Contacts of the helix formed by residues 439 - 452 (chain A) in PDB entry 3OFN
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 ALA 439 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A GLN* 5.4 0.2 - - - -
190A ARG* 3.5 33.5 - - - +
438A LEU* 1.3 77.4 - - - +
440A THR* 1.3 60.4 + - - +
441A GLU* 3.2 28.9 - - - +
442A GLU* 3.0 22.5 + - + +
443A GLN* 2.9 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A GLN* 2.4 42.7 + - - +
156A ASP* 4.0 4.6 + - - +
382A VAL* 3.8 31.9 - - + -
384A ALA* 5.3 0.7 - - + -
385A LEU* 4.3 14.6 - - + -
438A LEU 3.9 0.4 + - - -
439A ALA* 1.3 73.0 - - - +
441A GLU* 1.3 60.7 + - - +
442A GLU 3.0 0.2 - - - -
443A GLN* 3.0 8.8 + - + +
444A VAL* 2.9 51.4 + - + +
485A ILE* 4.7 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A ALA* 3.3 24.0 - - + +
440A THR* 1.3 75.8 + - - +
442A GLU* 1.3 63.6 + - + +
445A PRO* 3.2 10.6 - - - +
482A LEU* 3.1 58.8 - - + +
485A ILE* 3.7 20.5 - - + +
486A ARG* 3.2 49.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ARG* 4.3 4.3 + - - -
437A PRO 5.1 0.5 - - - +
438A LEU* 3.4 24.7 - - + +
439A ALA* 3.0 35.6 + - + +
441A GLU* 1.3 83.2 - - + +
443A GLN* 1.3 64.2 + - - +
444A VAL 3.6 0.2 - - - -
445A PRO* 3.4 11.6 - - - +
446A LEU* 3.6 12.9 - - - +
471A LEU* 3.6 34.6 - - + +
475A LYS* 3.2 34.9 + - - -
482A LEU* 5.1 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A GLY* 4.1 9.1 - - - -
153A LYS* 3.6 36.1 - - + +
156A ASP* 3.0 47.9 + - - +
157A ALA 4.3 0.2 + - - -
385A LEU* 3.8 16.9 - - + +
438A LEU* 3.9 23.7 + - + -
439A ALA 2.9 10.6 + - - +
440A THR* 3.4 13.6 - - - +
442A GLU* 1.3 77.7 - - - +
444A VAL* 1.3 60.8 + - - +
446A LEU* 3.3 7.4 + - - +
447A ILE* 3.0 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ALA* 4.0 6.7 - - + +
385A LEU* 3.9 26.5 - - + +
388A VAL* 3.8 18.5 - - + +
440A THR* 2.9 31.2 + - + +
443A GLN* 1.3 73.6 - - - +
445A PRO* 1.4 72.4 - - + +
447A ILE 3.2 0.5 + - - -
448A TYR* 2.8 32.6 + - - +
485A ILE* 3.7 29.2 - - + -
491A LEU* 4.3 13.7 - - + -
499A LEU* 4.4 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A GLU 3.2 26.7 - - - +
442A GLU* 3.4 14.4 - - - +
444A VAL* 1.4 99.0 - - + +
446A LEU* 1.3 57.9 + - - -
448A TYR* 3.8 8.3 - - + +
449A ALA* 3.4 14.4 + - - +
470A PHE* 3.3 18.5 - - + -
471A LEU* 4.6 2.7 - - + -
474A LEU* 3.6 26.9 - - + -
482A LEU* 4.0 10.1 - - + -
485A ILE* 4.3 2.2 - - + -
499A LEU* 4.1 20.2 - - + -
503A THR* 4.9 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LYS* 4.5 5.4 - - + -
429A LEU* 3.3 33.6 - - + +
438A LEU* 4.3 10.5 - - + -
442A GLU 3.6 15.3 - - - +
443A GLN* 3.3 9.3 + - - +
444A VAL 3.1 0.4 - - - -
445A PRO* 1.3 80.8 - - - +
447A ILE* 1.3 66.0 + - + +
449A ALA* 3.7 3.3 + - - +
450A GLY 3.4 8.3 + - - -
455A LEU* 4.7 0.5 - - - +
466A PHE* 4.4 8.1 - - + -
467A GLU* 3.3 60.1 - - + +
470A PHE* 4.3 16.4 - - + -
471A LEU* 4.2 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LYS* 4.6 8.7 - - + +
157A ALA* 3.8 28.5 - - + -
385A LEU* 4.0 15.3 - - + -
388A VAL* 3.8 24.0 - - + +
389A ALA* 3.9 17.3 - - + -
392A LEU* 4.7 11.4 - - + -
426A LEU* 4.8 2.2 - - + +
429A LEU* 4.5 8.7 - - + -
430A LEU* 4.8 12.3 - - + -
443A GLN* 3.0 27.4 + - + +
444A VAL 4.1 1.8 - - - +
446A LEU* 1.3 76.5 - - + +
448A TYR* 1.3 61.3 + - - +
450A GLY* 3.0 2.3 + - - +
451A VAL* 2.9 37.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A VAL* 3.6 28.2 - - + +
444A VAL 2.8 17.8 + - - +
445A PRO 3.8 4.5 - - - +
446A LEU 3.3 0.2 - - - -
447A ILE* 1.3 76.9 - - - +
449A ALA* 1.3 66.6 + - - +
451A VAL* 5.3 0.9 - - - -
452A ASN* 2.8 52.6 + - - +
454A HIS* 3.9 12.2 - + - -
496A LEU* 3.7 27.0 + - + +
499A LEU* 3.8 22.9 - - + -
500A LYS* 3.1 52.1 - - - +
503A THR* 3.7 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A PRO 3.4 13.2 + - - +
446A LEU 3.8 5.2 - - - +
447A ILE 3.4 0.2 - - - -
448A TYR* 1.3 81.7 - - - +
450A GLY* 1.3 62.6 + - - +
453A GLY 3.7 0.5 + - - -
454A HIS* 3.1 41.8 + - + +
455A LEU* 3.7 5.5 + - + -
466A PHE* 4.2 23.8 - - + -
470A PHE* 4.3 1.1 - - + -
503A THR* 3.7 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A ARG* 3.7 12.0 - - - -
425A ARG* 5.9 1.5 - - - +
426A LEU* 3.8 12.1 - - - +
429A LEU* 4.0 10.1 - - - -
446A LEU 3.4 4.4 + - - -
447A ILE 3.0 7.3 + - - -
449A ALA* 1.3 79.3 - - - +
451A VAL* 1.3 62.9 + - - +
453A GLY* 3.2 13.2 + - - -
455A LEU* 3.6 23.4 + - - +
456A ASP* 4.5 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A VAL 4.0 22.9 - - - +
389A ALA 5.2 0.2 - - - +
390A GLY 5.6 4.3 - - - +
391A SER* 6.0 1.3 - - - +
392A LEU* 4.4 18.6 - - + -
422A ARG* 2.8 23.6 + - - +
426A LEU* 3.8 24.4 - - + +
447A ILE* 2.9 27.7 + - + +
448A TYR* 4.5 1.8 - - - +
450A GLY* 1.3 69.9 - - - -
452A ASN* 1.3 68.0 + - - +
453A GLY 3.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 452 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A VAL* 5.6 1.0 - - - +
422A ARG* 3.8 3.4 - - - +
448A TYR* 2.8 60.0 + - - +
450A GLY 3.2 0.4 - - - -
451A VAL* 1.3 84.8 - - - +
453A GLY* 1.3 55.0 + - - +
454A HIS* 3.2 31.3 + - + +
----------------------------------------------------------
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