Contacts of the helix formed by residues 417 - 433 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A GLN* 3.1 37.5 + - - +
337A SER* 3.8 5.2 - - - -
338A TRP* 4.8 2.0 - - - -
341A LYS* 3.9 4.1 - - - +
415A PRO 3.6 2.6 + - - -
416A SER* 1.3 69.9 - - - +
418A HIS* 1.4 64.6 + - - +
420A THR* 4.4 1.1 - - - -
421A GLN* 3.0 22.9 + - - +
600A VO4 2.9 17.1 + - - -
315B PHE* 6.0 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A THR* 3.4 6.0 + - - -
278A ASP* 2.9 40.5 + - - -
280A ILE* 5.8 2.1 + - + -
416A SER* 3.3 2.2 + - - +
417A GLY* 1.4 77.3 - - - +
419A ALA* 1.3 56.5 + - - +
421A GLN* 3.2 20.0 + - - -
422A ASN* 2.9 36.5 + - - +
476A VAL* 3.8 16.6 - - + +
477A ALA* 5.2 1.1 - - - -
480A ARG* 3.2 45.4 + - + -
600A VO4 3.1 27.0 + - - +
315B PHE* 6.3 3.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A SER* 3.1 18.8 + - - +
418A HIS* 1.3 73.9 - - - +
420A THR* 1.3 61.7 - - - +
422A ASN* 3.3 0.6 + - - -
423A GLY 2.9 26.0 + - - -
477A ALA* 3.8 17.2 - - + +
490A ASP 3.9 1.3 - - - +
491A GLY* 3.2 41.7 - - - +
494A GLY* 3.7 3.4 - - - -
495A LEU* 3.4 14.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ALA* 3.9 36.3 - - + +
334A GLN* 4.6 1.1 - - - +
337A SER* 3.8 20.9 - - - -
415A PRO* 3.9 5.2 - - - +
416A SER 3.0 18.3 + - - -
417A GLY 3.9 3.8 - - - -
418A HIS 3.4 0.2 - - - -
419A ALA* 1.3 77.7 - - - +
421A GLN* 1.3 62.0 + - - +
423A GLY 3.3 0.2 + - - -
424A ALA* 3.1 18.7 + - - +
494A GLY* 3.2 22.1 - - - -
497A LEU* 4.2 9.1 - - + +
498A GLY* 3.3 22.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ILE* 3.4 34.2 - - - +
331A GLU* 2.8 43.7 + - - +
333A ALA* 5.6 1.3 - - - -
334A GLN* 3.1 17.8 - - - +
417A GLY 3.0 16.6 + - - +
418A HIS* 3.2 36.3 + - - +
420A THR* 1.3 76.1 - - - +
422A ASN* 1.3 67.9 + - - +
424A ALA* 3.1 9.2 + - - +
425A PHE* 2.9 43.7 + - + -
315B PHE* 4.9 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ILE 4.3 6.1 + - - +
281A ASN* 5.8 0.3 - - - -
283A GLU* 4.7 5.9 + - - +
284A ALA* 4.4 11.4 + - - +
418A HIS* 2.9 29.0 + - - +
419A ALA* 4.2 2.5 - - - +
421A GLN* 1.3 89.1 + - - +
423A GLY* 1.3 58.4 + - - +
425A PHE* 4.1 13.0 - - - +
426A ALA* 2.9 31.4 + - - +
472A LEU* 5.2 2.9 - - - +
473A ALA* 3.6 30.2 - - + +
476A VAL* 3.5 37.3 - - + +
495A LEU* 4.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A ALA 2.9 14.0 + - - -
420A THR 3.3 0.9 + - - -
422A ASN* 1.3 76.9 - - - +
424A ALA* 1.4 56.6 - - - +
426A ALA* 3.5 1.7 + - - +
427A THR* 2.7 34.5 + - - -
495A LEU* 3.6 24.8 - - - +
498A GLY 4.0 5.4 - - - -
499A GLU 4.0 0.2 - - - -
524A PHE* 3.8 16.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ALA* 3.8 24.5 - - + +
333A ALA* 4.5 3.8 - - + -
420A THR 3.1 13.4 + - - +
421A GLN* 3.1 11.9 + - - +
423A GLY* 1.4 75.5 - - - +
425A PHE* 1.4 63.6 + - - +
427A THR* 3.2 4.3 + - - -
428A VAL* 3.0 26.9 + - - +
498A GLY* 3.7 8.3 - - - +
502A THR* 3.1 27.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ILE* 3.3 27.8 - - + -
281A ASN* 3.4 14.8 - - + -
284A ALA* 3.6 33.4 - - + -
327A ILE* 3.1 34.7 - - + +
330A ALA* 4.2 7.9 - - + -
331A GLU* 3.7 43.3 - - + -
421A GLN* 2.9 35.1 + - + -
422A ASN* 3.3 10.7 + - - +
424A ALA* 1.4 75.1 - - - +
426A ALA* 1.3 63.8 + - - +
