Contacts of the helix formed by residues 200 - 212 (chain X) in PDB entry 2W6C
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 SER 200 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118X GLY 3.4 16.5 + - - -
199X GLU* 1.3 95.2 + - - +
201X ALA* 1.3 63.8 + - - -
203X GLY* 2.7 23.0 + - - -
204X ALA* 2.9 10.4 + - - +
225X GLN 2.8 13.1 + - - -
226X SER 3.2 13.9 - - - -
227X GLY* 3.8 3.0 - - - -
233X TRP* 3.8 10.8 - - - -
440X HIS* 3.4 11.2 - - - -
601X BM4 3.4 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 201 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116X TYR 4.5 0.9 - - - -
117X GLY* 3.8 6.5 - - - -
118X GLY 4.3 0.2 - - - +
119X GLY* 3.8 9.8 - - - +
120X PHE* 3.5 52.5 - - + +
148X TYR* 4.3 4.0 - - - +
200X SER* 1.3 80.3 + - - +
202X GLY* 1.3 55.6 + - - +
204X ALA* 3.7 2.9 - - - -
205X SER* 2.8 34.2 + - - -
233X TRP* 3.7 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 202 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115X ILE* 3.3 26.4 - - - +
116X TYR 3.7 6.5 + - - -
117X GLY* 3.4 4.9 - - - -
198X GLY* 3.6 6.9 - - - -
199X GLU 3.0 8.0 + - - -
201X ALA* 1.3 75.0 - - - +
203X GLY* 1.3 65.4 + - - +
205X SER* 3.4 8.5 + - - -
206X VAL* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 203 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198X GLY* 3.2 24.7 - - - -
199X GLU 3.3 2.2 - - - +
200X SER 2.7 14.6 + - - -
202X GLY* 1.3 71.2 - - - +
204X ALA* 1.3 60.0 + - - -
206X VAL* 3.2 4.3 + - - +
207X GLY 3.2 17.2 + - - -
224X LEU* 3.3 14.6 - - - +
225X GLN 4.3 6.5 - - - -
227X GLY 3.8 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 204 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120X PHE* 4.4 4.5 - - + -
200X SER 2.9 10.4 + - - +
201X ALA* 3.8 7.9 - - - +
203X GLY* 1.3 76.4 - - - +
205X SER* 1.3 56.9 + - - +
207X GLY* 3.2 4.7 + - - -
208X MET* 2.8 34.9 + - + +
227X GLY 3.8 3.0 - - - -
228X SER 3.5 31.2 - - - +
229X PRO* 3.8 3.1 - - + +
233X TRP* 4.2 8.3 - - + -
234X ALA* 4.1 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 205 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115X ILE* 4.2 4.7 - - - -
120X PHE* 3.5 13.9 - - - -
148X TYR* 4.6 0.5 + - - -
170X LEU* 4.1 3.6 - - - +
173X GLN* 3.1 39.1 + - - -
201X ALA 2.8 26.2 + - - -
202X GLY* 3.4 9.9 - - - -
204X ALA* 1.3 71.6 - - - +
206X VAL* 1.3 55.5 + - - +
208X MET* 2.7 32.3 + - - +
209X HIS* 2.8 19.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 206 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115X ILE* 4.2 10.3 - - + -
196X ILE* 3.8 20.8 - - + +
197X PHE* 3.9 13.0 - - - +
198X GLY* 3.8 21.3 - - - +
202X GLY 3.0 20.8 + - - +
203X GLY 3.2 6.5 + - - +
205X SER* 1.3 72.8 - - - +
207X GLY* 1.3 65.8 + - - +
209X HIS* 2.9 14.7 + - - +
210X ILE* 3.0 13.1 + - + +
222X ALA* 3.4 33.7 - - + -
223X ILE 3.9 8.1 - - - +
