Contacts of the helix formed by residues 472 - 480 (chain B) in PDB entry 4KZM
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 472 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B GLY* 2.8 21.8 + - - +
462B LEU* 3.7 13.1 - - - +
471B HIS* 1.3 78.1 - - + +
473B LEU* 1.3 94.7 + - - +
475B CYS* 3.0 7.3 + - - +
476B ALA* 3.0 28.3 + - + +
483B ILE* 4.3 11.9 - - + +
484B ASP* 2.7 31.4 + - - -
487B LEU* 3.5 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 473 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B VAL* 3.6 42.2 - - + +
471B HIS* 3.2 11.3 - - + +
472B ARG* 1.3 114.3 - - + +
474B GLN* 1.3 59.9 + - - +
475B CYS 3.2 0.6 + - - -
476B ALA* 3.9 18.7 + - + +
477B ARG* 4.6 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 474 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B LYS 2.8 25.5 + - - -
387B PHE* 3.7 0.5 - - - -
388B GLN* 3.1 32.9 + - + +
391B VAL* 3.9 22.2 - - + -
402B ASP* 5.5 2.1 - - - +
405B GLN* 3.1 22.6 + - - +
470B LEU* 3.6 21.7 - - + +
471B HIS* 2.8 34.9 + - + +
473B LEU* 1.3 77.9 - - - +
475B CYS* 1.3 57.8 + - - +
477B ARG* 5.4 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 475 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B GLN* 3.9 7.9 - - - +
409B LEU* 4.9 2.0 - - - -
462B LEU* 4.1 18.4 - - - -
464B PHE* 4.1 22.9 - - - -
470B LEU* 4.3 15.0 - - - -
471B HIS 4.0 11.0 - - - -
472B ARG 3.0 6.3 + - - +
474B GLN* 1.3 79.5 - - - +
476B ALA* 1.3 64.4 + - - +
477B ARG 3.2 2.9 - - - -
478B GLY* 3.2 6.8 + - - -
479B PHE* 3.0 41.1 + - + -
483B ILE* 4.5 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 476 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B ARG* 3.0 19.4 + - + +
473B LEU* 3.9 22.8 + - + +
474B GLN 3.7 1.2 - - - -
475B CYS* 1.3 78.8 - - - +
477B ARG* 1.3 60.8 + - + +
479B PHE 4.5 0.4 - - - +
480B GLY* 2.7 32.0 + - - +
483B ILE* 4.1 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 477 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B VAL* 5.5 6.5 - - - +
397B LYS 4.4 18.6 + - - +
398B GLU* 3.4 23.6 - - + +
399B ASP* 4.0 9.1 + - - -
402B ASP* 2.9 46.3 + - - +
473B LEU 4.6 13.9 + - - +
474B GLN* 5.4 2.2 + - - +
475B CYS 3.2 0.8 - - - -
476B ALA* 1.3 77.8 - - + +
478B GLY* 1.3 60.1 + - - +
480B GLY* 4.0 0.5 + - - -
572B ARG* 2.9 22.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 478 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B GLU* 5.4 0.2 - - - -
402B ASP* 3.4 32.4 - - - +
403B VAL* 4.7 2.0 - - - -
405B GLN* 5.1 2.4 + - - -
406B PHE* 3.7 18.6 - - - -
475B CYS 3.2 7.2 + - - -
477B ARG* 1.3 79.2 - - - +
479B PHE* 1.3 57.3 + - - +
572B ARG* 2.9 24.0 + - - -
576B LEU* 4.1 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 479 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B GLN* 5.9 0.7 - - - -
406B PHE* 3.6 33.2 - + + -
409B LEU* 3.9 29.8 - - + -
410B LEU* 4.6 1.8 - - + -
447B PHE* 4.2 29.4 - + - -
451B LEU* 5.2 0.9 - - + -
464B PHE* 4.4 7.9 - + - -
475B CYS* 3.0 40.6 + - + +
476B ALA 4.5 0.2 - - - +
478B GLY* 1.3 76.2 - - - +
480B GLY* 1.3 61.7 + - - +
482B TRP* 3.6 33.5 - + - +
483B ILE* 3.8 37.7 - - + +
486B ILE* 4.3 6.1 - - + -
572B ARG* 3.3 20.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 480 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B ALA* 2.7 23.2 + - - +
477B ARG 4.7 0.2 - - - -
478B GLY 3.3 3.0 + - - -
479B PHE* 1.3 69.3 - - - +
481B ASP* 1.3 58.6 + - - -
482B TRP 2.9 11.7 + - - -
483B ILE* 3.1 23.1 + - - +
484B ASP* 5.6 0.2 - - - -
572B ARG* 3.8 18.6 - - - +
----------------------------------------------------------
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