - 433 (chain B) in PDB entry 1QI9
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 GLY 417 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A PHE* 6.0 0.4 - - - -
334B GLN* 3.2 31.9 + - - +
337B SER* 3.8 6.5 - - - -
338B TRP* 4.6 2.7 - - - -
341B LYS* 3.9 4.4 - - - +
415B PRO 3.5 2.2 + - - -
416B SER* 1.3 70.3 - - - +
418B HIS* 1.3 64.8 + - - +
420B THR* 4.3 0.7 - - - -
421B GLN* 3.0 26.7 + - - +
600B VO4 2.7 16.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A PHE* 6.5 1.1 - + - -
275B THR 3.4 4.0 + - - -
278B ASP* 2.8 41.9 + - - -
280B ILE 5.6 1.7 + - - -
416B SER* 3.2 1.0 + - - -
417B GLY* 1.3 77.3 - - - +
419B ALA* 1.3 61.8 + - - +
421B GLN* 3.4 19.9 + - - +
422B ASN* 3.0 31.3 + - - +
476B VAL* 3.7 18.6 - - + +
477B ALA* 5.1 0.9 - - - -
480B ARG* 3.1 46.1 + - + -
600B VO4 3.1 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B SER* 3.0 17.3 + - - +
418B HIS* 1.3 78.5 - - - +
420B THR* 1.4 62.9 + - - +
422B ASN* 4.7 0.7 - - - -
423B GLY 2.9 17.7 + - - -
477B ALA* 3.4 25.7 - - + +
490B ASP 4.0 1.3 - - - +
491B GLY* 3.1 35.4 - - - +
494B GLY 3.8 0.9 - - - -
495B LEU* 3.2 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ALA* 4.0 20.6 - - + +
334B GLN* 4.6 1.6 - - - +
337B SER* 3.7 28.9 - - - -
415B PRO* 3.8 5.4 - - - +
416B SER 2.8 19.7 + - - -
417B GLY 3.3 4.7 + - - -
419B ALA* 1.4 77.1 - - - +
421B GLN* 1.3 63.5 + - - +
423B GLY 3.3 1.4 + - - -
424B ALA* 3.1 18.0 + - - +
494B GLY* 3.3 20.5 - - - +
497B LEU* 4.1 8.9 - - + +
498B GLY* 3.3 29.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A PHE* 4.9 0.9 - - - -
280B ILE* 3.4 44.9 - - - +
330B ALA 5.5 1.1 - - - -
331B GLU* 2.8 40.1 + - - +
333B ALA* 5.6 2.7 - - - -
334B GLN* 3.1 16.3 - - + +
417B GLY 3.0 18.1 + - - +
418B HIS* 3.4 35.1 + - - +
420B THR* 1.3 76.7 - - - +
422B ASN* 1.3 64.8 + - - +
424B ALA* 3.2 8.3 + - - +
425B PHE* 2.8 38.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ILE 4.3 5.7 + - - +
281B ASN* 5.9 0.5 - - - -
283B GLU* 4.7 4.3 + - - +
284B ALA* 4.6 13.2 + - - +
418B HIS* 3.0 25.5 + - - +
419B ALA* 4.3 2.0 - - - +
421B GLN* 1.3 86.0 + - - +
423B GLY* 1.4 64.4 + - - +
425B PHE* 3.9 14.0 - - - +
426B ALA* 3.0 26.3 + - - +
472B LEU* 4.9 3.3 - - - +
473B ALA* 3.7 26.0 - - + +
476B VAL* 3.4 38.1 - - + +
495B LEU* 4.1 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B ALA 2.9 13.2 + - - -
420B THR 3.8 0.7 - - - -
421B GLN 3.2 0.2 - - - -
422B ASN* 1.4 76.7 - - - +
424B ALA* 1.3 55.3 + - - +
426B ALA* 3.6 1.9 + - - +
427B THR* 2.7 34.3 + - - -
495B LEU* 3.5 33.3 - - - +
498B GLY 4.0 5.2 - - - -
499B GLU 4.1 0.4 + - - -
524B PHE* 3.9 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 424 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ALA* 3.6 26.7 - - + +
333B ALA* 4.5 3.6 - - + -
420B THR 3.1 13.1 + - - +
421B GLN* 3.3 9.6 - - - +
423B GLY* 1.3 77.9 - - - +
425B PHE* 1.3 63.5 + - - +
427B THR* 3.2 3.6 + - - -
428B VAL* 3.0 25.6 + - - +
498B GLY* 3.7 9.4 - - - +
502B THR* 3.1 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 425 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ILE* 3.3 26.5 - - + -
281B ASN* 3.4 17.5 - - + -
284B ALA* 3.8 31.4 - - + -
327B ILE* 3.3 32.8 - - + -
330B ALA* 4.2 7.2 - - + -
331B GLU* 3.7 42.0 - - + -
421B GLN* 2.8 35.8 + - + +
422B ASN* 3.9 11.2 - - - +
