Contacts of the helix formed by residues 193 - 212 (chain R) in PDB entry 6CNB
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 193 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192R ALA* 1.3 77.0 - - - +
194R LYS* 1.3 64.9 + - + +
195R LYS 3.1 1.4 + - - -
196R ILE* 3.2 38.8 + - + +
197R LYS* 4.3 0.5 + - - +
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Residues in contact with LYS 194 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191R LEU* 6.4 0.2 - - + -
192R ALA* 3.0 15.7 - - + +
193R ASP* 1.3 77.5 - - + +
195R LYS* 1.3 63.3 + - + +
197R LYS* 2.9 27.0 + - + +
198R VAL* 3.0 10.8 + - - +
235R ASN* 3.5 27.3 + - - +
237R LEU* 5.6 1.8 - - + -
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Residues in contact with LYS 195 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186R ALA* 3.3 33.0 - - + +
187R GLU* 5.1 1.8 - - - +
189R LEU* 4.0 9.4 - - + -
190R ASP 2.3 28.6 + - - +
191R LEU* 3.5 37.0 - - + -
192R ALA 2.5 33.5 + - - +
193R ASP 3.1 1.2 - - - -
194R LYS* 1.3 77.2 - - + +
196R ILE* 1.3 53.7 + - + +
198R VAL* 2.9 17.6 + - + +
199R VAL* 2.3 47.4 + - + +
232R CYS* 5.8 0.4 - - - -
237R LEU* 5.3 1.8 - - + -
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Residues in contact with ILE 196 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47L ARG* 6.3 0.7 - - - +
49L LYS 4.8 5.8 - - - +
50L ASP 3.7 20.4 - - - +
51L CYS* 4.5 1.6 - - - -
52L GLY* 3.6 33.4 - - - +
193R ASP* 3.5 30.5 - - + +
194R LYS 3.0 0.4 + - - -
195R LYS* 1.3 75.5 - - + +
197R LYS* 1.3 53.3 + - - +
199R VAL* 2.9 14.5 + - + +
200R LYS* 2.7 34.5 + - + +
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Residues in contact with LYS 197 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193R ASP 4.3 0.6 + - - -
194R LYS* 2.9 18.2 + - + +
196R ILE* 1.3 77.3 - - - +
198R VAL* 1.3 51.6 + - + +
200R LYS* 2.9 13.6 + - + +
201R ASP* 2.4 56.7 + - - +
235R ASN* 5.1 11.8 + - - +
276R ARG* 5.7 8.1 - - - +
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Residues in contact with VAL 198 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194R LYS 3.0 8.8 + - - +
195R LYS* 2.9 25.5 + - + +
197R LYS* 1.3 70.5 - - - +
199R VAL* 1.3 50.6 + - + +
201R ASP* 2.9 11.0 + - - +
202R ALA* 2.3 43.3 + - + +
228R ILE* 4.9 2.7 - - + +
231R ALA* 3.6 21.3 - - + -
232R CYS* 4.1 19.1 - - - +
235R ASN* 3.3 44.6 - - + +
237R LEU* 4.8 4.3 - - + -
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Residues in contact with VAL 199 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182R ILE* 3.7 16.4 - - + -
183R GLN* 3.3 24.2 - - - +
186R ALA* 4.0 26.9 - - + -
195R LYS* 2.3 35.9 + - + +
196R ILE* 2.9 13.8 + - + +
198R VAL* 1.3 70.3 - - + +
200R LYS* 1.3 65.2 + - - +
202R ALA* 2.9 12.5 + - - +
203R VAL* 3.0 22.5 + - + +
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Residues in contact with LYS 200 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49L LYS* 4.0 30.0 - - + +
196R ILE* 2.7 15.9 + - + +
197R LYS* 3.3 12.8 - - + +
199R VAL* 1.3 74.4 - - - +
201R ASP* 1.3 64.2 + - - +
203R VAL* 4.6 3.1 - - - +
204R LYS* 3.9 13.0 + - - +
276R ARG* 3.9 33.4 + - - +
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Residues in contact with ASP 201 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197R LYS* 2.4 54.0 + - - +
198R VAL* 2.9 24.3 + - - +
200R LYS* 1.3 72.0 - - - +
202R ALA* 1.3 60.6 + - - +
203R VAL 3.3 0.3 + - - -
204R LYS* 3.4 5.0 + - - +
205R LEU* 3.3 16.2 + - - +
231R ALA* 4.2 11.3 - - + +
234R MET* 5.8 6.3 - - + +
235R ASN* 5.2 5.2 - - - +
276R ARG* 3.5 39.2 + - + +
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Residues in contact with ALA 202 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182R ILE* 5.6 6.7 - - + -
198R VAL* 2.3 32.0 + - + +
199R VAL* 2.9 5.4 + - - +
201R ASP* 1.3 67.9 - - - +
203R VAL* 1.3 53.9 + - + +
205R LEU* 2.8 13.6 - - - +
206R ALA* 2.8 34.0 + - - +
227R CYS* 4.0 18.2 - - + +
228R ILE* 4.8 8.5 - - + +
231R ALA* 3.7 20.9 - - + -
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Residues in contact with VAL 203 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179R SER* 3.9 25.8 - - - +
182R ILE* 3.7 35.9 - - + -
199R VAL* 3.0 20.0 + - + +
