Contacts of the helix formed by residues 273 - 280 (chain A) in PDB entry 2VZE
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 LEU 273 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 4.0 10.8 - - + -
119A TRP* 4.2 5.4 - - + -
120A TRP* 3.9 26.0 - - + +
123A ILE* 4.0 16.8 - - + -
124A LEU* 4.5 7.9 - - + -
127A ILE* 5.7 1.1 - - + -
268A ASN 3.2 8.7 + - - +
269A ILE* 3.4 31.2 - - + +
272A SER* 1.3 80.3 - - - +
274A MET* 1.3 84.1 + - + +
275A GLU 3.6 0.9 - - - -
276A PRO* 3.7 2.1 - - - +
277A TRP* 3.3 64.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 3.6 37.4 - - + -
127A ILE* 4.6 12.1 - - + -
133A PHE* 5.8 0.4 - - + -
235A TYR 5.4 0.4 - - - +
238A LEU* 3.6 38.4 - - + +
239A GLY* 3.6 24.9 - - - +
242A ALA* 3.5 16.8 - - + -
269A ILE* 3.0 36.1 + - + +
270A LEU* 3.7 8.0 + - - +
273A LEU* 1.3 81.5 - - + +
275A GLU* 1.3 68.3 + - - +
278A ALA* 2.8 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ALA* 4.7 4.8 - - - +
245A ASP* 4.2 0.5 - - - +
246A ALA* 3.3 10.6 + - - -
247A GLY* 3.2 31.6 + - - -
248A TRP* 3.8 11.7 - - - +
249A THR* 2.7 47.5 + - + +
251A LEU* 4.2 5.3 - - + +
257A MET* 4.2 9.9 - - + -
270A LEU 3.0 17.2 + - - +
271A CYS* 3.9 10.1 - - + +
274A MET* 1.3 78.3 - - - +
276A PRO* 1.3 76.0 - - + +
278A ALA* 3.2 13.5 + - - +
279A LEU* 3.5 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LEU* 3.6 24.9 - - + -
257A MET* 4.8 4.7 - - + -
271A CYS 3.0 24.7 - - - +
272A SER 3.6 19.1 - - - +
273A LEU 3.7 5.4 - - - +
275A GLU* 1.3 88.9 - - + +
277A TRP* 1.3 60.3 + - + +
279A LEU* 3.2 3.3 + - - -
280A GLY 3.1 6.4 + - - -
281A ALA* 2.8 38.1 + - + +
282A CYS 4.1 6.1 - - - +
283A THR* 3.6 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 4.2 12.6 - + + -
50A VAL* 3.4 7.2 - - - +
51A LEU* 4.1 17.0 - - + -
54A TRP* 2.9 25.3 + - - -
68A ALA* 2.9 29.0 + - - +
69A LEU* 4.1 8.7 - - + -
83A PHE* 3.8 13.9 - + + -
86A LEU* 3.5 31.0 - - + -
120A TRP* 3.9 22.0 - + + -
124A LEU* 3.5 22.0 - - + -
273A LEU* 3.3 48.4 + - + +
275A GLU 3.2 0.8 - - - -
276A PRO* 1.3 75.6 - - + +
278A ALA* 1.3 66.2 + - - +
279A LEU 3.1 1.1 - - - -
280A GLY 3.5 2.2 + - - +
281A ALA 3.4 15.9 - - - -
283A THR* 4.1 18.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 4.0 4.4 - - + -
50A VAL* 3.7 15.4 - - + +
54A TRP* 3.5 15.2 + - - -
242A ALA 4.3 2.2 - - - +
243A LYS* 4.2 21.0 - - + +
246A ALA* 3.5 24.6 - - + +
274A MET 2.8 18.5 + - - +
275A GLU 3.5 5.6 - - - +
277A TRP* 1.3 79.0 - - - +
279A LEU* 1.3 57.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A TRP* 3.5 13.7 - - - -
246A ALA* 3.8 27.6 - - + +
247A GLY* 3.7 16.4 - - - +
251A LEU* 3.3 48.9 - - + +
252A GLN* 4.4 0.9 - - - +
253A ALA* 3.2 30.8 - - + +
275A GLU* 3.9 10.8 - - - +
276A PRO 3.2 7.6 + - - +
277A TRP 3.1 0.4 - - - -
278A ALA* 1.3 75.9 - - - +
280A GLY* 1.3 57.8 - - - +
281A ALA* 4.3 6.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A TRP* 3.4 29.2 - - - +
63A ARG* 2.7 30.6 + - - -
66A SER* 4.7 1.0 - - - -
67A PRO 4.7 0.9 - - - +
83A PHE* 3.3 24.8 - - - -
253A ALA 2.9 4.4 - - - +
276A PRO 3.1 2.4 + - - -
277A TRP 3.5 0.8 + - - -
278A ALA 3.5 0.2 - - - -
279A LEU* 1.3 78.8 - - - +
281A ALA* 1.3 57.6 + - - +
----------------------------------------------------------
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