Contacts of the helix formed by residues 438 - 450 (chain A) in PDB entry 3KMU
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 438 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A HIS* 5.8 7.5 + - - +
371A ARG* 4.9 23.1 - - + +
375A MSE 3.5 3.9 - - - +
436A ARG 5.4 1.1 - - - +
437A PRO* 1.3 78.5 - - - +
439A PHE* 1.3 66.0 + - - +
440A ASP* 3.3 31.3 + - - +
441A MSE 3.0 16.7 + - + +
442A ILE 3.3 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ALA* 3.7 15.3 - - - +
305A MSE 3.6 31.9 - - + -
306A ALA* 3.7 22.7 - - - +
309A HIS* 3.5 37.7 + + - +
320A LEU* 4.2 2.2 - - + -
371A ARG 4.4 1.1 - - - -
374A ASP* 3.6 29.4 - - + -
375A MSE 3.4 23.4 - - + +
378A PHE* 3.6 36.1 - + + -
438A LYS* 1.3 74.1 - - - +
440A ASP* 1.3 62.0 + - - +
442A ILE* 3.1 7.7 + - + +
443A VAL* 3.1 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ALA* 4.0 15.9 - - + +
438A LYS* 3.3 36.0 + - - +
439A PHE* 1.3 77.6 - - - +
441A MSE 1.3 61.4 + - - +
443A VAL* 4.3 4.5 - - - +
444A PRO* 3.2 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A PRO* 4.3 12.1 - - + -
438A LYS* 3.0 20.7 + - + +
440A ASP* 1.3 84.1 + - - +
442A ILE* 1.3 63.9 + - - +
443A VAL 3.3 0.4 - - - -
444A PRO* 3.3 22.7 - - + +
445A ILE* 3.6 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ALA* 4.1 9.4 - - + -
375A MSE 3.7 17.7 - - + -
378A PHE* 3.1 46.7 - - + -
424A LEU* 4.1 24.0 - - + -
428A CYS* 4.1 3.6 - - - -
437A PRO* 3.6 35.2 - - + -
438A LYS 3.3 2.0 + - - +
439A PHE* 3.1 11.8 + - + +
441A MSE 1.3 78.3 - - - +
443A VAL* 1.3 68.2 + - - +
445A ILE* 3.2 10.8 + - + +
446A LEU* 2.9 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU* 3.6 14.0 - - + +
302A ALA* 3.7 33.2 - - + +
303A ARG* 3.7 18.8 - - + +
306A ALA* 4.5 5.2 - - + -
439A PHE 3.1 22.1 + - - +
440A ASP* 4.3 4.3 - - - +
442A ILE* 1.3 75.8 - - - +
444A PRO* 1.4 67.2 - - + +
446A LEU* 3.2 3.3 + - - -
447A GLU* 2.8 50.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ASP 3.2 19.3 - - - +
441A MSE 3.3 31.0 - - + +
443A VAL* 1.4 93.0 - - + +
445A ILE* 1.3 59.1 + - - +
447A GLU* 3.3 16.5 + - - +
448A LYS* 3.1 46.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A HIS* 3.9 25.3 + - + +
424A LEU* 4.1 28.9 - - + -
427A ILE* 6.5 0.4 - - + -
437A PRO* 6.2 0.4 - - + -
441A MSE 3.6 33.7 - - + +
442A ILE* 3.2 17.4 + - + +
444A PRO* 1.3 76.6 - - + +
446A LEU* 1.3 61.9 + - - +
448A LYS* 3.4 12.2 + - - +
449A MSE 3.3 27.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
295A VAL* 4.1 8.0 - - + +
298A ALA* 3.7 32.1 - - + +
299A LEU* 4.0 16.1 - - + +
302A ALA* 3.7 28.5 - - + -
378A PHE* 3.8 10.8 - - + -
382A LEU* 4.8 3.8 - - + -
424A LEU* 4.0 24.9 - - + -
442A ILE* 2.9 25.3 + - + +
443A VAL 3.7 3.1 - - - +
445A ILE* 1.3 76.3 - - - +
447A GLU* 1.3 65.1 + - - +
449A MSE 3.1 30.7 + - + +
450A GLN* 3.3 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU* 3.9 10.1 - - + -
303A ARG* 2.8 33.4 + - - +
443A VAL* 2.8 33.2 + - - +
444A PRO* 3.3 20.0 + - - +
446A LEU* 1.3 71.2 - - - +
448A LYS* 1.3 65.3 + - + +
450A GLN* 3.2 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A HIS* 6.2 0.7 - - - +
444A PRO* 3.1 37.4 + - - +
445A ILE* 3.8 10.7 - - - +
446A LEU 3.2 0.4 - - - -
447A GLU* 1.3 79.6 + - + +
449A MSE 1.3 60.7 + - + +
450A GLN 3.6 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A VAL* 4.0 32.2 - - + +
382A LEU* 6.4 0.7 - - + -
420A HIS* 3.8 31.6 - - + +
421A VAL* 4.2 24.5 - - + -
424A LEU* 4.3 15.7 - - + -
445A ILE* 3.3 16.8 + - - +
446A LEU* 3.1 34.2 + - + +
448A LYS* 1.3 75.4 - - + +
450A GLN* 1.3 63.9 - - - +
451A ASP 3.9 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A VAL* 4.0 13.9 - - + +
296A LYS* 3.6 29.2 - - + +
299A LEU* 3.4 32.1 - - + +
303A ARG* 4.8 3.6 - - - +
446A LEU 3.3 5.6 + - - +
447A GLU* 3.2 24.2 + - - +
448A LYS 3.9 6.8 - - - +
449A MSE 1.3 82.0 - - - +
451A ASP* 1.3 69.3 + - - +
----------------------------------------------------------
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