Contacts of the helix formed by residues 237 - 245 (chain A) in PDB entry 2VLA
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 ALA 237 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A TYR* 3.0 32.3 + - + +
235A ARG 3.4 2.0 + - - -
236A GLU* 1.3 76.3 - - - +
238A GLU* 1.3 62.5 + - + +
240A ILE* 4.2 11.2 - - - -
241A ASN* 3.0 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ARG 5.4 0.2 + - - -
236A GLU 3.1 1.2 + - - -
237A ALA* 1.3 79.7 - - + +
239A ASN* 1.3 64.7 + - - +
241A ASN* 3.5 3.6 + - - +
242A TYR* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LYS* 3.1 25.4 - - + +
222A LEU* 3.9 14.1 - - + -
236A GLU* 2.8 31.3 + - - +
238A GLU* 1.3 78.4 - - - +
240A ILE* 1.3 67.7 + - - +
242A TYR* 3.4 9.9 + - - +
243A ILE* 3.1 33.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LEU* 4.1 15.8 - - + +
146A LEU* 4.2 26.5 - - + -
222A LEU* 3.7 33.8 - - + +
232A LEU* 4.0 29.2 - - + -
233A ASN 3.2 31.4 - - - +
234A TYR* 4.4 5.2 - - + -
236A GLU* 2.9 18.8 + - + +
237A ALA* 3.7 9.2 - - - +
239A ASN* 1.3 75.0 - - - +
241A ASN* 1.3 61.1 + - - +
243A ILE 3.9 0.2 - - - -
244A ALA* 2.9 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU* 3.9 23.1 - - - +
234A TYR* 6.2 1.6 - - - -
237A ALA* 3.0 31.5 + - - +
238A GLU* 4.0 3.6 - - - +
240A ILE* 1.3 78.7 - - - +
242A TYR* 1.3 66.2 + - - +
244A ALA* 3.9 3.0 - - - +
245A GLN* 3.2 44.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A PHE* 3.6 29.0 - + - -
238A GLU 3.1 17.9 + - - +
239A ASN* 3.4 10.3 + - - +
241A ASN* 1.3 79.1 - - - +
243A ILE* 1.3 72.9 + - + +
245A GLN* 3.4 16.7 + - - +
246A PHE* 3.1 45.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LYS* 4.5 25.1 - - + +
110A CYS* 5.3 2.0 - - + -
111A PHE* 4.2 22.0 - - + +
138A PHE* 4.6 3.6 - - + -
139A PRO* 3.1 39.6 - - + +
142A LEU* 3.7 18.2 - - + -
222A LEU* 3.8 26.5 - - + -
239A ASN* 3.1 20.1 + - + +
242A TYR* 1.3 86.4 - - + +
244A ALA* 1.3 67.0 + - - +
245A GLN 3.1 1.0 + - - -
246A PHE* 3.1 16.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A PRO* 3.7 11.4 - - - -
142A LEU* 3.9 13.2 - - + +
143A GLN* 3.7 18.8 - - - +
146A LEU* 3.7 18.4 - - + -
240A ILE 2.9 20.3 + - - +
241A ASN* 3.9 4.3 - - - +
243A ILE* 1.3 77.2 - - - +
245A GLN* 1.3 57.5 + - + +
246A PHE 3.1 0.2 - - - -
247A TRP* 3.0 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A GLN* 5.3 1.1 - - - +
241A ASN* 3.2 34.5 + - - +
242A TYR* 3.6 17.2 - - - +
243A ILE 3.1 1.4 - - - -
244A ALA* 1.3 76.2 - - + +
246A PHE* 1.3 62.5 + - + +
247A TRP* 3.3 10.8 + - - -
248A GLY 4.7 1.4 + - - -
249A ASN* 4.3 5.7 - - - +
----------------------------------------------------------
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