Contacts of the helix formed by residues 398 - 409 (chain A) in PDB entry 2KFZ
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 ARG 398 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ASN* 3.9 20.3 + - - +
368A LEU* 2.8 40.8 + - + -
385A VAL* 3.7 29.9 + - + +
386A ALA* 3.8 16.5 - - + +
396A ILE 3.8 1.8 + - - -
397A SER* 1.3 71.9 - - - +
399A GLU* 1.3 64.5 + - + +
401A ALA* 3.9 0.9 - - - +
402A LEU* 3.1 44.3 + - + +
431A TYR* 3.6 38.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A SER* 3.1 6.3 + - - +
398A ARG* 1.3 86.7 + - + +
400A ARG* 1.3 61.2 + - - +
402A LEU* 3.5 5.9 + - - +
403A GLU* 3.1 26.4 + - - +
431A TYR* 4.3 19.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A GLU* 2.9 46.8 + - + +
340A LYS* 4.3 7.9 - - - +
396A ILE* 4.1 12.3 - - + -
397A SER* 3.1 22.2 + - - +
399A GLU* 1.3 75.0 - - - +
401A ALA* 1.3 65.3 + - - +
403A GLU* 3.0 39.5 + - - +
404A LEU* 3.3 51.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LEU* 4.5 12.5 - - + +
371A LEU* 5.0 4.3 - - + -
383A ILE* 4.9 4.5 - - + -
385A VAL* 3.7 24.7 - - + -
396A ILE* 3.9 13.0 - - + +
397A SER 2.9 15.9 + - - +
398A ARG 3.9 1.8 - - - +
400A ARG* 1.3 76.8 - - - +
402A LEU* 1.3 60.1 + - + +
404A LEU* 3.5 2.3 + - - +
405A LEU* 3.0 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A LEU* 3.8 21.8 - - + -
371A LEU* 4.5 14.4 - - + -
385A VAL* 6.5 0.2 - - + -
398A ARG* 3.1 33.1 + - + +
399A GLU* 4.1 7.4 - - - +
401A ALA* 1.3 78.2 - - + +
403A GLU* 1.3 59.1 + - - +
405A LEU* 4.4 2.5 - - + -
406A LYS* 2.8 32.6 + - - +
409A LEU* 5.2 4.3 - - + -
428A LEU* 4.3 10.5 - - + -
431A TYR* 3.6 45.1 - - + -
433A ILE* 4.0 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A GLU 3.1 15.8 + - - +
400A ARG* 3.0 49.0 + - - +
402A LEU* 1.3 76.5 - - - +
404A LEU* 1.3 65.0 + - - +
406A LYS* 4.0 7.5 - - - +
407A PRO* 3.5 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A GLU* 4.3 13.9 - - + -
339A LEU* 3.7 21.8 - - + -
340A LYS* 4.2 29.8 - - + -
343A ILE* 3.4 26.4 - - + +
396A ILE* 5.7 0.4 - - + -
400A ARG* 3.3 60.1 + - + +
401A ALA 3.9 3.1 - - - +
403A GLU* 1.3 77.9 - - - +
405A LEU* 1.3 59.5 + - - +
407A PRO* 3.6 11.0 - - - +
408A LEU* 5.2 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LEU* 4.3 10.3 - - + -
343A ILE* 3.6 32.1 - - + -
346A LEU* 5.3 1.6 - - + -
371A LEU* 4.2 19.1 - - + -
373A PHE* 3.9 37.2 - - + -
383A ILE* 4.3 11.2 - - + -
401A ALA* 3.0 25.1 + - + +
402A LEU* 4.1 4.3 - - + +
404A LEU* 1.3 77.5 - - - +
406A LYS* 1.3 64.0 + - - +
407A PRO* 3.4 1.1 - - - -
408A LEU* 3.2 18.8 + - + +
409A LEU* 3.1 34.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A LEU 2.8 22.4 + - - +
403A GLU* 4.0 7.9 - - - +
405A LEU* 1.3 73.1 - - - +
407A PRO* 1.3 72.7 - - + +
409A LEU* 3.2 4.8 + - - +
410A GLU* 2.9 58.3 + - + +
431A TYR 5.2 1.2 + - - -
432A GLY 3.3 20.7 + - - -
433A ILE* 3.9 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A GLU* 5.9 2.7 - - - +
403A GLU 3.5 14.6 - - - +
404A LEU 3.6 8.5 - - - +
405A LEU 3.5 4.0 - - - -
406A LYS* 1.3 94.9 - - + +
408A LEU* 1.3 60.9 + - - +
410A GLU* 3.4 4.4 + - + +
411A ASP* 3.2 24.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
343A ILE* 4.8 14.6 - - + -
346A LEU* 3.8 30.1 - - + -
347A GLU* 3.9 35.4 + - + +
352A PHE* 3.8 30.3 - - + -
373A PHE* 4.6 4.5 - - + -
404A LEU 5.2 0.9 + - - +
405A LEU* 3.2 24.5 + - + +
407A PRO* 1.3 79.2 - - - +
409A LEU* 1.3 60.9 + - + +
411A ASP* 3.5 8.2 + - - +
414A ALA* 3.6 18.9 - - + +
416A LYS* 2.9 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A PHE* 5.1 1.6 - - + -
354A PHE* 4.5 10.8 - - + -
371A LEU* 4.9 8.1 - - + -
373A PHE* 4.3 24.5 - - + -
402A LEU* 5.2 1.3 - - + -
405A LEU* 3.1 39.1 + - + +
406A LYS* 3.7 6.1 - - - +
408A LEU* 1.3 84.7 - - + +
410A GLU* 1.3 57.7 + - - +
411A ASP 3.3 0.7 - - - -
416A LYS* 3.1 21.7 + - - +
428A LEU* 4.2 32.8 - - + -
433A ILE* 4.3 16.4 - - + -
434A GLU 4.3 0.9 - - - -
435A LEU* 3.4 9.5 - - + +
436A ARG 3.0 22.7 + - - -
----------------------------------------------------------
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