Contacts of the helix formed by residues 204 - 221 (chain B) in PDB entry 3C6G
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 204 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B PHE* 3.7 29.9 - - + +
201B THR* 3.2 21.1 + - - +
202B TYR 3.5 0.2 - - - -
203B GLU* 1.3 71.6 - - - +
205B THR* 1.3 61.6 + - - +
206B ASP* 3.1 10.2 + - - +
207B PHE* 3.2 32.8 + - + +
208B GLN* 3.3 17.6 + - - +
256B PHE* 5.6 0.3 - - - -
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Residues in contact with THR 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ARG* 2.9 27.7 + - - -
263A LYS* 4.7 6.2 - - - +
202B TYR 5.3 0.7 - - - +
203B GLU* 2.7 22.5 + - - +
204B ASP* 1.3 72.3 - - - +
206B ASP* 1.3 59.5 + - - +
208B GLN* 3.5 20.3 - - - +
209B HIS* 2.8 31.5 + - - +
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Residues in contact with ASP 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ASP* 5.8 0.2 - - - +
259A ARG* 3.2 27.9 + - - +
263A LYS* 2.8 33.8 + - - -
204B ASP* 3.1 8.8 - - - +
205B THR* 1.3 74.5 - - - +
207B PHE* 1.3 65.4 - - - +
209B HIS* 3.3 7.4 + - - +
210B MET* 3.1 21.3 + - - +
256B PHE* 3.8 19.5 - - + -
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Residues in contact with PHE 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B SER* 4.0 14.8 - - - -
192B ASN* 3.4 34.1 - - - -
196B PHE* 4.6 2.2 - + - -
200B PHE* 3.6 30.5 - + + -
204B ASP* 3.2 26.9 + - + +
206B ASP* 1.3 79.1 - - - +
208B GLN* 1.3 67.8 + - + +
210B MET* 3.1 32.3 + - + +
211B ILE* 3.0 41.5 + - + +
256B PHE* 3.6 12.7 - + + -
260B LEU* 3.8 17.9 - - + -
308B ILE* 4.6 5.8 - - + -
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Residues in contact with GLN 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B GLN* 3.5 39.4 + - - +
184B THR* 5.9 1.6 - - + -
185B ASN* 3.4 26.8 + - - +
201B THR 4.3 2.3 - - - +
202B TYR* 3.6 24.2 + - - +
204B ASP* 3.3 19.6 + - - +
205B THR* 3.5 24.8 - - - +
207B PHE* 1.3 86.7 - - + +
209B HIS* 1.3 56.5 + - - +
211B ILE* 3.3 8.6 + - + +
212B GLU* 2.9 27.5 + - - +
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Residues in contact with HIS 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ASP* 3.0 40.5 + - - -
258A SER* 5.4 3.1 - - - -
259A ARG* 3.8 33.5 + - + +
205B THR 2.8 19.8 + - - +
206B ASP* 3.5 6.5 - - - +
208B GLN* 1.3 75.3 - - - +
210B MET* 1.3 66.4 + - - +
212B GLU* 3.3 26.5 + - - +
213B LEU* 3.1 38.9 + - + +
252B VAL* 5.5 0.2 - - + -
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Residues in contact with MET 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ASP 3.1 11.1 + - - +
207B PHE* 3.1 38.6 + - + +
209B HIS* 1.3 81.4 - - + +
211B ILE* 1.3 70.1 + - + +
213B LEU* 3.2 8.8 + - - +
214B PHE* 2.9 42.9 + - - +
252B VAL* 6.2 1.8 - - + -
253B VAL* 3.8 17.7 - - + +
256B PHE* 3.4 56.3 - - + -
257B LEU* 4.0 20.4 - - + -
260B LEU* 4.7 0.4 - - + -
308B ILE* 4.8 2.9 - - + -
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Residues in contact with ILE 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B THR* 3.7 28.3 - - + -
188B SER* 4.9 3.1 - - - -
207B PHE* 3.0 39.1 + - + +
208B GLN* 3.3 11.2 + - - +
210B MET* 1.3 83.3 - - - +
212B GLU* 1.3 57.7 + - - +
214B PHE* 3.7 3.4 - - + +
215B SER* 2.9 31.4 + - - -
308B ILE* 3.3 33.7 - - + -
309B ILE* 4.2 10.7 - - + +
312B THR* 3.9 20.2 - - + +
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Residues in contact with GLU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B GLN* 6.0 2.0 - - - +
208B GLN 2.9 14.1 + - - +
209B HIS* 3.4 32.5 + - - +
210B MET 3.2 0.2 - - - -
211B ILE* 1.3 77.1 - - - +
213B LEU* 1.3 60.1 + - + +
215B SER* 3.6 5.9 + - - -
216B GLU* 3.0 39.4 + - + +
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Residues in contact with LEU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ASP* 3.7 6.5 - - - +
