Contacts of the helix formed by residues 422 - 430 (chain A) in PDB entry 3MYV
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 HIS 422 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLY 4.1 0.4 + - - -
68A ASP* 4.6 1.2 + - - -
152A ARG* 5.6 1.6 + - - -
224A ARG* 3.7 17.6 + - - -
228A TYR* 5.0 5.5 + - - -
357A VAL 5.1 1.8 + - - -
362A GLU* 3.6 35.8 + - - +
413A ARG* 4.4 3.0 + - + -
417A LEU* 3.7 45.7 + - + +
420A GLU* 3.4 32.9 + - + +
421A GLY* 1.3 78.5 - - - +
423A ARG* 1.3 68.6 + - - +
424A PHE 3.4 2.2 - - - -
425A PHE* 3.0 10.4 + - - +
426A ASP* 2.9 42.1 + - - +
516A EDO 4.4 6.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLY 3.6 6.7 + - - +
68A ASP* 4.9 11.7 + - - +
71A GLY* 4.2 9.9 - - - -
72A ASP* 2.8 42.4 + - - +
73A ASP* 3.2 20.6 + - + +
308A LYS* 3.4 12.1 - - - +
410A LEU* 3.4 32.7 + - - +
411A ASP* 4.6 8.5 + - - -
413A ARG* 5.6 1.5 - - - +
414A SER* 3.8 17.7 - - - +
417A LEU 5.6 1.0 + - - -
418A VAL* 6.4 2.0 - - - -
422A HIS* 1.3 77.3 - - - +
424A PHE* 1.3 64.1 + - - +
426A ASP* 3.3 7.9 + - - +
427A LEU* 3.0 57.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TYR* 3.8 27.6 - + - -
67A GLY 2.9 24.8 + - - +
70A LYS* 3.4 39.7 - - + -
71A GLY* 3.8 8.9 - - - +
89A PHE* 4.0 18.2 - + - -
152A ARG 5.4 1.3 - - - -
423A ARG* 1.3 72.8 - - - +
425A PHE* 1.3 80.0 + + - +
427A LEU* 3.5 0.7 + - - -
428A LEU* 3.0 60.3 + - + +
434A ILE* 3.5 16.5 - - + +
449A VAL* 4.2 2.9 - - + -
456A CYS* 3.7 23.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A MSE 3.7 23.1 - - + -
66A TYR* 3.6 31.0 - + - -
67A GLY* 4.1 10.1 - - - -
152A ARG* 3.5 61.9 - - + -
153A CYS* 4.4 1.6 - - - -
228A TYR* 3.2 24.2 - + + +
421A GLY 3.5 26.0 - - - -
422A HIS* 3.0 4.9 + - - +
424A PHE* 1.3 85.8 - + - +
426A ASP* 1.3 59.3 + - - +
428A LEU* 4.8 3.1 - - + -
429A ARG* 2.9 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A TYR* 3.8 10.7 + - - -
410A LEU* 4.3 7.3 - - + +
413A ARG* 3.0 41.1 + - + +
422A HIS* 2.9 34.2 + - - +
423A ARG* 3.3 10.1 + - - +
425A PHE* 1.3 78.4 - - - +
427A LEU* 1.3 61.8 + - + +
429A ARG* 2.8 36.1 + - - +
430A ASN* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASP* 4.0 9.2 - - - +
410A LEU* 4.5 10.1 - - + -
423A ARG* 3.0 68.4 + - + +
424A PHE 4.0 0.4 - - - +
426A ASP* 1.3 76.3 - - - +
428A LEU* 1.3 66.3 + - - +
430A ASN 3.2 7.1 + - - -
432A LYS* 3.0 51.4 + - + +
433A THR 5.4 1.8 - - - +
434A ILE* 3.8 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A PRO* 4.3 11.4 - - + -
424A PHE* 3.0 36.5 + - + +
425A PHE* 4.3 3.6 - - - +
427A LEU* 1.3 78.4 - - - +
429A ARG* 1.3 57.0 + - - +
431A GLY* 3.0 17.2 + - - -
432A LYS 3.7 9.4 - - - +
434A ILE* 3.7 22.9 - - + -
449A VAL* 3.8 1.8 - - + +
450A ASP* 3.6 31.0 - - - +
451A TRP* 3.2 28.0 - - + +
456A CYS* 3.4 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A PRO* 4.1 12.7 - - + +
159A THR* 2.5 39.7 + - + +
227A LEU* 3.6 21.8 + - - +
228A TYR* 3.5 45.4 - - + +
369A GLU* 2.8 43.6 + - - -
373A LYS* 4.1 5.3 + - - +
413A ARG* 3.4 15.0 - - - +
425A PHE 2.9 21.4 + - - +
426A ASP* 2.8 37.2 + - - +
428A LEU* 1.3 76.6 - - - +
430A ASN* 1.3 67.5 + - - +
431A GLY 3.3 1.2 + - - -
451A TRP* 4.0 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A GLU* 3.2 19.5 + - - -
373A LYS* 2.9 31.3 + - - -
406A LEU* 3.6 15.4 - - + +
410A LEU* 3.6 17.2 - - + +
426A ASP 3.0 23.1 + - - +
427A LEU 3.2 4.5 + - - +
428A LEU 3.2 0.8 - - - -
429A ARG* 1.3 88.6 - - - +
431A GLY* 1.3 62.9 + - - +
432A LYS* 3.2 23.6 + - + +
451A TRP* 4.5 1.6 - - - -
----------------------------------------------------------
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