Contacts of the helix formed by residues 211 - 228 (chain A) in PDB entry 3FWQ
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 TYR 211 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA* 4.1 9.2 - - + -
11A VAL* 3.5 20.9 - - + -
12A TYR* 3.0 35.3 + + + -
15A VAL* 3.3 4.0 - - - +
148A HIS* 3.3 71.1 + + + +
151A GLY* 3.3 18.2 - - - -
152A ILE 3.5 17.0 - - - -
153A MET* 3.7 15.9 - - + +
182A TYR* 3.5 33.0 - + + +
210A ASP* 1.3 72.6 - - - +
212A SER* 1.3 55.5 + - - +
213A LEU 2.9 12.1 + - - -
214A ASP* 3.0 15.0 + - - +
215A MET* 3.9 1.4 + - - +
339A CL 4.6 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A GLU* 4.2 0.2 - - - -
210A ASP* 2.8 18.7 + - - -
211A TYR* 1.3 75.9 - - - +
213A LEU* 1.3 56.4 + - - +
214A ASP 3.4 0.2 - - - -
215A MET* 3.5 13.8 + - - +
216A TRP 3.5 10.6 + - - -
309A HIS* 2.4 45.2 + - - -
312A ARG* 2.8 33.0 + - - +
313A LEU 5.3 0.7 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
153A MET* 5.8 1.3 - - + -
155A ARG* 4.1 22.4 - - + -
192A VAL* 4.0 21.1 - - + -
193A ALA* 5.2 2.5 - - + -
197A PHE 5.5 0.4 - - - +
199A GLY* 4.1 11.2 - - - +
201A GLU* 3.6 27.0 + - + +
202A LEU* 3.6 31.9 - - + -
209A TYR* 3.6 24.5 - - + -
210A ASP 3.2 15.0 + - - +
211A TYR 4.6 0.2 - - - -
212A SER* 1.3 76.5 - - - +
214A ASP* 1.3 65.2 + - - +
215A MET 3.1 1.1 + - - -
216A TRP* 3.3 10.9 + - - +
217A SER* 3.1 22.2 + - - +
312A ARG* 4.2 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LEU* 3.7 21.0 - - + +
148A HIS* 2.8 30.3 + - + +
153A MET* 3.6 5.6 - - - +
154A HIS* 2.9 24.4 + - - +
155A ARG* 2.9 28.3 + - - -
157A VAL* 3.7 11.8 + - + +
211A TYR 3.0 10.5 + - - +
213A LEU* 1.3 77.8 - - - +
215A MET* 1.3 58.8 - - - +
217A SER* 3.6 7.1 + - - -
218A LEU* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 3.8 15.7 - - + -
144A LEU* 4.4 8.5 - - - -
148A HIS* 4.5 7.9 - - + -
211A TYR 4.4 10.1 - - - +
212A SER* 3.5 14.1 + - - +
213A LEU 3.1 0.6 - - - -
214A ASP* 1.3 78.3 - - - +
216A TRP* 1.3 59.4 + - - +
218A LEU* 3.5 13.9 + - + +
219A GLY* 3.0 21.3 + - - -
304A LEU* 3.7 35.0 - - + +
312A ARG* 4.8 6.7 - - + -
313A LEU 3.4 28.3 - - - +
314A THR* 3.5 16.8 - - - +
315A ALA* 3.6 24.0 - - - +
318A ALA* 3.9 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PHE 3.9 4.7 - - - -
198A LYS 3.4 12.7 + - - -
199A GLY* 3.4 24.0 - - - -
200A PRO* 3.5 21.1 - - + -
212A SER 3.5 3.4 + - - -
213A LEU* 3.3 9.5 + - - +
215A MET* 1.3 75.9 - - - +
217A SER* 1.3 60.2 + - - +
219A GLY* 2.8 21.5 + - - -
220A CYS* 2.9 26.4 + - - -
233A PHE* 4.1 7.0 - + - -
241A GLN* 5.9 0.4 - - - +
245A ILE* 3.6 45.0 - - + +
249A LEU* 3.8 11.0 - - + -
304A LEU 4.0 8.3 - - - -
305A LEU* 3.6 50.4 - - + +
306A ARG 3.6 22.7 - - - -
307A TYR* 4.8 0.2 - - - -
312A ARG* 3.8 18.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ARG 6.0 0.9 - - - -
157A VAL* 3.4 34.5 + - - +
193A ALA* 5.0 4.3 - - - +
197A PHE* 2.9 34.1 + - - +
213A LEU* 3.1 17.7 + - - +
214A ASP* 3.6 9.7 + - - -
216A TRP* 1.3 78.7 - - - +
218A LEU* 1.3 57.9 + - - +
220A CYS* 3.1 6.9 + - - +
221A MET* 2.9 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A MET* 3.7 33.7 - - + +
140A ILE* 3.8 32.8 - - + -
141A LEU* 3.6 34.3 - - + -
144A LEU* 4.5 5.4 - - + -
157A VAL* 3.9 11.2 - - + +
214A ASP 3.0 18.5 + - - +
215A MET* 3.7 18.8 - - + +
216A TRP 3.2 0.2 - - - -
217A SER* 1.3 72.7 - - - +
219A GLY* 1.3 60.8 + - - +
221A MET* 3.4 7.2 + - + +
222A LEU* 2.9 27.4 + - - +
300A PHE* 4.8 0.9 - - + -
304A LEU* 4.4 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A MET 3.0 9.3 + - - -
216A TRP 2.8 9.5 + - - -
218A LEU* 1.3 76.6 - - - +
220A CYS* 1.3 55.8 + - - -
222A LEU* 3.4 1.7 + - - -
223A ALA* 2.9 26.2 + - - +
