Contacts of the helix formed by residues 231 - 243 (chain C) in PDB entry 1VLP
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 231 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C TYR* 3.6 34.0 - - + -
19C MSE 4.6 6.1 - - - +
229C THR 3.8 1.0 + - - -
230C VAL* 1.3 82.2 - - - +
232C HIS* 1.3 65.9 + - - +
233C GLU* 4.1 17.0 - - + +
234C TRP* 3.2 18.2 + - - +
235C VAL* 4.3 1.0 + - - +
269C LEU* 3.5 8.1 - - - +
294C ARG* 4.4 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 232 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C ALA* 1.3 73.0 - - - +
233C GLU* 1.3 66.0 + - - +
234C TRP 2.8 1.9 + - - -
235C VAL* 3.1 6.4 + - - +
236C MSE 2.9 37.3 + - - +
269C LEU* 3.3 21.0 - - + +
271C ASP* 2.9 36.1 + - - -
272C THR* 3.0 25.2 + - + -
294C ARG* 5.2 3.4 - - - -
296C ASP* 2.8 26.7 + - - -
379C LYS* 5.8 4.9 - - - -
390C LYS* 3.7 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 233 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C TYR* 4.8 1.4 - - - -
16C LYS* 2.6 31.7 + - - -
19C MSE 3.5 12.3 - - + -
34C TYR* 2.3 36.0 + - + -
125C TRP* 3.2 20.0 + - - -
129C ILE* 2.9 15.9 - - - +
132C GLU* 3.9 4.9 - - - +
231C ALA* 3.2 12.0 - - + +
232C HIS* 1.3 78.3 - - - +
234C TRP* 1.3 55.7 + - - +
236C MSE 3.8 13.8 - - - -
237C GLY 2.9 22.9 + - - -
380C LEU* 3.7 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 234 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C MSE 3.7 23.8 - - + +
22C ALA* 3.7 39.0 - - + -
23C VAL* 4.0 6.5 - - + -
26C ASN* 3.9 4.9 - - - -
27C PHE* 3.5 35.4 - + - -
125C TRP* 4.2 7.1 - + - -
230C VAL* 3.5 34.8 - - + -
231C ALA 3.2 2.9 + - - +
232C HIS 2.8 2.2 + - - -
233C GLU* 1.3 78.0 - - - +
235C VAL* 1.3 65.8 + - + +
237C GLY* 3.8 0.5 - - - -
238C VAL* 3.1 32.7 + - + +
252C ALA* 3.0 35.1 + - + +
255C CYS* 3.7 24.0 - - + -
256C TRP* 3.7 18.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 235 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C ALA 4.3 1.0 + - - +
232C HIS* 3.1 6.1 + - - +
234C TRP* 1.3 81.5 - - + +
236C MSE 1.3 66.4 + - - +
238C VAL* 3.9 0.8 - - - -
239C ALA* 3.0 22.9 + - - +
248C ALA* 3.6 33.9 - - + +
249C ASN* 3.6 21.3 - - - +
252C ALA* 3.6 16.2 - - + -
269C LEU 5.9 0.7 - - - +
272C THR* 3.2 42.2 - - + +
273C PHE* 3.9 7.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 236 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C HIS* 2.9 38.7 + - - +
233C GLU* 3.9 10.1 - - - +
235C VAL* 1.3 78.6 - - - +
237C GLY* 1.3 52.4 + - - +
239C ALA* 3.4 2.4 + - - +
240C SER* 2.6 37.5 + - - -
245C TYR* 5.1 0.7 + - - -
272C THR* 3.6 14.6 - - + -
273C PHE* 4.2 8.0 - - - -
379C LYS* 6.0 2.2 - - + -
380C LEU* 3.9 32.5 - - + +
388C ALA* 4.0 9.7 - - + +
389C ILE* 3.3 44.3 + - - +
390C LYS* 4.1 12.1 - - + +
399C MSE 5.4 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 237 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C TRP* 3.6 22.7 - - - -
233C GLU 2.9 12.6 + - - -
236C MSE 1.3 73.4 - - - +
238C VAL* 1.3 66.2 + - - +
240C SER* 3.4 6.4 + - - -
241C ILE* 3.0 36.4 + - - +
380C LEU* 4.1 1.2 - - - +
383C VAL* 4.2 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 238 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C PHE* 3.8 32.1 - - + -
125C TRP* 4.5 0.6 - - + -
234C TRP* 3.1 37.2 + - + +
235C VAL* 3.9 6.3 - - - +
237C GLY* 1.3 76.3 - - - +
239C ALA* 1.3 61.6 + - - +
241C ILE* 3.8 15.8 + - - +
242C SER 4.7 1.4 + - - -
244C ASP* 4.9 4.2 + - - +
248C ALA* 3.9 23.1 - - - +
251C ASN* 4.0 22.7 - - + +
252C ALA* 4.1 9.9 - - + +
255C CYS* 5.5 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 239 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C VAL 3.0 18.5 + - - +
236C MSE 3.7 1.8 - - - +
238C VAL* 1.3 80.0 - - - +
240C SER* 1.3 57.6 + - - +
241C ILE 3.5 0.2 + - - -
243C GLU* 2.9 30.0 + - - -
244C ASP 3.2 8.9 + - - -
245C TYR* 3.6 31.6 - - + -
248C ALA* 3.6 22.6 - - + +
273C PHE* 3.7 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 240 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C MSE 2.6 23.8 + - - -
237C GLY 3.4 1.9 + - - -
239C ALA* 1.3 75.8 - - - +
241C ILE* 1.3 66.1 + - - +
242C SER 3.3 0.2 + - - -
243C GLU* 3.6 4.1 + - - +
245C TYR* 4.1 7.9 - - - -
383C VAL* 3.2 35.8 - - - +
386C ASN* 2.8 27.6 + - - +
387C HIS 3.6 24.9 - - - -
388C ALA* 4.1 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 241 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C PHE* 3.5 43.1 - - + -
30C VAL* 3.8 24.0 - - + -
125C TRP* 4.3 4.0 - - + -
237C GLY 3.0 29.3 + - - +
238C VAL* 4.1 6.7 - - - +
239C ALA 3.3 1.4 - - - -
240C SER* 1.3 79.0 - - - +
242C SER* 1.3 65.8 + - - +
383C VAL* 3.7 14.6 - - + -
384C ASN* 2.9 39.1 + - + +
386C ASN* 3.2 6.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 242 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C VAL 4.7 1.8 + - - -
239C ALA 3.9 2.0 + - - -
241C ILE* 1.3 86.0 + - - +
243C GLU* 1.3 73.3 + - - +
244C ASP* 3.3 12.7 + - - +
386C ASN* 4.6 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 243 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C ALA 2.9 13.6 + - - -
240C SER* 3.6 2.8 + - - +
242C SER* 1.3 80.5 - - - +
244C ASP* 1.3 59.4 + - - +
245C TYR* 3.1 27.8 + - + +
386C ASN* 3.9 37.6 - - + +
387C HIS* 4.7 8.0 + - - +
404C THR* 4.6 7.4 + - - +
407C ARG* 3.4 29.0 + - - +
411C GLU* 5.5 0.9 - - - +
----------------------------------------------------------
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