224X LEU* 3.8 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 207 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203X GLY 3.2 8.5 + - - -
204X ALA 3.2 4.2 + - - -
206X VAL* 1.3 79.9 - - - +
208X MET* 1.3 61.9 + - - +
210X ILE* 3.3 14.3 + - - +
211X LEU* 3.1 26.0 + - - +
224X LEU* 3.8 7.9 - - - +
229X PRO* 3.7 25.9 - - - +
407X PHE* 4.7 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 208 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120X PHE* 4.4 5.4 - - + -
170X LEU* 4.1 11.9 - - + -
204X ALA* 2.8 20.8 + - + +
205X SER* 2.7 14.2 + - - +
207X GLY* 1.3 74.8 - - - +
209X HIS* 1.3 58.6 + - - +
211X LEU* 3.2 2.3 + - - +
212X SER* 2.8 31.4 + - - -
229X PRO* 3.5 31.9 - - + +
234X ALA* 3.4 33.0 - - + +
235X SER* 4.3 5.6 - - - -
294X PRO* 3.8 19.1 - - + -
300X PHE* 4.0 7.5 - - + -
301X PHE* 3.7 37.8 - - + -
305X LEU* 5.0 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 209 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115X ILE* 4.4 12.8 - - + -
170X LEU* 3.6 23.7 - - + +
173X GLN* 2.9 33.4 + - + +
174X ARG* 4.2 11.0 - - + -
177X LEU* 4.4 10.4 - - + +
196X ILE* 4.2 4.7 - - + -
205X SER 2.8 22.9 + - - -
206X VAL* 2.9 7.2 + - - +
208X MET* 1.3 75.8 - - - +
210X ILE* 1.3 64.4 + - - +
211X LEU 3.6 0.2 + - - -
212X SER 3.6 7.1 - - - +
215X SER* 2.9 46.2 + - - -
216X ARG* 3.8 3.5 + - - -
219X PHE* 3.6 22.2 - - + -
300X PHE* 3.9 13.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 210 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206X VAL* 3.0 14.5 + - + +
207X GLY* 3.3 17.0 - - - +
209X HIS* 1.3 78.6 - - - +
211X LEU* 1.3 60.5 + - + +
216X ARG* 3.8 2.8 + - - -
219X PHE* 4.0 22.7 - - + -
222X ALA* 3.8 23.3 - - + -
224X LEU* 4.7 1.8 - - + -
314X PHE* 3.6 8.4 - - + +
315X LYS* 2.9 45.1 + - + +
317X THR* 5.3 2.2 - - + -
319X ILE* 3.9 19.3 - - + -
407X PHE* 4.5 13.2 - - + -
411X TYR* 4.1 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207X GLY 3.1 19.0 + - - +
208X MET* 3.2 6.2 + - - +
210X ILE* 1.3 80.6 - - + +
212X SER* 1.3 65.4 + - - +
213X PRO 3.2 1.2 - - - -
216X ARG* 3.0 22.4 + - - -
229X PRO* 3.8 22.9 - - + -
301X PHE* 4.7 4.0 - - + -
305X LEU* 3.7 30.7 - - + +
308X MET* 3.2 43.1 - - + +
309X LEU* 4.0 22.9 - - + -
313X ASN 3.9 0.7 - - - +
314X PHE* 3.9 20.2 - - + -
407X PHE* 5.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 212 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174X ARG* 2.9 25.9 + - - -
208X MET 2.8 13.8 + - - -
209X HIS 3.6 1.9 - - - +
210X ILE 3.8 0.2 - - - -
211X LEU* 1.3 71.6 - - - +
213X PRO* 1.3 71.3 - - - +
214X GLY 3.9 0.7 + - - -
215X SER* 3.0 16.1 + - - -
216X ARG* 3.1 13.6 + - - +
300X PHE* 2.6 50.3 + - - -
301X PHE* 5.1 1.6 - - - -
308X MET* 5.2 0.4 - - - -
----------------------------------------------------------
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