Contacts of the helix formed by residues 199 - 212 (chain A) in PDB entry 3G33
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 PRO 199 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A GLU* 4.4 0.2 - - - -
197A ALA* 3.1 18.8 - - + -
198A THR* 1.3 96.3 - - - +
200A VAL* 1.3 60.1 + - - -
201A ASP 3.1 1.3 - - - -
202A MET* 3.2 20.6 + - + +
285A PRO* 3.5 39.5 - - + +
288A ARG* 2.9 35.0 + - + +
289A ILE 6.4 0.2 - - - -
290A SER* 6.4 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A VAL* 5.1 2.7 - - + -
143A HIS 5.3 0.9 - - - +
144A ARG* 4.7 26.0 - - - +
187A ALA* 3.7 23.0 - - + +
189A GLU* 3.5 30.7 - - + +
190A VAL* 3.7 20.2 - - + -
196A TYR* 4.7 1.1 - - - -
197A ALA* 3.3 35.7 - - + +
198A THR 2.7 6.6 + - - +
199A PRO* 1.3 76.1 - - - +
201A ASP* 1.3 61.1 + - - +
203A TRP* 3.6 8.1 + - - +
204A SER* 3.9 8.3 + - - +
288A ARG* 4.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LEU* 4.0 13.0 - - + -
137A HIS* 2.8 40.0 + - + +
142A VAL* 3.3 10.5 - - - +
143A HIS* 2.1 53.8 + - - +
146A LEU* 3.4 10.2 + - + +
198A THR 3.0 4.0 + - - +
200A VAL* 1.3 76.2 - - - +
202A MET* 1.3 60.6 + - - +
204A SER* 2.9 24.4 + - - +
205A VAL* 3.1 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LEU* 4.1 13.9 - - + -
133A LEU* 3.9 20.2 - - + -
137A HIS* 5.5 2.9 - - + -
198A THR 5.5 0.2 - - - +
199A PRO* 3.2 19.8 + - + +
201A ASP* 1.3 77.4 - - + +
203A TRP* 1.3 61.9 + - - +
205A VAL* 3.2 16.4 + - + +
206A GLY* 3.2 9.7 + - - -
280A MET* 3.7 38.7 - - - +
288A ARG* 3.9 10.8 - - + -
289A ILE* 3.3 32.8 - - + +
290A SER* 3.9 15.5 - - - +
291A ALA* 3.6 21.1 - - - +
294A ALA* 4.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A TRP 4.9 0.4 + - - -
185A TYR 3.7 6.3 - - - -
186A ARG 3.0 30.1 + - - -
187A ALA* 3.7 7.9 - - + -
188A PRO* 3.4 18.2 - - + -
199A PRO 3.6 2.4 + - - -
200A VAL 3.6 8.8 + - - +
201A ASP 3.1 0.6 - - - -
202A MET* 1.3 77.9 - - - +
204A SER* 1.3 62.4 + - - +
206A GLY* 3.2 10.7 + - - -
207A CYS* 3.3 24.0 + - - -
219A PHE* 4.2 7.2 - + - -
231A ILE* 3.4 46.8 - - + +
235A ILE* 4.0 7.9 - - + -
280A MET 4.1 5.6 - - - -
281A LEU* 3.3 54.5 - - + +
282A THR 3.7 10.3 - - - -
283A PHE 4.4 1.3 - - - -
288A ARG* 3.4 33.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ARG 5.6 0.7 + - - -
145A ASP* 5.3 1.6 + - - -
146A LEU* 3.6 38.7 + - - +
185A TYR* 2.7 31.3 + - - +
186A ARG* 5.0 0.3 + - - -
187A ALA 5.1 0.3 + - - -
200A VAL* 3.9 8.3 + - - +
201A ASP* 2.9 12.0 + - - -
203A TRP* 1.3 75.1 - - - +
205A VAL* 1.3 64.5 + - - +
207A CYS* 3.5 3.1 + - - +
208A ILE* 3.2 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A MET* 3.7 16.3 - - + +
129A PHE* 3.4 35.2 - - + -
130A LEU* 3.8 13.5 - - + -
133A LEU* 3.5 24.2 - - + -
146A LEU* 4.3 1.6 - - + -
201A ASP 3.1 14.6 + - - +
202A MET* 3.3 15.0 - - + +
203A TRP 3.2 0.2 - - - -
204A SER* 1.3 78.5 - - - +
206A GLY* 1.3 57.2 + - - +
208A ILE* 3.5 1.8 + - - +
