Contacts of the helix formed by residues 463 - 471 (chain D) in PDB entry 4ZZ7
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 TYR 463 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D ASN* 3.5 24.0 - - - +
157D TRP* 3.4 63.8 + + - +
161D MET* 5.8 1.3 - - + -
244D GLN* 5.3 1.2 + - - -
442D VAL* 3.8 5.5 - - - +
443D PRO* 2.5 25.3 + - - +
444D VAL 3.4 13.7 - - - -
445D ALA* 3.7 8.3 - - - -
447D HIS 3.1 31.0 - - - -
448D SER* 2.7 20.5 + - - -
449D PHE* 3.2 38.1 - - + +
462D ALA* 1.3 82.1 - - - +
464D GLY* 1.3 63.9 + - - +
467D ALA* 3.0 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 464 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D TYR* 3.5 16.7 - - - -
161D MET* 3.9 3.6 - - - +
445D ALA 3.3 18.9 + - - -
447D HIS 3.4 2.7 - - - -
463D TYR* 1.3 85.7 - - - +
465D PRO* 1.3 74.2 - - - +
467D ALA* 3.1 8.5 + - - +
468D VAL* 3.4 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 465 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLU* 4.7 0.7 - - - +
119B LYS* 3.7 19.7 - - - +
121C GLU* 3.9 11.7 - - - +
474C ARG* 4.1 16.8 - - - +
110D TYR* 3.6 17.2 - - - +
117D LEU* 6.1 0.4 - - + -
446D TYR 3.7 6.5 - - - +
447D HIS* 3.6 16.4 - - - -
448D SER* 3.3 11.2 - - - +
464D GLY* 1.3 82.2 - - - +
466D ASP* 1.3 60.9 + - - +
468D VAL* 3.2 22.5 + - + +
469D ARG* 3.4 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 466 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469C ARG* 2.8 25.1 + - - -
474C ARG* 2.6 42.3 + - - +
448D SER* 3.1 10.3 + - - +
459D ASP 4.7 0.2 - - - +
460D LEU* 3.9 8.1 - - + +
461D HIS* 3.0 44.8 + - - +
465D PRO* 1.3 78.1 - - - +
467D ALA* 1.3 58.3 + - - +
469D ARG* 3.0 11.0 + - - +
470D PHE* 2.8 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 467 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D MET* 3.8 17.3 - - + -
244D GLN* 5.5 2.5 - - - +
461D HIS 3.9 3.5 + - - -
463D TYR* 3.0 40.4 + - - +
464D GLY 3.1 2.9 + - - +
466D ASP* 1.3 78.0 - - - +
468D VAL* 1.3 57.0 + - - +
470D PHE* 4.3 6.5 - - - -
471D TYR* 2.9 50.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 468 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D LEU* 3.6 41.3 - - + +
118D LEU* 4.3 8.5 - - + -
136D PHE* 5.6 4.9 - - + -
161D MET* 3.6 28.3 - - + -
165D CYS* 4.1 15.7 - - - -
464D GLY 3.6 11.0 - - - +
465D PRO* 3.4 12.1 - - + +
466D ASP 3.1 0.4 - - - -
467D ALA* 1.3 78.6 - - - +
469D ARG* 1.3 59.0 + - + +
472D THR* 2.5 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 469 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459C ASP 4.4 9.8 + - - +
460C LEU* 3.9 10.0 - - + +
466C ASP* 2.5 45.3 + - - -
469C ARG* 6.1 6.0 - - + +
136D PHE* 3.9 41.8 - - - -
242D ARG* 3.4 6.1 + - - +
460D LEU* 3.8 22.3 - - + +
465D PRO 3.4 9.8 + - - +
466D ASP* 3.0 10.1 + - - +
468D VAL* 1.3 81.2 - - + +
470D PHE* 1.3 59.5 + - - +
472D THR* 3.0 24.1 + - - +
474D ARG* 3.7 16.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 470 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459C ASP* 3.7 18.4 - - - -
139D MET* 4.1 2.4 - - - +
219D ALA* 4.1 12.2 - - + +
220D VAL 3.8 7.2 - - - -
221D SER* 3.4 19.5 - - - -
242D ARG* 2.8 37.9 + - - +
243D CYS* 3.5 36.6 - - - -
244D GLN* 3.6 39.5 - - + +
460D LEU* 3.7 16.1 - - + +
466D ASP 2.8 16.0 + - - +
467D ALA* 4.0 4.7 - - - +
469D ARG* 1.3 78.3 - - - +
471D TYR* 1.3 76.5 + + - +
472D THR 3.3 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 471 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D PRO* 4.2 0.3 - - - +
139D MET* 3.7 10.0 + - - +
142D VAL* 3.6 33.9 - - + -
157D TRP 4.7 0.4 - - - -
158D MET* 3.3 42.0 - - + +
161D MET* 4.1 4.0 - - + -
162D ALA* 3.4 27.8 - - + -
165D CYS* 4.2 6.1 - - + -
167D ASN* 2.7 39.6 + - - +
169D PHE* 4.5 0.6 - + - -
219D ALA* 5.1 0.2 - - + -
221D SER* 2.7 29.9 + - - -
244D GLN* 3.8 4.2 + - - -
467D ALA* 2.9 43.2 + - + +
470D PHE* 1.3 88.6 - + - +
472D THR* 1.3 64.9 + - - +
----------------------------------------------------------
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