Contacts of the helix formed by residues 204 - 221 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A PHE* 3.5 26.3 - - + +
201A THR* 3.3 28.1 + - - +
202A TYR 3.3 0.6 - - - -
203A GLU* 1.3 73.5 - - - +
205A THR* 1.3 58.0 + - - +
206A ASP* 3.3 8.7 + - - +
207A PHE* 3.1 26.4 + - + +
208A GLN* 3.4 23.2 + - - +
256A PHE* 5.5 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A TYR 5.2 0.9 - - - +
203A GLU* 2.8 22.5 + - - +
204A ASP* 1.3 70.3 - - - +
206A ASP* 1.3 63.7 + - - +
208A GLN* 3.8 20.4 - - - +
209A HIS* 3.0 28.9 + - - +
259B ARG* 3.5 17.3 + - - -
263B LYS* 5.3 5.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ASP* 3.2 7.5 + - - +
205A THR* 1.3 77.3 + - - +
207A PHE* 1.3 64.9 + - - +
209A HIS* 3.3 6.1 + - - +
210A MET 3.2 16.8 + - - -
256A PHE* 3.8 26.9 - - + -
206B ASP* 5.8 0.2 - - - +
259B ARG* 2.7 37.5 + - - +
263B LYS* 3.2 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A SER* 3.7 15.3 - - - -
192A ASN* 3.5 25.8 - - - -
196A PHE* 4.5 2.7 - + - -
200A PHE* 3.5 33.0 - + + -
204A ASP* 3.1 25.7 + - + +
206A ASP* 1.3 78.8 - - - +
208A GLN* 1.3 69.6 + - + +
210A MET* 3.2 21.9 + - + +
211A ILE* 3.1 51.7 + - + +
256A PHE* 3.7 12.7 - + + -
260A LEU* 3.8 22.7 - - + -
308A ILE* 4.8 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A GLN* 3.5 23.6 + - - +
185A ASN* 3.2 35.4 + - - +
201A THR 4.0 3.2 + - - -
202A TYR* 3.0 33.8 + - - +
204A ASP* 3.4 17.5 + - - +
205A THR* 3.8 21.8 - - - +
206A ASP 3.3 0.4 - - - -
207A PHE* 1.3 85.2 - - + +
209A HIS* 1.3 55.6 + - - +
211A ILE* 3.2 7.7 + - - +
212A GLU* 3.0 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A THR 3.0 19.2 + - - +
206A ASP 3.5 6.5 - - - +
207A PHE 3.3 0.2 - - - -
208A GLN* 1.3 76.4 - - - +
210A MET* 1.3 63.4 + - + +
212A GLU* 3.1 10.1 + - - +
213A LEU* 3.1 50.0 + - + +
252A VAL* 5.1 1.1 - - + -
255B ASP* 2.9 38.6 + - - -
259B ARG* 3.7 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ASP 3.2 7.6 + - - +
207A PHE* 3.2 36.3 + - + +
209A HIS* 1.3 82.5 - - + +
211A ILE* 1.3 74.8 + - + +
213A LEU* 3.5 5.1 + - - -
214A PHE* 3.1 38.5 + - - +
252A VAL* 5.8 1.8 - - + -
253A VAL* 3.7 21.5 - - + +
256A PHE* 3.6 42.8 - - + -
257A LEU* 3.9 23.6 - - + -
260A LEU* 4.5 0.2 - - + -
308A ILE* 4.8 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A THR* 3.8 24.7 - - + -
188A SER* 3.9 19.3 - - - +
207A PHE* 3.1 46.5 + - + +
208A GLN* 3.7 9.0 - - - +
209A HIS 3.2 0.2 - - - -
210A MET* 1.3 88.9 - - + +
212A GLU* 1.3 61.7 + - - +
214A PHE* 3.7 5.3 - - + +
215A SER* 2.9 33.1 + - - -
308A ILE* 4.1 11.0 - - + -
309A ILE* 4.6 5.8 - - + +
312A THR* 3.9 17.0 - - + +
313A GLU* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LYS* 3.6 27.4 + - - +
181A GLN* 4.0 19.6 + - - +
184A THR* 6.1 0.7 - - - +
208A GLN 3.0 13.0 + - - +
209A HIS* 3.1 14.1 + - - +
211A ILE* 1.3 77.8 - - - +
213A LEU* 1.3 60.4 + - + +
215A SER* 3.6 9.4 + - - -
216A GLU* 3.1 41.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A HIS* 3.1 45.5 + - + +
210A MET* 3.9 2.5 - - - +
212A GLU* 1.3 74.6 - - + +
