Contacts of the helix formed by residues 345 - 351 (chain B) in PDB entry 2VZI
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 345 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B PHE* 4.1 2.4 - - - -
343B LYS 3.9 0.8 + - - +
344B PRO* 1.3 79.5 - - - +
346B PRO* 1.4 72.5 - - + +
347B GLU* 3.4 34.3 + - + +
348B ASP* 2.9 36.1 + - - +
349B ILE* 3.8 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B VAL* 3.9 17.7 - - + +
327B VAL* 3.7 24.1 - - + +
328B SER* 3.5 27.4 - - - +
331B PHE* 3.9 12.5 - - + -
344B PRO 4.4 0.4 - - - +
345B ARG* 1.4 85.3 - - + +
347B GLU* 1.3 79.4 + - - +
349B ILE* 3.3 6.2 + - - +
350B VAL* 3.2 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B PHE* 3.7 27.8 - - + -
321B GLU* 5.7 0.3 - - - +
324B VAL* 4.0 17.2 - - + +
345B ARG* 3.1 33.7 + - + +
346B PRO* 1.3 97.1 - - - +
348B ASP* 1.3 56.3 + - - +
350B VAL* 3.3 7.7 + - - +
351B ASN* 2.7 46.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B PRO* 3.7 6.0 - - + +
345B ARG* 2.9 40.7 + - - +
347B GLU* 1.3 77.3 - - - +
349B ILE* 1.3 58.7 - - - +
351B ASN* 3.5 9.3 + - - +
352B CYS 3.4 2.9 + - - -
353B ASP* 2.9 37.5 + - + +
356B SER* 3.5 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B PHE* 3.5 27.1 - - + +
291B ALA* 3.3 12.2 + - - +
296B LEU* 4.3 10.1 - - + -
327B VAL* 3.8 18.2 - - + -
331B PHE* 3.9 24.5 - - + -
344B PRO* 4.7 2.0 - - + -
345B ARG 3.8 4.7 + - - +
346B PRO 3.3 7.7 + - - +
347B GLU 3.2 0.4 - - - -
348B ASP* 1.3 74.1 - - - +
350B VAL* 1.3 64.5 + - - +
351B ASN 3.1 0.2 - - - -
352B CYS* 3.1 13.5 + - - -
356B SER* 3.5 31.0 - - - +
357B THR* 3.6 25.5 + - + +
360B VAL* 4.1 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ALA* 3.3 22.2 - - - +
320B PHE* 3.4 34.5 - - + -
323B LYS* 3.7 18.6 - - + +
324B VAL* 3.6 29.8 - - + +
327B VAL* 3.9 3.1 - - + -
346B PRO 3.2 13.8 + - - +
347B GLU 3.3 6.7 + - - +
349B ILE* 1.3 76.2 - - - +
351B ASN* 1.3 57.7 + - - +
352B CYS* 3.2 4.4 + - - -
1373B PG4 3.3 33.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B PHE* 3.9 18.8 - - - -
347B GLU* 2.7 33.7 + - - +
348B ASP* 3.8 10.9 + - - +
349B ILE 3.1 0.4 - - - -
350B VAL* 1.3 72.4 - - - +
352B CYS* 1.3 70.7 + - - +
353B ASP* 3.3 4.5 + - + +
----------------------------------------------------------
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