Contacts of the helix formed by residues 219 - 235 (chain R) in PDB entry 6CNC
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 ARG 219 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218R ARG* 1.3 68.6 - - - +
220R PRO* 1.3 72.2 - - + +
221R ALA 3.3 1.8 - - - +
222R GLY* 3.2 13.4 + - - +
223R ILE* 3.7 7.4 + - - +
250R VAL* 5.9 1.8 - - + -
513R PRO 4.2 3.6 - - - +
514R GLU* 2.4 44.5 + - - +
515R LEU* 4.4 6.9 - - - +
516R PHE 4.9 5.3 - - - +
408S TYR* 3.1 64.5 - - + +
11X A 6.2 1.0 - - - -
12X T 5.2 13.7 + - - -
53Y T 4.7 7.4 + - - +
54Y A 2.3 64.8 + - - +
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Residues in contact with PRO 220 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142R MET* 3.9 22.0 - - + -
176R ALA* 5.0 9.6 - - + +
177R ASP 5.1 1.1 - - - -
178R PRO* 4.1 17.5 - - + +
181R PHE* 4.7 14.6 - - + -
215R PHE* 4.9 7.0 - - + -
218R ARG 3.1 7.6 - - - +
219R ARG* 1.3 83.3 - - - +
221R ALA* 1.3 64.2 + - - +
222R GLY 3.0 0.3 + - - -
223R ILE* 3.1 14.6 - - + +
224R ALA* 2.9 23.6 + - - +
513R PRO* 3.6 28.3 - - + -
514R GLU* 4.3 7.6 - - + +
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Residues in contact with ALA 221 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142R MET* 4.2 23.5 - - + +
144R ILE* 5.0 3.6 - - + -
181R PHE* 5.5 4.5 - - + -
185R PHE* 4.0 17.6 - - + -
219R ARG 3.2 0.8 + - - -
220R PRO* 1.3 79.6 - - - +
222R GLY* 1.3 61.9 + - - +
224R ALA* 3.5 8.7 - - - +
225R GLY 3.1 17.7 + - - -
248R SER* 3.2 29.5 + - - +
250R VAL* 4.4 4.5 - - + -
408S TYR* 4.6 7.0 - - + +
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Residues in contact with GLY 222 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219R ARG* 3.2 9.7 + - - +
220R PRO 3.1 1.4 - - - -
221R ALA* 1.3 75.7 - - - +
223R ILE* 1.3 66.1 + - - +
225R GLY* 3.0 4.5 + - - -
226R ALA* 2.9 21.6 + - - +
248R SER* 4.6 0.2 + - - -
250R VAL* 3.5 28.4 - - - +
254R THR* 5.5 8.3 - - - -
255R LEU* 4.3 7.0 - - - +
258R ARG* 5.7 3.1 - - - -
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Residues in contact with ILE 223 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178R PRO* 3.7 6.1 - - + -
209R MET* 3.9 22.2 - - + -
215R PHE* 3.4 52.0 - - + +
218R ARG* 5.6 7.6 - - + -
219R ARG 3.7 6.0 + - - +
220R PRO* 3.1 18.8 + - + +
222R GLY* 1.3 73.1 - - - +
224R ALA* 1.3 61.7 + - - +
226R ALA* 3.2 6.3 + - - +
227R CYS* 2.9 32.7 + - - -
258R ARG* 3.4 43.2 - - + +
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Residues in contact with ALA 224 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178R PRO* 3.7 26.5 - - + -
181R PHE* 4.6 2.9 - - + -
182R ILE* 4.2 10.1 - - + +
185R PHE* 4.0 19.7 - - + -
220R PRO 2.9 12.9 + - - +
221R ALA* 3.5 10.5 - - - +
223R ILE* 1.3 77.6 - - - +
225R GLY* 1.3 64.3 + - - +
227R CYS* 3.0 10.7 + - - +
228R ILE* 2.9 25.1 + - - +
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Residues in contact with GLY 225 (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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185R PHE* 4.7 1.9 - - - -
221R ALA 3.1 7.4 + - - -
222R GLY 3.0 7.3 + - - -
224R ALA* 1.3 78.7 - - - +
226R ALA* 1.3 57.4 + - - +
228R ILE* 3.2 13.7 + - - +
229R LEU* 2.9 28.6 + - - +
244R ILE* 4.0 14.6 - - - +
248R SER* 4.1 13.2 - - - -
255R LEU* 3.9 7.2 - - - -
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Residues in contact with ALA 226 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209R MET* 5.3 4.3 - - + -
222R GLY 2.9 11.8 + - - +
223R ILE* 3.4 15.0 - - + +
225R GLY* 1.3 75.7 - - - +
227R CYS* 1.3 63.7 + - - +
229R LEU* 3.2 6.7 + - - +
230R LEU* 2.9 30.9 + - + +
255R LEU* 3.5 23.4 - - + +
258R ARG* 4.6 15.9 - - + -
259R LEU* 4.8 10.2 - - + +
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Residues in contact with CYS 227 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178R PRO* 5.5 1.1 - - - -
182R ILE* 5.1 4.9 - - + -
202R ALA* 4.6 10.3 - - + +
205R LEU* 3.8 14.6 - - + +
206R ALA* 3.4 28.7 - - + -
209R MET* 3.4 30.7 - - - -
223R ILE* 2.9 29.9 + - - -
