Contacts of the helix formed by residues 412 - 430 (chain A) in PDB entry 1F9O
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 412 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A THR 3.8 1.6 + - - -
411A TRP* 1.3 73.5 - - + +
413A GLY* 1.3 53.6 + - - +
415A GLN* 2.7 59.1 + - + +
416A VAL* 3.6 33.7 + - + -
441A TRP* 4.9 1.1 - + - -
444A TRP* 4.1 13.5 - + - -
445A ILE* 3.6 34.5 - - + -
459A ILE* 4.2 18.6 - - + -
460A PRO* 3.3 42.4 - - + +
461A SER* 2.9 17.5 + - - +
463A ILE* 4.3 13.8 - - + +
497A CYS* 4.2 15.3 - - + -
501A LEU* 4.7 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A TRP* 3.0 40.5 + - - +
412A PHE* 1.3 78.8 - - - +
414A MET* 1.3 62.7 + - - +
415A GLN 3.0 1.0 + - - -
416A VAL* 3.2 9.5 - - - +
417A TRP* 3.1 24.8 + - - +
497A CYS* 3.8 10.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A TRP* 4.3 10.8 - - + -
320A HIS* 3.8 25.1 - - + +
321A PHE* 3.5 11.9 - - + -
322A GLY* 4.3 14.1 - - - +
323A TYR* 4.2 24.9 - - + -
408A SER* 3.8 21.3 - - - +
409A ASN* 3.8 16.4 - - - +
411A TRP* 3.3 29.1 + - + +
412A PHE 3.0 1.6 + - - -
413A GLY* 1.3 74.4 - - - +
415A GLN* 1.3 65.3 + - - +
417A TRP* 4.8 13.7 - - - -
418A SER* 3.3 25.6 + - - -
3C BGC 5.1 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A PHE* 3.5 15.9 - - - -
369A ALA* 3.7 7.6 - - - -
370A ILE* 3.0 47.8 + - - +
409A ASN* 4.2 3.4 + - - -
411A TRP 5.2 0.4 + - - +
412A PHE* 2.7 49.5 + - + +
414A MET* 1.3 74.2 - - - +
416A VAL* 1.3 59.7 + - - +
418A SER* 4.3 0.3 - - - -
419A MET* 3.2 28.2 + - - +
441A TRP* 3.1 24.6 + - + -
444A TRP* 4.3 4.9 - - + -
463A ILE* 4.1 12.3 - - + +
465A TRP* 4.0 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A PHE* 3.6 30.3 - - + -
413A GLY* 3.2 23.3 - - - +
415A GLN* 1.3 71.4 - - - +
417A TRP* 1.3 66.5 + - + +
420A GLN* 2.9 28.4 + - - +
441A TRP* 4.0 11.4 - - + -
497A CYS* 4.0 11.4 - - - +
500A SER* 3.4 30.7 - - - +
501A LEU* 3.8 30.1 - - + -
504A THR* 3.4 2.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLU* 3.5 30.5 - - - -
59A TYR* 3.0 26.1 + + - -
230A ASP* 4.9 7.9 - - - -
234A ARG* 4.0 15.5 - - - -
322A GLY 5.0 3.1 - - - +
411A TRP* 3.8 27.8 - + - -
413A GLY 3.1 16.8 + - - +
414A MET* 4.3 14.6 - - - +
416A VAL* 1.3 79.7 - - + +
418A SER* 1.3 62.2 + - - +
420A GLN* 3.7 7.9 + - - +
421A ARG* 3.0 36.6 + - - +
497A CYS* 6.0 0.6 - - - +
500A SER* 3.3 22.2 + - - -
611A TRP* 3.4 43.4 - + - -
615A GLU* 3.1 8.8 + - - -
3C BGC 3.8 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A PHE* 2.8 34.7 + - - -
322A GLY* 3.7 8.3 - - - -
324A GLN 3.9 2.1 + - - -
360A TYR* 2.6 41.0 + - - -
414A MET 3.3 16.5 + - - -
417A TRP* 1.3 80.8 - - - +
419A MET* 1.3 58.5 + - - +
421A ARG* 3.0 32.2 + - - +
422A VAL 3.5 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A PHE* 5.0 1.6 - - + -
360A TYR* 4.1 15.7 - - + -
370A ILE* 4.2 19.1 - - + -
415A GLN 3.2 19.9 + - - +
416A VAL 4.3 0.7 - - - +
418A SER* 1.3 70.8 - - - +
420A GLN* 1.3 59.6 + - - +
421A ARG 3.1 2.7 - - - -
422A VAL* 3.2 20.0 + - + +
423A ALA* 3.0 26.2 + - - +
437A LEU* 4.0 19.3 - - + +
438A LEU* 3.6 25.5 - - + +
441A TRP* 3.6 59.0 - - + +
504A THR* 3.7 5.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A TRP* 3.7 14.5 - - + -
237A GLN* 3.4 17.0 + - - +
416A VAL 2.9 15.1 + - - +
417A TRP* 3.8 6.2 - - - +
418A SER 3.2 0.4 - - - -
419A MET* 1.3 77.3 - - - +
421A ARG* 1.3 63.1 + - - +
423A ALA* 3.3 3.7 + - - +
424A GLU* 2.8 53.0 + - - +
500A SER* 4.5 5.8 - - - +
503A ASN* 3.2 38.0 + - + +
504A THR* 3.1 27.6 + - - +
