Contacts of the helix formed by residues 221 - 229 (chain A) in PDB entry 1VPE
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 MET 221 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LEU* 4.1 31.0 - - - -
194A GLY* 4.2 12.8 - - - +
195A GLY 3.4 3.7 + - - +
198A VAL* 3.9 33.8 - - + +
201A LYS* 3.6 32.1 - - + -
202A ILE* 3.6 22.9 - - + +
205A ILE* 4.8 1.3 - - - -
217A ILE* 3.7 13.0 - - + -
218A GLY 3.5 9.4 - - - +
219A GLY 3.2 0.6 - - - -
220A ALA* 1.3 79.8 - - - +
222A MET* 1.3 62.5 + - - +
223A PHE 3.0 1.2 + - - -
224A THR* 3.2 13.0 + - - +
225A PHE* 3.6 24.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ILE* 3.6 10.3 - - - +
218A GLY* 3.1 14.2 + - - +
219A GLY 3.3 20.9 - - - +
220A ALA 3.2 0.6 - - - -
221A MET* 1.3 75.9 - - - +
223A PHE* 1.3 85.7 + - + +
225A PHE* 3.4 4.2 + - - +
226A LEU* 2.8 47.9 + - + +
262A LEU* 4.5 1.6 - - - -
263A PRO* 3.6 54.1 - - + -
265A ASP 4.5 1.8 - - - +
266A ALA* 4.0 20.6 - - + -
283A ILE* 6.3 1.1 - - + -
295A ASP 5.4 2.0 - - - +
296A ILE* 4.3 16.6 - - + -
320A MET 5.3 0.9 - - - +
400A ANP 5.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A GLY 4.0 0.4 - - - -
220A ALA* 3.5 17.9 - - + +
221A MET 3.0 1.6 + - - -
222A MET* 1.3 109.6 - - + +
224A THR* 1.3 59.9 + - - +
225A PHE 3.2 1.3 - - - -
226A LEU* 3.8 9.6 - - + -
227A LYS* 3.0 30.7 + - - +
233A VAL* 3.6 15.2 - - + +
236A SER* 3.6 26.0 - - - -
237A ARG 3.6 19.3 - - - +
238A VAL* 3.8 12.8 - - + +
266A ALA* 5.0 0.4 - - + -
287A ILE* 3.8 17.5 - - + -
293A GLY* 3.4 39.3 - - - -
295A ASP 5.9 0.2 - - - -
400A ANP 3.7 15.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A VAL* 4.0 14.8 - - + +
202A ILE* 4.7 5.2 - - + -
220A ALA 4.2 1.8 + - - -
221A MET 3.2 9.8 + - - -
223A PHE* 1.3 76.8 - - - +
225A PHE* 1.3 63.3 + - - +
228A ALA* 3.2 22.7 + - - +
238A VAL* 3.7 9.0 - - - +
239A GLU* 2.9 45.5 + - + +
242A LYS* 4.0 26.2 - - + +
243A ILE* 4.1 9.2 - - + +
246A ALA* 3.9 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ILE* 4.2 24.9 - - + -
205A ILE* 3.6 28.0 - - + -
217A ILE* 3.6 27.8 - - + -
221A MET* 3.7 23.8 - - + -
222A MET 3.4 3.1 + - - +
224A THR* 1.3 80.5 - - - +
226A LEU* 1.3 64.6 + - - +
228A ALA* 3.2 15.1 + - - +
229A LEU* 3.2 17.0 + - - +
246A ALA* 3.9 23.6 - - + -
249A LEU* 4.3 11.4 - - + -
250A VAL* 3.6 26.0 - - + +
260A ILE* 4.8 6.3 - - + -
262A LEU* 3.6 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A MET* 2.8 54.7 + - + +
223A PHE* 4.0 13.0 - - + -
225A PHE* 1.3 70.8 - - - +
227A LYS* 1.3 64.4 + - - +
229A LEU* 3.0 16.1 + - + +
231A LYS* 3.3 31.1 - - + +
233A VAL* 4.3 6.7 - - + -
262A LEU* 3.7 33.4 - - + -
263A PRO* 4.3 14.4 - - + +
283A ILE* 3.9 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A PHE 3.0 19.7 + - - +
224A THR 4.2 2.7 - - - +
226A LEU* 1.3 77.3 - - - +
228A ALA* 1.3 57.2 + - - +
230A GLY* 2.8 23.3 + - - +
231A LYS 3.9 13.0 - - - +
233A VAL* 4.0 20.3 - - + +
238A VAL* 3.7 27.9 - - + +
240A GLU* 5.6 6.3 + - - +
243A ILE* 3.9 26.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A THR 3.2 14.4 + - - +
225A PHE* 3.2 13.4 + - - +
227A LYS* 1.3 79.2 - - - +
229A LEU* 1.3 58.6 + - + +
230A GLY 3.2 3.1 + - - -
243A ILE* 3.8 30.9 - - + +
246A ALA* 4.1 9.6 - - + -
247A LYS* 4.1 31.3 - - + +
250A VAL* 5.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A PHE 3.2 10.2 + - - +
226A LEU* 3.0 15.5 + - + +
228A ALA* 1.3 78.8 - - + +
230A GLY* 1.3 56.0 + - - +
231A LYS* 3.4 26.4 + - + +
247A LYS* 6.5 0.4 - - + -
250A VAL* 4.7 24.0 - - + -
262A LEU* 3.8 27.1 - - + -
----------------------------------------------------------
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