224R ALA* 3.0 10.3 + - - +
226R ALA* 1.3 75.3 - - - +
228R ILE* 1.3 63.6 + - - +
230R LEU* 3.2 4.3 + - - +
231R ALA* 2.9 26.0 + - - +
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Residues in contact with ILE 228 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182R ILE* 4.3 24.0 - - + +
185R PHE* 3.5 42.4 - - + -
186R ALA* 4.6 2.0 - - + +
189R LEU* 3.6 31.0 - - + -
198R VAL* 5.8 2.2 - - + -
202R ALA* 4.9 10.1 - - + -
224R ALA 2.9 18.3 + - - +
225R GLY* 3.2 12.3 + - - +
227R CYS* 1.3 76.4 - - - +
229R LEU* 1.3 63.9 + - - +
231R ALA* 5.0 0.4 - - - -
232R CYS* 2.9 39.0 + - - -
244R ILE* 5.3 9.6 - - + -
247R VAL* 6.2 0.4 - - + -
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Residues in contact with LEU 229 (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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225R GLY 2.9 11.2 + - - +
226R ALA* 3.5 9.0 - - - +
228R ILE* 1.3 75.9 - - - +
230R LEU* 1.3 65.8 + - + +
232R CYS* 3.6 4.9 - - + +
233R ARG* 2.9 30.9 + - + +
237R LEU* 6.4 0.7 - - + -
239R ARG* 4.1 12.1 - - + +
241R HIS* 3.7 35.4 - - + +
244R ILE* 3.5 29.1 - - + +
255R LEU* 4.4 9.2 - - + -
259R LEU* 4.3 23.1 - - + -
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Residues in contact with LEU 230 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205R LEU* 3.5 24.7 - - + -
209R MET* 4.5 7.9 - - + -
226R ALA* 2.9 20.5 + - + +
227R CYS* 3.2 9.2 + - - +
229R LEU* 1.3 76.1 - - + +
231R ALA* 1.3 52.0 - - - +
233R ARG* 3.0 15.1 + - - +
234R MET* 2.5 36.7 + - - +
259R LEU* 3.5 29.2 - - + -
262R PHE* 3.8 39.5 - - + -
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Residues in contact with ALA 231 (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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198R VAL* 3.6 19.2 - - + +
201R ASP* 3.9 9.1 - - + +
202R ALA* 3.5 41.7 - - + +
205R LEU* 4.3 3.3 - - + +
227R CYS 2.9 10.7 + - - +
228R ILE 4.2 0.7 - - - +
230R LEU* 1.3 72.7 - - - +
232R CYS* 1.3 51.8 + - - +
234R MET* 3.1 12.4 + - - +
235R ASN* 2.7 35.3 + - - +
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Residues in contact with CYS 232 (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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189R LEU* 4.6 11.0 - - - -
191R LEU* 4.8 5.2 - - - -
195R LYS* 6.0 0.4 - - - -
198R VAL* 4.2 14.6 - - - -
228R ILE* 2.9 42.6 + - - +
229R LEU* 3.6 7.6 - - + +
231R ALA* 1.3 76.5 - - - +
233R ARG* 1.3 61.7 + - - +
235R ASN* 2.9 12.4 + - - -
236R ASN 3.0 8.5 + - - -
237R LEU* 3.2 47.1 - - + +
239R ARG* 5.5 4.3 - - + -
244R ILE* 6.2 1.6 - - + -
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Residues in contact with ARG 233 (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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229R LEU* 2.9 28.8 + - + +
230R LEU* 3.5 11.1 - - - +
232R CYS* 1.3 72.4 - - - +
234R MET* 1.3 60.4 + - - +
236R ASN* 2.8 21.7 + - - +
237R LEU* 4.5 11.6 - - - +
272R VAL* 5.2 11.9 - - - +
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Residues in contact with MET 234 (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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201R ASP* 5.1 14.4 - - + +
230R LEU 2.5 18.4 + - - +
231R ALA* 3.2 19.1 - - - +
233R ARG* 1.3 74.1 - - - +
235R ASN* 1.3 56.5 + - - +
236R ASN* 3.2 6.8 + - - +
272R VAL 4.5 12.8 - - - +
273R GLN 3.8 19.7 - - - +
274R LYS* 4.6 8.1 - - + -
276R ARG* 3.9 32.3 - - + +
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Residues in contact with ASN 235 (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* 3.3 33.0 + - - +
197R LYS* 4.8 15.2 + - - +
198R VAL* 3.3 29.7 - - + +
201R ASP* 4.8 8.5 - - - +
231R ALA 2.7 18.3 + - - +
232R CYS* 2.9 5.6 + - - +
234R MET* 1.3 70.7 - - - +
236R ASN* 1.3 81.7 + - - +
237R LEU* 3.7 8.8 - - + +
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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
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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