Contacts of the helix formed by residues 404 - 418 (chain A) in PDB entry 4ZPK
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 ASP 404 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A CYS* 3.5 15.3 - - - -
401A HIS* 2.7 23.5 + - - +
403A GLU* 1.3 82.5 - - - +
405A GLN* 1.3 53.6 + - - +
406A GLN* 3.2 3.4 - - - -
407A LEU* 2.8 40.5 + - + +
408A LEU* 3.5 2.4 + - - +
426A MET 5.6 0.9 - - - +
427A PHE* 4.3 11.6 - - + +
428A ARG* 2.6 56.2 + - - +
438A TRP* 4.5 4.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A VAL* 3.1 37.6 + - + +
398A GLU* 4.6 5.3 - - - +
400A CYS* 2.7 35.8 + - + -
401A HIS 2.9 14.3 + - - +
402A PRO* 3.5 26.7 + - - +
403A GLU 3.9 0.4 - - - -
404A ASP* 1.3 75.6 - - - +
406A GLN* 1.3 61.9 + - - +
408A LEU* 3.1 7.1 - - - +
409A ARG* 3.0 21.0 + - - +
430A ARG* 4.7 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A PRO 5.3 1.0 + - - -
403A GLU 6.4 0.2 - - - -
404A ASP 3.0 1.2 + - - -
405A GLN* 1.3 74.9 - - - +
407A LEU* 1.3 66.7 + - - +
409A ARG* 3.1 25.4 + - - +
410A ASP* 2.8 57.0 + - - +
413A GLN* 5.1 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A ASP* 2.8 18.8 + - + +
406A GLN* 1.3 77.9 - - - +
408A LEU* 1.3 50.5 + - + +
410A ASP* 2.7 23.1 - - - +
411A SER* 2.7 29.4 + - - -
414A GLN* 6.2 1.6 - - - +
425A VAL* 3.9 22.9 - - + -
426A MET* 3.3 28.3 - - + +
427A PHE* 5.2 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ILE* 4.3 15.7 - - + +
397A VAL* 3.7 29.8 - - + +
400A CYS* 3.5 25.1 - - + -
404A ASP 3.5 2.4 + - - -
405A GLN* 3.1 13.2 + - - +
406A GLN 3.1 0.4 - - - -
407A LEU* 1.3 77.8 - - - +
409A ARG* 1.3 65.4 + - - +
411A SER* 2.4 22.0 + - - +
412A PHE* 2.9 22.5 + - + -
425A VAL* 4.2 9.4 - - + -
427A PHE* 3.4 48.0 - - + -
441A THR* 5.4 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A VAL* 4.6 10.0 - - + +
405A GLN 3.0 8.8 + - - +
406A GLN* 3.1 25.4 + - - +
408A LEU* 1.3 79.6 - - - +
410A ASP* 1.3 59.3 + - - +
412A PHE* 3.1 7.1 + - - +
413A GLN* 3.0 51.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A GLN* 2.8 38.9 + - - +
407A LEU* 2.7 37.6 - - - +
409A ARG* 1.3 71.8 - - - +
411A SER* 1.3 65.8 + - - +
413A GLN* 3.2 23.3 - - - +
414A GLN* 2.9 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A LEU* 2.7 16.0 + - - -
408A LEU* 2.4 25.6 + - - +
410A ASP* 1.3 80.9 + - - +
412A PHE* 1.3 65.1 + - - +
414A GLN* 3.1 15.5 + - - +
415A VAL* 2.9 32.5 + - - +
423A LEU* 4.0 7.1 - - - +
425A VAL* 3.4 32.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A HIS* 4.2 15.5 - + + -
369A ILE 4.4 10.1 - - - +
370A GLU 5.0 1.3 - - - -
371A GLY* 3.7 30.1 - - - -
396A ILE* 4.4 20.0 - - + -
408A LEU* 2.9 25.0 + - + +
409A ARG* 3.5 10.1 - - - +
411A SER* 1.3 79.2 + - - +
413A GLN* 1.3 66.2 + - + +
415A VAL* 3.0 20.8 + - + +
416A VAL* 3.0 19.4 + - - +
441A THR* 5.8 6.7 - - + -
443A SER* 5.0 6.3 - - - -
457A ILE* 3.7 27.1 - - + -
459A CYS* 4.1 24.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A GLN* 5.1 0.6 - - - +
409A ARG* 3.0 55.0 + - + +
410A ASP* 3.2 22.3 - - - +
412A PHE* 1.3 75.2 - - - +
414A GLN* 1.3 56.9 + - + +
416A VAL* 3.1 13.6 - - - +
417A LYS* 3.0 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A LEU* 6.2 2.0 - - - +
410A ASP* 2.9 27.3 + - - +
411A SER* 3.1 17.0 + - - +
413A GLN* 1.3 72.6 - - + +
415A VAL* 1.3 56.6 + - - +
417A LYS* 3.8 27.8 - - - +
418A LEU* 2.4 40.6 + - + +
423A LEU* 3.9 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A SER* 2.9 22.4 + - - +
412A PHE* 3.0 13.2 + - + +
414A GLN* 1.3 74.6 - - - +
416A VAL* 1.3 60.2 + - - +
418A LEU* 2.9 23.0 - - - +
421A GLN 5.4 0.7 - - - -
423A LEU* 3.7 23.8 - - + +
443A SER* 3.2 25.4 - - - +
444A PHE* 3.8 7.4 - - - -
445A THR* 2.8 35.7 + - - +
457A ILE* 3.8 25.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
369A ILE* 4.0 33.0 - - + +
412A PHE 3.0 9.4 + - - +
413A GLN* 3.1 21.3 - - - +
415A VAL* 1.3 72.7 - - - +
417A LYS* 1.3 66.8 + - - +
419A LYS* 3.8 11.8 + - - +
445A THR* 3.2 18.3 + - + +
454A ILE* 5.2 4.7 - - + -
457A ILE* 3.9 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A GLN* 3.0 17.9 + - - +
414A GLN* 3.3 29.4 - - - +
416A VAL* 1.3 79.2 - - + +
418A LEU* 1.3 53.8 + - + +
419A LYS* 2.6 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A GLN* 2.4 32.1 + - + +
415A VAL 2.9 12.5 - - - +
417A LYS* 1.3 64.1 - - + +
419A LYS* 1.3 65.7 + - - +
420A GLY 3.1 3.1 + - - -
421A GLN* 3.1 56.1 + - + +
422A VAL 4.0 10.5 - - - +
423A LEU* 3.9 22.9 - - + -
----------------------------------------------------------
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