Contacts of the helix formed by residues 425 - 429 (chain B) in PDB entry 2VRM
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 GLY 425 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B SER* 2.8 19.7 + - - -
263B ALA* 4.1 12.2 - - - +
264B ILE 4.9 4.5 - - - -
424B ALA* 1.3 71.3 - - - +
426B THR* 1.3 65.8 + - - -
427B GLU* 3.0 8.2 + - - -
428B THR* 2.8 22.5 + - - -
442B ALA* 3.2 7.8 - - - +
600B FAD 3.1 12.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 426 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ARG* 3.8 10.1 - - - +
425B GLY* 1.3 70.8 - - - -
427B GLU* 1.3 73.2 + - - +
429B ALA* 3.0 11.1 + - - +
433B SER* 2.9 18.7 + - - -
434B GLY* 2.8 27.7 + - - +
435B TYR 2.7 26.4 + - - -
438B GLY* 3.5 3.8 - - - -
439B ALA* 3.4 18.4 + - - +
600B FAD 2.7 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ARG* 3.1 40.5 + - - -
187B TRP* 4.6 5.9 - - - -
265B PRO* 4.1 2.9 - - - +
266B PRO* 3.6 32.8 - - + +
291B LEU* 3.9 3.3 - - - +
399B THR* 3.4 15.4 + - - +
400B THR* 2.8 40.1 + - + +
402B PHE* 6.1 2.4 - - + -
414B LEU* 3.5 18.9 - - + +
415B ARG* 5.5 0.3 + - - -
425B GLY* 3.0 3.6 + - - -
426B THR* 1.3 77.7 + - - +
428B THR* 1.3 59.8 + - + +
429B ALA 3.3 3.1 + - - +
433B SER* 3.4 15.0 + - - -
600B FAD 4.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B PRO* 5.5 2.5 - - + -
414B LEU* 3.9 34.5 - - + +
415B ARG* 3.1 41.5 + - + +
423B PHE* 4.2 5.2 - - + +
424B ALA 3.3 18.3 + - - +
425B GLY 2.8 16.5 + - - -
427B GLU* 1.3 79.6 - - + +
429B ALA* 1.3 62.5 + - - +
430B THR* 4.5 0.9 - - - +
441B GLU* 4.4 1.6 - - - +
442B ALA* 3.2 13.4 - - - +
445B ARG* 3.2 17.4 + - - -
463B TRP* 4.9 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B SER 5.1 0.2 - - - +
187B TRP* 3.8 10.7 - - - -
415B ARG* 4.3 2.8 + - - -
425B GLY 4.1 0.2 + - - -
426B THR 3.0 13.0 + - - +
427B GLU 3.3 1.1 - - - +
428B THR* 1.3 83.5 + - - +
430B THR* 1.3 62.3 + - - +
431B HIS 3.6 1.6 - - - +
433B SER* 3.5 20.9 - - - +
438B GLY* 3.3 39.7 - - - +
441B GLU* 3.3 16.6 - - - +
442B ALA* 4.1 2.0 - - + +
----------------------------------------------------------
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