209A PHE* 2.9 26.9 + - - +
280A MET* 3.5 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A MET 3.2 7.7 + - - -
203A TRP 3.2 7.7 + - - -
205A VAL* 1.3 76.5 - - - +
207A CYS* 1.3 63.8 + - - +
209A PHE 3.4 0.2 + - - -
210A ALA* 3.1 25.1 + - - +
218A LEU* 4.8 0.3 - - - +
277A LEU* 3.6 16.0 - - - +
280A MET* 3.4 18.8 - - - +
281A LEU* 4.1 13.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A TRP 4.1 8.7 - - - +
185A TYR* 3.6 27.7 - - + -
203A TRP* 3.3 39.2 + - - -
204A SER 3.9 3.4 - - - +
205A VAL 3.4 0.4 - - - -
206A GLY* 1.3 76.1 - - - +
208A ILE* 1.3 58.0 + - - +
210A ALA* 3.7 2.9 + - - +
211A GLU* 3.3 25.6 + - - +
218A LEU* 4.3 18.8 + - + +
219A PHE* 3.8 26.9 - - + +
281A LEU* 4.3 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 3.6 28.5 - - + -
109A LEU* 5.6 0.8 - - + +
126A MET* 5.9 1.1 - - - -
129A PHE* 4.3 10.1 - - + -
146A LEU* 4.2 5.4 - - + +
147A LYS* 3.8 20.4 - - - +
148A PRO* 3.9 9.6 - - + -
151A ILE* 3.1 30.5 - - + -
185A TYR* 3.9 19.1 - - + -
204A SER 3.2 18.4 + - - +
205A VAL* 4.1 3.6 - - - +
206A GLY 3.2 0.6 - - - -
207A CYS* 1.3 72.6 - - - +
209A PHE* 1.3 65.5 + - - +
210A ALA 3.2 1.6 - - - -
211A GLU* 3.2 16.5 + - + +
212A MET* 3.2 22.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ILE* 4.1 4.0 - - + -
126A MET* 3.3 48.4 - - + -
205A VAL 2.9 19.9 + - - +
206A GLY 3.4 3.3 + - - +
208A ILE* 1.3 77.1 - - - +
210A ALA* 1.3 61.2 + - - +
212A MET* 3.5 8.3 - - - +
213A PHE* 3.4 41.8 - + - -
269A MET* 3.7 26.9 - - + -
273A GLY 4.0 8.5 - - - -
276A LEU* 4.7 10.8 - - + -
277A LEU* 3.8 22.0 - - + -
280A MET* 3.8 8.7 - - + -
299A TYR* 3.9 29.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLY 3.1 16.7 + - - +
207A CYS 4.0 4.5 - - - +
209A PHE* 1.3 77.4 - - - +
211A GLU* 1.3 60.2 + - - +
212A MET 3.1 4.9 - - - -
213A PHE* 3.1 12.2 + - - -
214A ARG* 3.2 21.8 - - - +
218A LEU* 4.1 20.9 - - + -
266A VAL* 3.9 29.5 - - + +
269A MET* 5.9 0.4 - - - -
277A LEU* 4.3 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ARG* 5.1 6.4 + - - +
109A LEU* 3.9 18.6 - - + +
148A PRO* 4.2 13.2 - - - +
185A TYR* 3.0 36.3 + - - -
207A CYS 3.3 12.7 + - - +
208A ILE* 3.2 10.6 + - + +
210A ALA* 1.3 77.2 - - - +
212A MET* 1.3 57.7 + - - +
213A PHE 3.2 0.2 - - - -
214A ARG* 3.7 8.3 - - - +
215A ARG* 2.8 28.3 + - - -
216A LYS* 3.8 21.6 + - - +
217A PRO* 3.5 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 4.2 27.1 - - + -
109A LEU* 4.3 26.9 - - + +
116A GLY* 5.4 2.8 - - - -
117A LEU* 5.0 9.4 + - + +
122A ILE* 3.4 52.5 - - + +
125A LEU* 4.2 22.7 - - + +
126A MET* 3.8 29.2 - - - +
129A PHE* 5.8 4.3 - - + -
208A ILE* 3.3 17.0 - - + +
209A PHE* 3.5 9.9 - - - +
210A ALA 3.1 0.4 - - - -
211A GLU* 1.3 81.1 - - - +
213A PHE* 1.3 56.3 + - - +
214A ARG 3.3 1.2 + - - -
215A ARG* 4.8 5.7 + - - +
----------------------------------------------------------
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