Contacts of the helix formed by residues 413 - 425 (chain A) in PDB entry 1KYO
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 THR 413 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A VAL* 4.8 4.0 - - - -
366A LYS* 5.7 0.9 - - - +
411A ALA 3.9 9.4 - - - +
412A ILE* 1.3 80.0 - - - +
414A VAL* 1.3 66.2 + - - +
415A LYS* 3.7 10.4 + - - +
416A ASP* 3.2 26.7 + - - +
417A VAL* 3.2 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A VAL* 3.7 15.3 - - + +
358A THR 4.2 0.9 - - - -
359A ASP* 3.7 37.2 - - - +
362A VAL* 3.7 24.4 - - + +
413A THR* 1.3 71.9 - - - +
415A LYS* 1.3 67.4 + - - +
417A VAL* 3.0 9.5 + - - +
418A LYS* 2.9 52.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A THR* 3.2 11.7 + - - +
414A VAL* 1.3 80.8 - - - +
416A ASP* 1.3 58.8 + - - +
418A LYS* 3.8 9.5 - - + +
419A ALA* 3.1 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A VAL* 4.0 11.1 - - + +
411A ALA 4.1 4.2 - - - +
412A ILE* 3.8 14.9 - - + +
413A THR* 3.2 35.2 + - - +
414A VAL 3.0 0.2 - - - -
415A LYS* 1.3 77.1 - - - +
417A VAL* 1.3 65.4 + - - +
418A LYS 3.1 1.6 - - - -
419A ALA* 3.2 6.0 + - - +
420A TRP* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A VAL* 4.0 12.8 - - + +
279A LEU* 4.0 16.4 - - + -
280A ALA* 5.0 9.2 - - + -
283A ILE* 4.3 9.6 - - + -
353A LEU* 4.1 31.0 - - + +
357A VAL* 4.4 9.6 - - + -
362A VAL* 4.4 12.1 - - + -
412A ILE* 3.8 16.4 - - + -
413A THR 3.4 13.9 - - - +
414A VAL* 3.0 7.9 + - - +
416A ASP* 1.3 74.9 - - - +
418A LYS* 1.3 56.8 + - - +
420A TRP* 3.5 4.4 + - + +
421A ALA* 3.1 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A LEU 3.4 16.9 - - - +
354A THR* 3.8 18.7 - - - +
355A ILE 3.6 26.6 + - - -
356A SER* 4.6 1.6 - - - +
357A VAL* 4.0 19.7 + - + -
414A VAL* 2.9 39.4 + - + +
415A LYS* 3.8 9.2 - - + +
417A VAL* 1.3 75.2 - - - +
419A ALA* 1.3 64.5 + - - +
421A ALA* 3.4 1.9 + - - +
422A GLY* 3.0 20.8 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
415A LYS 3.1 18.1 + - - +
416A ASP* 3.2 6.9 + - - +
418A LYS* 1.3 76.6 - - - +
420A TRP* 1.3 61.6 + - - +
422A GLY* 3.6 2.0 + - - -
423A LYS* 3.3 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLY* 5.7 0.4 - - - -
267A GLU* 3.0 35.3 + - + +
273A ASN* 3.9 25.4 - - + +
276A VAL* 4.0 13.9 - - + -
277A ALA* 3.8 14.8 - - + +
280A ALA* 3.8 20.0 - - + -
327A TRP* 3.5 48.0 - + + -
353A LEU* 4.4 3.1 - - + -
416A ASP 3.1 15.2 + - - +
417A VAL* 3.7 7.6 - - + +
419A ALA* 1.3 76.5 - - - +
421A ALA* 1.3 77.8 + - + +
423A LYS* 3.1 5.7 + - + +
424A ARG* 2.8 51.7 + - + +
425A LEU* 3.4 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A LEU* 3.2 37.0 - - + +
354A THR* 3.1 19.3 - - - +
417A VAL 3.1 10.8 + - - +
418A LYS 3.4 2.0 + - - +
420A TRP* 1.3 90.6 - - + +
422A GLY* 1.3 57.1 + - - +
425A LEU* 2.8 31.2 + - + +
426A TRP 3.0 10.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A THR* 3.7 18.7 + - - -
418A LYS 3.0 14.6 + - - -
419A ALA* 4.0 3.4 - - - -
420A TRP 3.3 0.2 - - - -
421A ALA* 1.3 75.8 - - - +
423A LYS* 1.3 67.6 + - - +
426A TRP* 4.2 18.1 - - - +
428A GLN* 4.7 2.9 + - - -
13I ARG* 5.2 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A ALA 3.3 13.4 + - - +
420A TRP* 3.1 9.4 + - + +
422A GLY* 1.3 83.6 + - - +
424A ARG* 1.3 73.7 + - - +
425A LEU 3.8 0.2 - - - -
428A GLN* 3.5 23.4 + - - +
13I ARG* 3.9 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A VAL* 3.7 12.2 - - + +
265A GLU* 3.4 52.0 + - - +
266A GLY* 3.5 17.0 + - - -
267A GLU* 2.7 33.8 + - - +
268A PRO* 5.1 4.6 - - - +
420A TRP* 2.8 44.6 + - + +
423A LYS* 1.3 88.1 + - - +
425A LEU* 1.3 65.0 + - + +
428A GLN* 3.4 16.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
264A VAL* 3.4 37.2 - - + -
327A TRP* 3.8 31.0 - - + -
350A TRP* 4.7 17.9 - - + +
353A LEU* 4.2 11.2 - - + -
354A THR* 4.9 2.2 - - - +
420A TRP* 3.4 32.3 - - + -
421A ALA* 2.8 21.8 + - + +
424A ARG* 1.3 74.5 - - - +
426A TRP* 1.3 65.6 + - - +
427A ASP 3.1 3.6 + - - -
428A GLN* 3.4 11.6 + - - +
451A MET* 3.6 26.4 - - + +
----------------------------------------------------------
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