209B HIS* 3.1 48.8 + - + +
210B MET* 3.7 7.6 - - - +
212B GLU* 1.3 75.8 - - + +
214B PHE* 1.3 64.8 + - - +
216B GLU* 3.4 18.9 - - - +
217B ASN* 3.2 25.5 + - - +
249B ASN* 3.5 27.8 + - - +
252B VAL* 3.6 33.7 - - + -
253B VAL* 4.1 11.0 - - + -
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Residues in contact with PHE 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B MET* 2.9 27.0 + - - +
211B ILE* 3.7 6.1 - - + +
213B LEU* 1.3 73.2 - - - +
215B SER* 1.3 66.7 + - - +
217B ASN* 3.1 17.2 + - + +
218B VAL* 3.2 11.8 + - + +
253B VAL* 3.7 29.7 - - + +
257B LEU* 4.3 1.8 - - + -
305B GLY* 3.1 38.4 - - - -
308B ILE* 5.1 4.3 - - + -
309B ILE* 3.7 36.3 - - + -
700B VD3 3.6 54.1 - - + -
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Residues in contact with SER 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B LYS* 5.1 7.6 + - - -
211B ILE* 2.9 23.4 + - - -
212B GLU* 3.7 6.7 - - - -
214B PHE* 1.3 77.3 - - - +
216B GLU* 1.3 63.0 + - - +
218B VAL* 3.0 15.4 + - - +
219B GLU* 3.1 11.3 + - - +
309B ILE* 3.7 9.6 - - - +
313B GLU* 2.8 34.6 + - - -
490B GLN* 4.7 7.1 + - - -
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Residues in contact with GLU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B GLU* 3.0 25.8 + - + +
213B LEU* 3.4 21.1 - - - +
215B SER* 1.3 76.7 - - - +
217B ASN* 1.3 57.0 + - - +
219B GLU* 3.1 18.9 + - - +
220B LEU* 2.9 34.3 + - + +
245B GLN* 2.5 32.0 + - - +
249B ASN* 3.0 15.5 + - - +
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Residues in contact with ASN 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B LEU 3.2 4.1 + - - -
214B PHE* 3.1 18.1 + - + +
216B GLU* 1.3 78.6 - - - +
218B VAL* 1.3 57.3 + - - +
220B LEU* 3.2 7.3 + - - +
221B ALA* 2.9 31.1 + - - +
246B LEU* 3.2 42.9 + - + +
249B ASN* 3.0 39.3 + - - +
250B ALA* 3.4 13.7 - - - +
253B VAL* 5.5 1.2 - - - +
700B VD3 4.2 22.3 + - + +
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Residues in contact with VAL 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B PHE* 3.2 12.5 + - + +
215B SER* 3.0 9.4 + - - +
217B ASN* 1.3 76.2 - - - +
219B GLU* 1.3 59.7 + - - +
221B ALA* 3.9 4.8 + - - -
309B ILE* 3.7 30.5 - - + -
313B GLU* 4.3 8.5 - - + +
487B MET* 3.2 42.2 + - + +
488B THR* 4.1 25.4 - - + +
700B VD3 4.2 33.2 - - + -
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Residues in contact with GLU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B SER 3.1 9.7 + - - +
216B GLU* 3.1 19.6 + - - +
218B VAL* 1.3 76.4 - - - +
220B LEU* 1.3 68.0 + - + +
222B ALA* 3.3 17.7 + - - +
223B SER* 4.1 3.1 + - - -
484B ARG* 3.1 38.0 + - - +
485B LEU* 3.4 21.8 - - - +
486B GLY* 3.9 10.5 - - - -
490B GLN* 3.3 26.2 + - - +
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Residues in contact with LEU 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B GLU* 2.9 27.6 + - + +
217B ASN* 3.2 20.4 + - - +
219B GLU* 1.3 71.7 - - + +
221B ALA* 1.3 58.7 + - - +
222B ALA 3.0 5.8 - - - -
223B SER* 2.7 31.7 + - - +
226B VAL* 3.2 12.8 - - + +
242B LYS* 3.7 40.6 - - + +
245B GLN* 4.1 28.3 - - - +
246B LEU* 3.9 31.0 - - + +
249B ASN* 4.2 0.7 - - - +
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Residues in contact with ALA 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B LEU* 4.4 7.2 - - + +
115B PHE* 5.8 0.2 - - + -
217B ASN 2.9 17.4 + - - +
218B VAL 4.0 0.7 - - - +
219B GLU 3.2 1.0 - - - -
220B LEU* 1.3 76.5 - - - +
222B ALA* 1.3 55.8 + - - +
223B SER 3.5 1.0 - - - +
226B VAL* 3.7 22.7 - - - +
227B PHE* 4.8 6.6 - - - -
246B LEU* 4.0 2.6 - - - +
487B MET* 3.8 26.2 - - + +
700B VD3 3.8 28.3 - - + -
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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