Contacts of the helix formed by residues 225 - 243 (chain R) in PDB entry 3TDD
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 ASP 225 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223R ILE* 3.3 5.9 + - - +
224R TYR* 1.3 74.9 - - - +
226R ASN* 1.3 67.3 + - - +
227R GLU* 3.4 23.2 - - - +
228R LYS* 2.9 39.1 + - - +
229R THR* 3.3 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 226 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20R ASN* 4.0 13.0 + - - +
52R LYS* 5.2 9.0 + - - +
61R SER* 5.4 1.7 + - - -
62R ASP* 5.3 9.6 - - - +
209R GLU* 3.1 41.4 + - + +
210R ALA 4.9 3.4 + - - -
211R GLN* 5.9 4.0 + - - +
224R TYR 4.8 3.6 + - - -
225R ASP* 1.3 70.7 - - - +
227R GLU* 1.3 64.9 + - - +
229R THR* 3.0 6.9 + - - -
230R ALA* 2.7 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 227 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225R ASP* 3.4 18.5 - - - +
226R ASN* 1.3 85.0 + - - +
228R LYS* 1.3 63.4 + - - +
230R ALA* 3.3 14.4 + - - +
231R GLU* 3.4 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 228 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190R GLU* 5.5 2.2 - - - -
222R LYS* 5.9 2.4 - - - +
224R TYR* 3.5 55.0 + - + -
225R ASP* 2.9 28.1 + - - +
227R GLU* 1.3 80.0 - - - +
229R THR* 1.3 61.6 + - - +
231R GLU* 3.7 10.4 + - - +
232R LEU* 3.5 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 229 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194R LEU* 4.2 19.7 - - + -
208R ASP 5.6 0.2 - - - +
209R GLU* 4.4 10.1 - - + -
210R ALA 4.9 9.6 - - - +
211R GLN* 5.2 0.7 - - - -
212R LEU* 3.9 16.6 + - + +
224R TYR* 3.4 26.5 + - - +
225R ASP 3.3 3.1 + - - -
226R ASN* 3.0 9.5 + - - -
228R LYS* 1.3 74.3 - - - +
230R ALA* 1.3 68.8 + - - +
231R GLU 3.1 1.8 - - - -
232R LEU* 2.9 20.1 + - - -
233R ILE* 2.9 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 230 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209R GLU* 3.7 32.2 - - + +
226R ASN 2.7 20.0 + - - +
227R GLU* 3.5 10.8 - - - +
229R THR* 1.3 71.4 - - - +
231R GLU* 1.3 63.1 + - + +
233R ILE* 3.1 10.0 + - - +
235R LYS* 3.1 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 231 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227R GLU* 3.4 20.5 - - - +
228R LYS* 3.8 9.5 - - - +
229R THR 3.1 0.4 - - - -
230R ALA* 1.3 74.0 - - + +
232R LEU* 1.3 60.2 + - + +
233R ILE 3.0 2.1 + - - -
235R LYS* 3.1 11.8 + - + +
236R GLU* 2.9 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 232 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187R LYS* 4.5 13.9 - - + +
190R GLU* 3.1 34.8 - - + +
191R LEU* 3.2 39.3 - - + +
194R LEU* 3.7 13.4 - - + +
212R LEU* 4.0 13.2 - - + -
224R TYR* 4.0 18.6 - - + -
228R LYS* 3.5 18.3 + - + +
229R THR* 2.9 9.2 + - - +
231R GLU* 1.3 79.2 - - + +
233R ILE* 1.3 60.3 - - - +
236R GLU* 3.7 17.9 + - - +
237R LEU* 3.2 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 233 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194R LEU* 4.0 8.5 - - + -
198R LYS* 6.4 2.0 - - + -
207R LEU* 3.3 41.5 - - + +
208R ASP* 3.4 4.3 - - - -
209R GLU* 3.3 36.3 - - + +
210R ALA* 5.8 0.2 - - + -
229R THR* 2.9 28.1 + - + +
230R ALA* 3.2 9.2 - - - +
231R GLU 3.0 0.2 - - - -
232R LEU* 1.3 75.1 - - - +
235R LYS* 1.3 67.7 + - - +
237R LEU* 2.9 19.7 + - + +
238R LYS* 2.9 15.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 235 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230R ALA 3.1 8.5 + - - +
231R GLU* 3.4 13.2 - - + +
233R ILE* 1.3 80.0 - - - +
236R GLU* 1.3 61.9 + - - +
237R LEU 3.0 1.2 + - - -
238R LYS* 3.1 21.8 + - - +
239R GLU* 2.9 51.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 236 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187R LYS* 3.8 26.0 + - - +
191R LEU* 3.1 30.5 - - + +
231R GLU 2.9 16.0 + - - +
232R LEU* 3.8 14.2 - - - +
233R ILE 3.2 0.2 - - - -
235R LYS* 1.3 77.6 - - - +
237R LEU* 1.3 58.7 + - - +
239R GLU* 3.8 12.8 - - - +
240R LYS* 3.2 49.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 237 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191R LEU* 4.0 37.7 - - + +
194R LEU* 4.9 5.8 - - + -
195R LYS* 4.1 24.2 - - + +
198R LYS* 4.5 13.5 - - + -
232R LEU 3.2 13.9 + - - +
233R ILE* 2.9 15.3 + - + +
236R GLU* 1.3 75.8 - - - +
238R LYS* 1.3 68.5 - - - +
240R LYS* 3.3 6.3 + - + -
241R GLU* 2.9 62.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 238 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233R ILE* 2.9 13.2 + - + +
235R LYS* 3.5 26.9 - - - +
237R LEU* 1.3 81.2 - - - +
239R GLU* 1.3 62.8 + - - +
241R GLU* 3.3 6.3 + - - +
242R ALA* 2.9 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 239 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235R LYS* 2.9 57.8 + - + +
236R GLU* 3.8 10.2 + - - +
238R LYS* 1.3 79.6 - - - +
240R LYS* 1.3 60.2 + - + +
241R GLU 3.0 4.4 + - - -
242R ALA* 3.1 6.9 + - - +
243R ALA* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 240 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191R LEU* 4.2 15.3 - - + +
236R GLU* 3.2 48.1 + - + +
237R LEU* 4.0 6.5 - - + +
239R GLU* 1.3 79.9 - - + +
241R GLU* 1.3 61.6 + - + +
243R ALA* 3.4 20.1 + - - +
244R GLU* 4.3 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 241 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195R LYS* 4.2 24.6 - - - +
198R LYS* 4.5 11.4 - - - +
237R LEU* 2.9 58.7 + - + +
238R LYS* 3.5 6.8 - - - +
240R LYS* 1.3 76.2 - - - +
242R ALA* 1.3 58.1 + - - +
243R ALA 2.9 5.5 + - - -
244R GLU* 2.8 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 242 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238R LYS* 2.9 21.7 + - + +
239R GLU* 3.6 5.4 - - - +
241R GLU* 1.3 71.6 - - - +
243R ALA* 1.3 55.2 + - - +
244R GLU* 3.0 10.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 243 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239R GLU 2.9 16.9 + - - +
240R LYS* 3.4 17.3 - - - +
241R GLU 2.9 1.2 - - - -
242R ALA* 1.3 77.0 - - - +
244R GLU* 1.3 70.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 244 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240R LYS 4.4 3.8 - - - +
241R GLU* 2.8 21.8 - - - +
242R ALA 3.0 5.8 + - - -
243R ALA* 1.3 85.7 - - - +
----------------------------------------------------------
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