Contacts of the helix formed by residues 470 - 476 (chain C) in PDB entry 2V4M
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 SER 470 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C SER 3.3 24.0 - - - -
442C GLY* 3.5 13.1 - - - -
443C GLU* 3.2 10.8 - - - -
465C THR* 4.1 2.9 + - - -
467C THR* 2.7 28.7 + - - +
468C VAL 3.2 1.8 + - - -
469C GLY* 1.3 80.4 - - - +
471C SER* 1.3 66.7 + - - +
473C SER* 3.1 17.2 + - - -
474C ARG* 2.9 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 471 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C GLY 3.4 2.4 + - - -
443C GLU* 2.6 36.2 + - - -
448C LEU* 3.8 24.5 - - - +
452C ARG* 5.1 0.9 + - - -
470C SER* 1.3 70.2 - - - +
472C ILE* 1.3 57.2 + - - +
474C ARG* 3.2 24.1 + - - +
475C GLU* 2.9 45.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 472 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C PHE* 4.0 26.0 - - + +
439C SER* 3.6 17.7 - - - +
442C GLY* 2.9 39.8 + - - +
443C GLU 3.8 1.8 - - - +
444C THR 4.3 2.7 - - - +
447C THR* 4.1 21.3 - - + +
448C LEU* 4.1 25.4 - - + +
451C LEU* 3.8 13.2 - - + -
463C GLY* 4.4 5.6 - - - -
465C THR* 3.7 16.2 - - + -
471C SER* 1.3 74.2 - - - +
473C SER* 1.3 60.2 + - - +
476C THR* 2.8 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 473 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463C GLY* 5.5 2.7 - - - -
465C THR* 3.9 18.7 + - - +
467C THR 3.9 6.6 + - - -
468C VAL* 4.5 4.3 - - - +
469C GLY 4.0 9.4 + - - -
470C SER* 3.1 26.5 + - - -
472C ILE* 1.3 79.6 - - - +
474C ARG* 1.3 62.3 + - - +
476C THR* 3.6 12.1 + - - +
478C CYS 5.7 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 474 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C GLU* 4.8 0.6 + - - -
469C GLY* 3.3 29.5 + - - +
470C SER 2.9 10.2 + - - +
471C SER* 3.2 32.0 + - - +
473C SER* 1.3 79.3 - - - +
475C GLU* 1.3 81.2 + - + +
476C THR 3.5 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 475 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448C LEU* 4.0 5.1 - - - +
451C LEU* 3.8 14.3 - - + +
452C ARG* 2.8 53.5 + - - +
455C LYS* 2.8 43.4 + - - +
461C THR* 4.3 0.3 + - - -
471C SER* 2.9 31.7 + - - +
472C ILE 3.6 0.2 + - - -
473C SER 3.5 0.2 - - - -
474C ARG* 1.3 89.3 + - + +
476C THR* 1.3 64.4 + - - +
477C ASP* 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 476 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C PHE* 4.1 5.2 - - + -
451C LEU* 3.3 28.3 - - + -
461C THR* 3.4 7.0 - - - -
462C VAL 3.8 9.9 - - - +
463C GLY* 3.6 20.6 + - - +
472C ILE* 2.8 22.0 + - + +
473C SER* 3.6 10.4 + - - +
474C ARG 3.8 8.1 - - - +
475C GLU* 1.3 78.8 - - - +
477C ASP* 1.3 65.7 + - - +
478C CYS* 3.1 20.3 + - - -
479C GLY* 4.9 0.3 - - - -
----------------------------------------------------------
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