424B ALA* 1.3 72.6 - - - +
426B ALA* 1.4 57.1 + - - +
428B VAL* 3.1 8.3 + - - +
429B LEU* 2.8 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 426 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B ALA* 5.8 0.2 - - - +
422B ASN 3.0 19.3 + - - +
423B GLY 3.8 3.6 - - - +
425B PHE* 1.4 75.8 - - - +
427B THR* 1.3 58.0 + - - +
429B LEU* 3.4 2.2 + - - -
430B LYS* 3.0 37.6 + - - +
469B ILE* 3.7 24.8 - - + +
473B ALA* 4.0 11.7 - - + -
524B PHE* 3.8 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B GLY 2.7 22.7 + - - -
424B ALA 3.4 5.8 - - - -
426B ALA* 1.3 77.0 - - - +
428B VAL* 1.3 63.1 + - - +
430B LYS* 4.1 9.3 - - - +
431B ALA* 3.1 23.6 + - - +
499B GLU* 3.5 31.3 + - + +
502B THR* 3.8 24.2 - - + -
503B VAL* 4.4 2.9 - - + -
506B LEU* 4.1 5.4 - - + -
521B PHE* 3.8 26.1 - - + -
524B PHE* 4.6 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B TYR* 4.4 0.7 - - + +
326B LEU* 3.7 40.8 - - + +
327B ILE* 4.3 14.6 - - + +
330B ALA* 3.7 24.5 - - + -
424B ALA 3.0 15.3 + - - +
425B PHE* 3.4 9.4 - - - +
427B THR* 1.3 72.1 - - - +
429B LEU* 1.3 70.2 + - + +
431B ALA* 3.4 4.7 + - - +
432B LEU* 3.1 37.6 + - + +
502B THR* 3.9 11.4 - - + -
506B LEU* 5.0 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B LEU* 5.7 2.2 - - + -
284B ALA* 4.2 24.2 - - + +
287B GLY* 5.2 1.3 - - - -
288B ALA* 3.8 7.6 - - + +
291B LEU* 4.2 16.6 - - + -
323B TYR* 3.8 29.1 - - + +
327B ILE* 3.7 31.4 - - + -
425B PHE* 2.8 24.9 + - + +
426B ALA* 3.9 4.3 - - - +
428B VAL* 1.3 77.9 - - + +
430B LYS* 1.3 57.5 + - - +
432B LEU* 3.9 0.9 - - - +
433B ILE* 2.9 36.1 + - + +
469B ILE* 4.1 22.9 - - + -
472B LEU* 5.8 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B ALA* 3.0 31.2 + - - +
427B THR* 4.1 6.3 + - - +
429B LEU* 1.3 74.7 - - - +
431B ALA* 1.3 56.8 + - - +
433B ILE* 4.0 5.5 - - - +
434B GLY* 2.8 26.9 + - - -
438B GLY* 6.4 0.2 - - - -
466B GLU* 4.1 24.2 - - + +
469B ILE* 4.1 18.6 - - + -
470B ASN* 2.9 31.0 + - - +
499B GLU* 4.5 2.8 + - - -
521B PHE* 3.5 26.4 - - + +
522B ARG 3.0 26.3 + - - +
523B LEU* 3.9 2.0 - - - +
524B PHE* 3.8 23.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B THR 3.1 19.5 + - - +
428B VAL 3.9 2.7 - - - +
430B LYS* 1.3 77.7 - - - +
432B LEU* 1.3 64.1 + - + +
434B GLY* 3.5 9.7 + - - -
506B LEU* 3.8 19.7 - - + -
519B PHE* 3.7 27.5 - - + +
520B GLU 4.5 3.5 + - - +
521B PHE* 3.7 30.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B PHE* 3.6 39.5 - - + -
303B ASN* 4.7 2.8 - - + +
304B GLY* 5.0 3.5 + - - -
318B PHE* 4.4 11.5 - - + -
322B HIS* 3.8 39.0 - - + +
323B TYR* 3.4 38.6 - - + +
326B LEU* 4.6 3.4 - - + -
428B VAL* 3.1 32.5 + - + +
429B LEU 4.0 1.6 - - - +
431B ALA* 1.3 75.6 - - + +
433B ILE* 1.3 66.1 + - - +
434B GLY* 3.5 0.9 + - - -
437B ARG* 3.6 5.5 + - - -
506B LEU* 5.8 0.9 - - + -
519B PHE* 4.4 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B LEU* 4.1 19.1 - - + -
296B ALA* 3.4 44.2 - - + +
297B PHE* 4.1 11.7 - - + +
323B TYR* 4.8 4.0 - - + +
429B LEU* 2.9 23.1 + - + +
430B LYS* 4.0 4.3 - - - +
432B LEU* 1.3 76.0 - - - +
434B GLY* 1.3 67.5 + - - +
437B ARG* 3.0 44.9 + - + +
438B GLY* 3.7 12.1 - - - +
465B PHE* 5.4 2.0 - - + -
469B ILE* 4.0 23.1 - - + -
----------------------------------------------------------
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