507A TYR* 3.8 1.4 - - - -
615A GLU* 5.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ASP* 4.8 10.8 + - - +
234A ARG* 3.3 33.3 - - - +
237A GLN* 3.9 12.7 + - - +
322A GLY 2.8 24.7 + - - -
323A TYR 3.8 6.1 + - - -
324A GLN 2.8 36.3 + - - -
325A ASN* 3.5 36.1 - - - +
326A PRO* 3.9 9.9 - - + -
327A PHE* 3.9 7.9 + - + +
417A TRP* 3.0 32.3 + - - +
418A SER* 3.0 13.6 + - - +
420A GLN* 1.3 82.9 + - - +
422A VAL* 1.3 60.1 + - - +
424A GLU* 3.3 7.3 + - - +
425A LEU* 3.1 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A PRO* 4.1 7.0 - - + -
357A LEU* 4.8 4.9 - - + -
360A TYR* 3.5 45.8 - - + +
418A SER 3.7 5.4 - - - +
419A MET* 3.2 17.2 + - + +
421A ARG* 1.3 76.9 - - - +
423A ALA* 1.3 57.8 + - - +
425A LEU* 3.5 6.6 + - + +
426A TYR* 3.1 26.5 + - - +
434A ALA* 3.8 27.3 - - + +
437A LEU* 4.5 13.0 - - + -
438A LEU* 3.6 14.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A MET 3.0 12.8 + - - +
420A GLN* 3.5 9.4 - - - +
421A ARG 3.2 0.2 - - - -
422A VAL* 1.3 77.5 - - - +
424A GLU* 1.3 59.5 + - - +
426A TYR* 3.4 2.0 + - - +
427A TYR* 2.9 29.8 + - - +
438A LEU* 3.7 16.4 - - + +
504A THR* 3.6 30.5 - - + +
507A TYR* 3.8 15.7 - - + +
508A TYR* 4.3 4.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A TRP* 3.7 10.0 + - - -
237A GLN* 2.9 26.7 + - - -
241A TRP* 2.7 34.2 + - + -
327A PHE* 3.6 22.3 - - + -
420A GLN* 2.8 37.7 + - - +
421A ARG* 3.3 8.7 + - - +
423A ALA* 1.3 76.9 - - - +
425A LEU* 1.3 61.7 + - - +
427A TYR* 3.5 2.4 + - - +
428A LYS* 3.2 25.5 + - - +
507A TYR* 3.7 30.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A PRO* 3.9 23.8 - - + +
327A PHE* 3.8 12.1 - - + +
330A TRP* 3.8 37.7 - - + -
353A LEU* 4.3 7.4 - - + -
357A LEU* 4.2 24.7 - - + -
421A ARG 3.1 16.0 + - - +
422A VAL* 3.7 6.7 - - - +
424A GLU* 1.3 75.6 - - - +
426A TYR* 1.3 60.3 + - - +
428A LYS* 3.3 0.9 + - - -
429A THR* 2.8 50.6 + - + +
431A ASP* 4.7 9.2 - - + +
434A ALA* 4.7 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A VAL 3.1 15.6 + - - +
423A ALA 3.8 1.8 - - - +
424A GLU 3.4 0.2 - - - -
425A LEU* 1.3 78.3 - - - +
427A TYR* 1.3 57.6 + - - +
430A GLY* 2.7 42.1 + - - +
431A ASP 3.7 18.4 - - - +
434A ALA* 3.8 10.1 - - + +
435A LYS* 3.6 47.4 - - + +
438A LEU* 3.8 22.4 - - + -
508A TYR* 3.9 29.6 - + - -
511A LYS* 3.5 36.0 + - + +
512A SER* 3.6 17.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A TRP* 4.5 7.9 - + - -
423A ALA 2.9 18.3 + - - +
424A GLU 3.7 4.0 - - - +
425A LEU 3.2 0.4 - - - -
426A TYR* 1.3 78.3 - - - +
428A LYS* 1.3 83.8 + - + +
507A TYR* 3.7 47.8 - + + +
510A ALA* 4.4 15.3 - - + -
511A LYS* 3.4 35.5 + - + -
626A LEU* 3.6 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A TYR* 2.7 35.1 + - - -
241A TRP* 3.7 29.9 - - + -
244A GLN* 3.5 13.9 + - - -
327A PHE* 4.2 13.0 - - + -
330A TRP* 4.4 13.4 - - + -
424A GLU 3.2 15.9 + - - +
425A LEU 4.1 1.6 - - - +
427A TYR* 1.3 95.7 - - + +
429A THR* 1.3 66.1 + - + +
511A LYS* 5.1 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A TRP* 3.5 38.8 - - + +
425A LEU* 2.8 31.6 + - + +
428A LYS* 1.3 84.0 - - + +
430A GLY* 1.3 65.7 + - - +
431A ASP* 3.0 24.2 + - - +
511A LYS* 4.8 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A TYR* 2.7 37.9 + - - -
428A LYS 3.8 0.4 - - - -
429A THR* 1.3 72.9 + - - +
431A ASP* 1.3 66.3 + - - +
432A ALA* 3.4 2.9 + - - +
435A LYS* 5.5 0.5 - - - +
511A LYS* 3.7 18.6 - - - +
----------------------------------------------------------
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