200R LYS* 4.6 3.6 - - - +
202R ALA* 1.3 76.2 - - + +
204R LYS* 1.3 52.3 + - - +
206R ALA* 2.9 9.2 + - + +
207R GLN* 2.6 56.7 + - + +
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Residues in contact with LYS 204 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200R LYS 3.9 9.8 + - - +
201R ASP 3.4 8.6 + - - +
202R ALA 3.4 0.2 - - - -
203R VAL* 1.3 78.0 - - - +
205R LEU* 1.3 64.8 + - - +
207R GLN* 3.3 23.6 - - - +
208R ARG* 3.2 18.7 + - - +
276R ARG* 4.3 26.1 + - + +
277R GLU 4.4 11.4 - - - -
278R ASN* 3.1 35.0 - - - +
280R VAL* 5.8 6.7 - - - -
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Residues in contact with LEU 205 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201R ASP 3.3 7.4 + - - +
202R ALA* 2.8 17.8 + - - +
204R LYS* 1.3 75.6 - - - +
206R ALA* 1.3 62.8 + - - +
208R ARG* 2.9 26.0 + - - +
209R MET* 3.2 15.7 + - + +
227R CYS* 3.9 19.7 - - + +
230R LEU* 3.5 38.4 - - + -
231R ALA* 4.4 6.1 - - + +
262R PHE* 4.4 27.6 - - + -
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Residues in contact with ALA 206 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178R PRO* 4.7 21.7 - - + +
182R ILE* 6.1 3.8 - - + -
202R ALA 2.8 13.4 + - - +
203R VAL* 3.5 11.0 - - + +
205R LEU* 1.3 72.5 - - - +
207R GLN* 1.3 64.0 + - - +
209R MET* 3.2 6.3 + - - +
210R SER* 3.0 24.7 + - - -
223R ILE* 5.1 4.8 - - + +
227R CYS* 3.5 29.6 - - + -
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Residues in contact with GLN 207 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179R SER* 5.7 1.7 + - - +
203R VAL* 2.6 35.3 + - + +
204R LYS* 3.3 32.6 - - - +
206R ALA* 1.3 72.1 - - - +
208R ARG* 1.3 63.2 + - - +
210R SER* 3.1 17.8 + - - -
211R LYS* 3.2 10.9 + - - +
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Residues in contact with ARG 208 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204R LYS 3.2 6.6 + - - +
205R LEU* 2.9 16.7 + - - +
207R GLN* 1.3 78.9 - - - +
209R MET* 1.3 51.1 + - - +
211R LYS* 2.9 14.0 + - + +
212R ASP* 2.3 81.0 + - - +
262R PHE* 3.5 33.5 - - - -
265R THR* 5.1 3.4 + - - -
266R LYS* 3.9 19.8 + - - +
267R ALA* 5.1 7.9 + - - +
271R SER* 5.3 2.4 + - - -
277R GLU* 5.9 4.7 + - - +
279R ASP* 3.6 24.9 - - - +
280R VAL* 5.2 8.1 - - + +
281R GLU 5.9 2.2 - - - -
282R ASP* 6.3 1.3 - - - +
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Residues in contact with MET 209 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205R LEU* 3.2 15.4 + - + +
206R ALA 3.2 7.8 + - - +
208R ARG* 1.3 75.6 - - + +
210R SER* 1.3 61.4 + - - +
212R ASP* 3.0 26.5 + - + +
213R TRP 3.1 9.2 + - - -
214R MET* 3.6 9.2 + - + -
215R PHE* 4.0 5.0 + - - -
223R ILE* 3.9 13.7 - - + -
226R ALA* 5.6 2.9 - - + -
227R CYS* 3.4 28.5 - - - -
230R LEU* 4.4 11.7 - - + -
258R ARG* 3.8 34.5 + - + +
262R PHE* 4.3 38.4 - - + -
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Residues in contact with SER 210 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178R PRO* 5.0 4.9 - - - +
206R ALA 3.0 13.0 + - - -
207R GLN* 3.3 11.6 - - - -
209R MET* 1.3 75.7 - - - +
211R LYS* 1.3 57.8 + - - +
213R TRP* 3.0 23.9 + - - -
215R PHE* 3.7 39.5 - - - +
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Residues in contact with LYS 211 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207R GLN 3.2 6.9 + - - +
208R ARG* 2.9 13.9 + - + +
210R SER* 1.3 73.8 - - - +
212R ASP* 1.3 58.9 + - - +
213R TRP* 2.9 15.5 + - - +
280R VAL* 3.0 34.2 + - + +
281R GLU* 4.7 1.8 - - - +
282R ASP* 3.7 42.0 + - + +
284R GLU 5.5 1.4 - - - +
285R ALA* 5.7 1.0 - - - +
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Residues in contact with ASP 212 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208R ARG* 2.3 84.0 + - - +
209R MET* 3.0 19.9 + - + +
211R LYS* 1.3 68.7 - - - +
213R TRP* 1.3 65.8 + - - +
214R MET* 3.0 28.3 + - + +
262R PHE* 4.8 3.1 - - - -
265R THR* 5.3 11.7 + - + +
282R ASP* 5.0 13.4 - - - +
284R GLU 5.3 3.7 - - - +
285R ALA* 5.2 1.4 - - - -
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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) + - + + + + + -
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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