Contacts of the helix formed by residues 416 - 426 (chain A) in PDB entry 4PKO
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 416 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A THR* 5.8 2.7 - - - -
414A GLY* 3.0 2.6 - - - -
415A GLY* 1.3 78.6 - - - +
417A VAL* 1.3 61.4 + - - +
418A ALA 3.1 3.8 - - - -
419A LEU* 3.2 29.8 + - - +
420A ILE* 2.9 21.1 + - - +
447A MET 4.5 0.3 - - - +
450A PRO* 4.6 15.6 - - - +
451A LEU 4.8 0.2 - - - -
454A ILE* 4.5 2.1 - - - +
495A ASP* 4.0 9.0 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
413A ALA* 3.1 29.6 - - + -
414A GLY 3.0 22.7 + - - +
415A GLY* 2.9 4.5 - - - +
416A GLY* 1.3 75.2 - - - +
418A ALA* 1.3 60.2 + - - +
420A ILE* 3.5 10.9 + - + -
421A ARG* 2.9 58.8 + - + +
451A LEU* 4.8 2.9 - - + -
469A VAL* 4.1 15.0 - - + -
474A GLY 4.6 4.5 - - - +
475A ASN 5.1 0.2 - - - +
476A TYR 3.7 12.3 - - - +
477A GLY* 4.6 3.6 - - - -
488A MET* 4.2 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU* 4.2 11.2 - - + -
134A LEU* 5.5 6.1 - - + -
412A VAL* 3.4 37.2 - - + -
413A ALA* 3.5 10.7 + - - +
416A GLY* 4.8 0.4 - - - -
417A VAL* 1.3 83.4 - - - +
419A LEU* 1.3 64.7 + - + +
421A ARG* 3.1 6.8 + - - +
422A VAL* 2.9 36.4 + - - +
500A THR* 4.5 1.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A THR* 5.5 5.6 - - + -
95A LEU* 5.0 7.4 - - + -
131A LEU* 4.5 9.0 - - + -
416A GLY* 3.2 22.6 + - - +
418A ALA* 1.3 77.7 - - + +
420A ILE* 1.3 57.1 + - - +
422A VAL* 3.4 6.0 - - - +
423A ALA* 3.0 31.0 + - - +
447A MET* 3.4 45.6 - - + +
450A PRO* 4.8 13.0 - - + -
495A ASP* 5.6 0.4 - - - +
500A THR* 3.4 38.1 - - + +
504A LEU* 4.4 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A GLY 2.9 26.5 + - - +
417A VAL* 3.7 7.4 - - + +
418A ALA 3.3 0.6 - - - -
419A LEU* 1.3 76.3 - - - +
421A ARG* 1.3 68.2 + - - +
423A ALA* 3.8 6.7 - - + +
424A SER* 3.3 21.1 + - - -
447A MET 3.9 4.7 - - - +
448A GLU* 3.9 28.9 - - + -
451A LEU* 3.1 47.8 - - + -
469A VAL* 5.2 8.5 - - + -
470A LYS* 4.1 29.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
134A LEU* 4.6 18.4 - - + -
417A VAL* 2.9 29.5 + - + +
418A ALA* 3.4 7.2 - - - +
419A LEU 3.1 0.2 - - - -
420A ILE* 1.3 83.6 + - - +
422A VAL* 1.3 62.5 + - - +
423A ALA 3.2 0.2 - - - -
424A SER* 2.5 31.4 + - - -
425A LYS* 3.4 16.3 + - - +
469A VAL* 3.7 16.7 + - - +
470A LYS* 4.8 5.9 + - - +
472A GLY 2.9 25.1 + - - -
473A ASP* 3.6 15.6 + - - +
474A GLY* 3.0 34.2 + - - +
476A TYR 3.3 24.4 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
127A ALA* 3.8 13.0 - - + +
130A GLU* 3.7 30.2 - - + +
131A LEU* 3.6 26.0 - - + -
134A LEU* 5.2 7.6 - - + -
418A ALA* 2.9 15.8 + - - +
419A LEU* 3.4 6.3 - - + +
421A ARG* 1.3 73.8 - - + +
423A ALA* 1.3 67.3 + - - +
425A LYS* 3.3 15.2 + - - +
426A LEU* 3.3 19.8 + - - +
447A MET* 3.2 31.2 - - + -
----------------------------------------------------------
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 LEU 3.0 19.4 + - - +
420A ILE* 3.8 7.4 - - - +
421A ARG 3.2 0.2 - - - -
422A VAL* 1.3 81.1 - - - +
424A SER* 1.3 61.7 + - - +
426A LEU 3.4 8.3 + - - -
427A ALA* 3.7 3.1 + - - +
444A LEU* 3.6 46.8 - - + +
447A MET* 3.9 17.3 - - + -
448A GLU* 5.7 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A ILE 3.3 9.4 + - - -
421A ARG* 2.5 36.6 + - - -
423A ALA* 1.3 81.1 - - - +
425A LYS* 1.3 62.6 + - - +
426A LEU 3.6 0.2 + - - -
427A ALA* 3.6 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLU* 3.3 38.2 + - - +
134A LEU* 6.2 3.2 - - - +
421A ARG* 3.4 18.4 + - + +
422A VAL* 3.3 10.4 + - - +
423A ALA 3.2 1.0 - - - -
424A SER* 1.3 83.6 + - - +
426A LEU* 1.3 62.7 + - - +
427A ALA 3.2 2.0 + - - -
428A ASP* 3.8 14.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ALA* 3.3 28.5 - - - +
126A ALA* 3.5 20.4 - - + -
127A ALA* 3.3 26.0 - - + +
130A GLU* 4.1 18.2 - - + +
422A VAL 3.3 15.6 + - - +
423A ALA 3.4 0.6 + - - -
424A SER 3.3 0.6 - - - -
425A LYS* 1.3 81.2 - - - +
427A ALA* 1.3 57.9 + - - +
428A ASP* 3.2 4.7 - - - -
429A LEU* 2.9 36.9 + - + +
441A LYS* 4.1 0.5 + - - -
444A LEU* 3.8 31.1 - - + +
----------------------------------------------------------
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