214A PHE* 1.3 66.6 + - - +
216A GLU* 3.3 17.4 + - - +
217A ASN* 3.1 20.3 + - - +
249A ASN* 3.3 40.0 + - - +
252A VAL* 3.5 38.6 - - + -
253A VAL* 3.9 15.0 - - + -
255B ASP* 4.1 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A MET* 3.1 27.9 + - - +
211A ILE* 3.7 6.3 - - + +
212A GLU 3.4 0.2 - - - -
213A LEU* 1.3 77.1 - - - +
215A SER* 1.3 62.0 + - - +
217A ASN* 3.2 11.3 + - + +
218A VAL* 3.1 21.0 + - + +
253A VAL* 3.8 30.2 - - + +
257A LEU* 4.2 2.2 - - + -
305A GLY* 3.2 37.7 - - - -
308A ILE* 5.0 4.7 - - + -
309A ILE* 3.7 35.2 - - + -
701A VD3 3.5 53.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LYS* 5.3 6.2 + - - -
211A ILE* 2.9 23.2 + - - -
212A GLU* 3.9 13.6 + - - -
214A PHE* 1.3 75.5 - - - +
216A GLU* 1.3 65.5 + - - +
218A VAL* 3.1 13.5 + - - +
219A GLU* 3.1 12.5 + - - +
309A ILE* 4.0 7.6 - - - +
313A GLU* 2.6 31.2 + - - +
490A GLN* 5.0 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A GLU* 3.1 32.4 + - - +
213A LEU* 3.3 20.3 - - - +
215A SER* 1.3 74.1 - - - +
217A ASN* 1.3 57.1 + - - +
219A GLU* 3.2 12.0 + - - +
220A LEU* 2.9 39.0 + - + +
245A GLN* 2.6 29.9 + - - +
249A ASN* 3.0 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LEU 3.1 9.7 + - - -
214A PHE* 3.4 19.3 - - + +
215A SER 3.1 0.6 - - - -
216A GLU* 1.3 73.9 - - - +
218A VAL* 1.3 64.8 + - - +
220A LEU* 3.4 6.5 + - - +
221A ALA* 3.0 24.1 + - - +
246A LEU* 3.3 40.2 + - + +
249A ASN* 3.0 38.1 + - - +
250A ALA* 3.5 17.0 - - - +
253A VAL* 5.2 0.8 - - - +
701A VD3 4.1 21.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A PHE* 3.1 14.6 + - + +
215A SER 3.1 7.4 + - - +
217A ASN* 1.3 74.6 - - - +
219A GLU* 1.3 62.2 + - - +
221A ALA* 3.4 17.5 - - - +
309A ILE* 3.7 23.6 - - + -
313A GLU* 4.0 22.2 - - + +
487A MET* 3.5 29.6 + - + +
488A THR* 4.2 16.8 - - + +
701A VD3 4.2 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A SER 3.1 10.6 + - - +
216A GLU* 3.4 13.9 - - - +
217A ASN 3.1 0.8 - - - -
218A VAL* 1.3 75.7 - - - +
220A LEU* 1.3 66.0 + - + +
221A ALA 3.1 2.6 + - - -
222A ALA* 3.1 18.0 + - - +
223A SER* 3.9 2.6 + - - -
484A ARG* 2.9 38.0 + - - +
485A LEU* 3.4 25.0 - - - +
486A GLY* 3.9 10.3 - - - -
490A GLN* 4.0 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A GLU* 2.9 33.9 + - + +
217A ASN* 3.4 15.0 + - - +
219A GLU* 1.3 75.0 - - + +
221A ALA* 1.3 58.8 + - - +
222A ALA 3.1 0.2 - - - -
223A SER* 2.9 27.6 - - - -
226A VAL* 3.1 13.0 - - + +
242A LYS* 3.5 48.5 - - + +
245A GLN* 3.8 31.0 - - - +
246A LEU* 3.8 24.7 - - + -
249A ASN* 4.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LEU* 4.6 4.4 - - + +
115A PHE* 5.4 2.2 - - + -
217A ASN 3.0 13.0 + - - +
218A VAL 3.4 15.0 - - - +
219A GLU 3.1 0.6 - - - -
220A LEU* 1.3 76.3 - - - +
222A ALA* 1.3 56.3 + - - +
223A SER 3.4 0.9 - - - -
226A VAL* 3.6 23.4 - - - +
227A PHE* 4.6 6.2 - - - -
246A LEU* 4.3 3.1 - - - +
487A MET* 3.7 17.9 - - + +
701A VD3 3.8 26.0 - - + -
----------------------------------------------------------
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