301A LEU* 3.2 11.3 - - - +
304A LEU* 3.8 21.7 - - - +
305A LEU* 3.7 17.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A TYR 3.7 14.8 - - - +
197A PHE* 3.7 20.3 - - + -
216A TRP* 2.9 43.2 + - - -
217A SER 3.1 8.0 + - - +
219A GLY* 1.3 72.1 - - - +
221A MET* 1.3 65.3 + - - +
223A ALA* 3.6 6.8 + - - +
224A SER* 3.1 22.7 + - - -
232A PHE* 4.2 6.6 + - + +
233A PHE* 3.6 29.8 - - + +
241A GLN* 5.6 0.4 - - - -
305A LEU* 4.2 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PHE* 3.5 32.5 - - + -
125A TYR* 4.3 3.4 - - + -
137A MET* 4.4 2.2 - - - -
140A ILE* 3.7 21.5 - - + -
157A VAL* 4.7 7.9 - - + -
158A LYS* 3.6 11.4 - - - +
159A PRO* 3.4 45.5 - - + -
162A VAL* 4.6 6.5 - - + -
197A PHE* 3.7 11.2 - - + -
217A SER 2.9 10.9 + - - +
218A LEU* 3.6 11.9 - - + +
219A GLY 3.3 0.2 - - - -
220A CYS* 1.3 73.5 - - - +
222A LEU* 1.3 63.9 - - - +
224A SER* 3.4 7.4 + - - -
225A MET* 3.2 40.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ILE* 4.4 3.4 - - + -
137A MET* 3.6 23.1 - - + -
218A LEU 2.9 18.1 + - - +
219A GLY* 3.6 4.3 - - - +
220A CYS 3.3 0.2 - - - -
221A MET* 1.3 73.9 - - - +
223A ALA* 1.3 63.6 + - - +
225A MET* 2.9 20.5 + - - +
226A ILE* 3.0 26.1 + - + +
297A ALA* 4.4 5.4 - - + +
300A PHE* 3.5 31.6 - - + -
301A LEU* 3.7 30.5 - - + +
304A LEU* 4.2 3.1 - - + -
323A TYR* 3.8 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A GLY 2.9 18.7 + - - +
220A CYS* 3.7 6.3 - - - +
222A LEU* 1.3 74.4 - - - +
224A SER* 1.3 61.7 + - - +
226A ILE* 4.2 6.1 - - - -
227A PHE* 3.3 35.5 + - + +
232A PHE* 3.5 36.7 - - + -
301A LEU* 3.5 17.6 - - + +
305A LEU* 4.4 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A TYR* 3.2 20.3 + - - -
126A GLN* 2.7 31.8 + - - -
197A PHE* 5.9 2.9 - - - -
220A CYS 3.1 13.4 + - - -
221A MET* 3.4 11.4 - - - -
223A ALA* 1.3 77.6 - - - +
225A MET* 1.3 56.6 + - - +
228A ARG* 3.0 23.4 + - - -
229A LYS 3.2 26.9 + - - -
230A GLU* 4.0 1.8 - - - -
231A PRO* 4.9 1.8 - - - -
232A PHE* 4.1 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PHE* 3.6 30.3 - - + -
125A TYR* 3.3 36.1 - - + +
133A ILE* 3.7 36.3 - - + +
137A MET* 3.2 38.8 - - + +
221A MET* 3.2 32.3 + - + +
222A LEU* 2.9 8.2 + - - +
224A SER* 1.3 77.3 - - - +
226A ILE* 1.3 65.2 + - - +
227A PHE 3.6 0.2 + - - -
228A ARG* 3.1 24.3 + - - -
292A LEU* 3.8 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ASP* 5.8 0.2 - - - +
133A ILE* 4.6 6.1 - - + -
222A LEU* 3.0 36.2 + - + +
223A ALA* 3.8 5.8 - - - +
225A MET* 1.3 76.7 - - - +
227A PHE* 1.3 92.0 + - + +
289A ASN* 3.2 18.2 - - - +
292A LEU* 3.4 31.1 - - - +
293A VAL* 3.4 15.2 - - + +
297A ALA* 4.5 19.3 - - + +
298A LEU* 4.5 9.6 - - + -
301A LEU* 4.1 16.6 - - + -
323A TYR* 4.1 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ALA* 3.3 23.3 + - - +
226A ILE* 1.3 100.9 - - + +
228A ARG* 1.3 68.9 + - - +
229A LYS* 3.5 9.6 + - + +
232A PHE* 3.4 26.5 - + + -
281A TRP* 3.7 58.1 - + + -
284A PHE* 3.7 23.6 - - + +
285A VAL* 4.1 13.5 - - + -
288A GLU* 5.0 0.9 - - - +
289A ASN* 2.6 27.0 + - - +
293A VAL* 4.2 12.6 - - + -
298A LEU* 4.0 4.3 - - + -
301A LEU* 4.0 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A TYR 3.0 25.7 + - - -
126A GLN* 2.9 40.9 + - - +
127A THR* 3.5 4.4 - - - +
128A LEU 2.7 39.6 + - - +
133A ILE* 4.1 5.7 - - - +
224A SER 3.0 12.5 + - - -
225A MET 3.1 17.6 + - - -
226A ILE 3.5 0.6 - - - -
227A PHE* 1.3 81.1 - - - +
229A LYS* 1.3 59.2 + - - +
230A GLU 4.1 0.7 + - - -
288A GLU* 5.0 13.2 + - + +
289A ASN* 4.3 8.3 - - + +
291A HIS* 5.3 2.0 + - - -
292A LEU* 3.3 31.7 - - + +
----------------------------------------------------------
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