428A VAL* 3.3 6.8 + - - +
429A LEU* 3.0 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A ASN 2.9 16.9 + - - +
423A GLY 3.8 4.3 - - - +
425A PHE* 1.3 78.0 - - - +
427A THR* 1.3 57.0 + - - +
429A LEU* 3.5 3.1 + - - +
430A LYS* 3.0 35.6 + - - +
469A ILE* 3.7 25.1 - - + +
470A ASN* 4.7 1.3 - - - +
473A ALA* 4.1 11.0 - - + -
524A PHE* 3.9 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A GLY 2.7 20.9 + - - -
424A ALA 3.2 5.1 + - - -
426A ALA* 1.3 75.0 - - - +
428A VAL* 1.3 64.4 + - - +
430A LYS* 3.4 11.5 + - - +
431A ALA* 2.9 27.3 + - - +
499A GLU* 3.5 30.3 + - + +
502A THR* 3.7 24.0 - - + -
503A VAL* 4.2 4.0 - - + -
506A LEU* 4.1 5.2 - - + -
521A PHE* 3.8 26.1 - - + -
524A PHE* 4.6 3.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A TYR* 4.3 2.2 - - + +
326A LEU* 3.7 35.7 - - + +
327A ILE* 4.0 19.7 - - + +
330A ALA* 3.5 26.2 - - + -
424A ALA 3.0 17.9 + - - +
425A PHE* 3.6 8.3 - - - +
427A THR* 1.3 76.0 - - - +
429A LEU* 1.3 64.2 + - + +
431A ALA* 3.3 4.9 + - - +
432A LEU* 3.1 36.7 + - + +
502A THR* 3.8 11.2 - - + +
506A LEU* 4.9 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 5.7 2.5 - - + -
284A ALA* 4.4 20.9 - - + +
287A GLY* 5.1 1.6 - - - -
288A ALA* 3.8 10.5 - - + +
291A LEU* 4.2 15.5 - - + -
323A TYR* 3.6 38.1 - - + +
327A ILE* 3.8 21.3 - - + -
425A PHE 3.0 24.8 + - - +
426A ALA* 4.0 3.8 - - - +
428A VAL* 1.3 74.5 - - - +
430A LYS* 1.3 63.7 + - - +
432A LEU* 3.3 1.3 + - - +
433A ILE* 3.0 32.5 + - + +
469A ILE* 4.1 23.6 - - + -
472A LEU* 5.8 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ALA* 3.0 27.6 + - - +
427A THR* 3.9 8.6 + - - +
429A LEU* 1.3 74.2 - - - +
431A ALA* 1.3 56.9 + - - +
433A ILE* 4.0 4.7 - - - +
434A GLY 2.8 28.6 + - - +
438A GLY* 6.5 0.2 - - - -
466A GLU* 4.0 27.6 - - + +
469A ILE* 4.1 15.7 - - + -
470A ASN* 2.9 30.9 + - - +
499A GLU* 4.3 3.4 + - - -
521A PHE* 3.6 22.9 - - + +
522A ARG 2.9 27.7 + - - +
523A LEU* 3.9 1.8 - - - +
524A PHE* 3.8 23.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A THR 2.9 18.1 + - - +
428A VAL 3.8 3.1 - - - +
430A LYS* 1.3 77.9 - - - +
432A LEU* 1.3 63.6 + - + +
434A GLY* 3.4 9.4 + - - -
506A LEU* 3.7 20.2 - - + -
519A PHE* 3.7 26.8 - - + +
520A GLU 4.6 2.9 + - - +
521A PHE* 3.5 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A PHE* 3.5 39.6 - - + -
303A ASN* 4.6 3.3 - - + +
318A PHE* 4.4 11.9 - - + -
322A HIS* 3.6 39.3 - - + +
323A TYR* 3.3 43.7 - - + +
326A LEU* 4.7 4.3 - - + -
428A VAL* 3.1 27.7 + - + +
429A LEU 4.1 2.0 - - - +
431A ALA* 1.3 75.6 - - + +
433A ILE* 1.3 66.6 + - - +
434A GLY* 3.6 0.3 + - - -
437A ARG* 3.7 5.5 + - - -
506A LEU* 5.9 1.1 - - + -
519A PHE* 4.4 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A LEU* 4.1 19.5 - - + -
296A ALA* 3.5 38.4 - - + +
297A PHE* 4.0 13.2 - - + -
307A ILE* 5.7 0.2 - - - +
323A TYR* 4.7 4.5 - - + +
429A LEU* 3.0 24.3 + - + +
430A LYS* 4.0 3.4 - - - +
432A LEU* 1.3 76.1 - - - +
434A GLY* 1.3 66.4 + - - +
437A ARG* 3.1 48.4 + - + +
438A GLY* 3.8 10.5 - - - +
465A PHE* 5.3 2.9 - - + -
469A ILE* 3.9 24.2 - - + -
----------------------------------------------------------
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