Contacts of the helix formed by residues 241 - 252 (chain C) in PDB entry 3RCY
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 ASN 241 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ARG* 4.9 17.0 + - - +
237C VAL* 4.6 3.8 - - - +
238C PRO 4.1 4.1 + - - +
239C PRO 3.5 3.2 + - - -
240C ASP* 1.3 89.3 - - - +
242C VAL* 1.3 63.6 + - - +
243C GLY* 3.3 6.4 + - - -
244C ALA* 2.9 36.3 + - + +
245C MET* 3.2 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 242 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C PRO 5.9 2.2 - - - +
240C ASP 4.3 0.2 - - - -
241C ASN* 1.3 71.8 + - - +
243C GLY* 1.3 60.8 + - - +
245C MET* 3.2 3.3 + - - -
246C ALA* 2.9 24.9 + - - +
262C LEU* 6.2 1.3 - - + -
267C GLU 5.2 1.8 - - - +
270C PRO* 3.7 36.8 - - + +
271C VAL* 4.1 19.1 - - + -
274C GLU* 3.8 20.2 - - + -
276C ALA* 3.6 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 243 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ARG* 5.7 5.5 - - - +
241C ASN* 3.3 5.0 + - - -
242C VAL* 1.3 79.8 - - - +
244C ALA* 1.3 55.6 + - - +
246C ALA* 3.3 8.0 + - - +
247C GLN* 3.0 34.7 + - - +
250C ARG* 4.7 1.4 + - - -
274C GLU* 5.7 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C THR* 3.3 20.9 - - - +
237C VAL* 4.3 10.3 - - + -
241C ASN* 2.9 36.4 + - + +
243C GLY* 1.3 75.0 - - - +
245C MET* 1.3 63.0 + - - +
247C GLN* 3.2 25.1 + - - +
248C VAL* 3.2 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 245 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C GLU* 4.3 1.6 - - + -
236C PRO* 4.0 14.4 - - + -
237C VAL* 3.7 39.4 - - + +
238C PRO 4.7 4.5 - - - +
239C PRO* 5.3 4.9 - - + -
241C ASN 3.2 7.7 + - - +
242C VAL* 3.2 9.7 + - - +
244C ALA* 1.3 78.4 - - - +
246C ALA* 1.3 62.6 + - - +
248C VAL* 3.0 6.1 + - - +
249C ALA* 3.0 21.0 + - - +
256C VAL* 3.8 13.2 - - + -
258C THR* 3.5 44.2 - - + +
271C VAL* 5.6 0.7 - - - -
276C ALA* 3.3 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 246 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C VAL 2.9 13.3 + - - +
243C GLY* 3.3 11.0 + - - +
245C MET* 1.3 77.0 - - - +
247C GLN* 1.3 61.0 + - - +
249C ALA* 3.3 1.6 + - - +
250C ARG* 3.0 42.7 + - - +
274C GLU* 3.4 29.4 - - + +
275C GLY 4.1 4.0 - - - +
276C ALA* 3.7 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 247 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C THR* 3.7 21.3 + - + +
219C ILE* 4.2 2.7 - - + +
243C GLY 3.0 14.6 + - - +
244C ALA* 3.2 24.8 + - - +
246C ALA* 1.3 75.5 - - - +
248C VAL* 1.3 61.1 + - - +
250C ARG* 3.5 24.0 + - - +
251C ALA* 3.2 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 248 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C THR* 3.7 18.4 - - + +
218C ALA* 3.8 25.6 - - + -
219C ILE* 4.1 7.4 - - + -
233C TYR* 4.0 13.2 - - + -
236C PRO* 3.9 26.7 - - + -
237C VAL* 3.8 12.3 - - + -
244C ALA 3.2 13.4 + - - +
245C MET* 3.0 8.1 + - - +
247C GLN* 1.3 75.9 - - - +
249C ALA* 1.3 64.9 + - - +
251C ALA* 3.0 2.3 + - - -
252C VAL* 2.9 35.5 + - + +
256C VAL* 4.6 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 249 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C MET 3.0 12.0 + - - +
246C ALA 3.3 4.9 + - - +
248C VAL* 1.3 75.9 - - - +
250C ARG* 1.3 57.8 + - + +
252C VAL* 3.2 21.4 - - - +
254C ILE 5.0 1.1 - - - +
256C VAL* 3.8 25.5 - - + +
275C GLY 3.6 24.2 - - - +
276C ALA 3.9 5.2 - - - +
277C ALA* 5.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 250 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C GLY 4.7 1.0 + - - -
246C ALA* 3.0 38.8 + - + +
247C GLN* 3.6 33.8 - - - +
249C ALA* 1.3 77.2 - - + +
251C ALA* 1.3 60.4 + - + +
252C VAL 3.9 1.6 + - - +
274C GLU 4.2 7.7 + - - -
275C GLY 5.8 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 251 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C ILE* 3.6 36.9 - - + +
223C GLN* 5.7 2.6 - - - +
226C GLU* 4.4 2.4 - - - +
247C GLN 3.2 15.7 + - - +
248C VAL 3.0 1.8 + - - +
250C ARG* 1.3 78.3 - - + +
252C VAL* 1.3 62.6 + - - +
253C ARG* 5.5 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 252 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C ALA 4.3 0.2 - - - +
219C ILE* 3.9 29.8 - - + +
222C GLY* 4.1 19.5 - - - -
223C GLN* 4.4 2.2 - - + +
226C GLU* 3.4 8.1 - - - +
233C TYR* 4.0 19.1 - - + -
248C VAL* 2.9 28.2 + - + +
249C ALA* 3.2 19.1 - - - +
250C ARG 4.7 1.3 - - - -
251C ALA* 1.3 84.5 - - - +
253C ARG* 1.3 61.2 + - - +
254C ILE* 3.2 26.3 + - + +
256C VAL* 4.6 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