Contacts of the helix formed by residues 205 - 229 (chain A) in PDB entry 5F0P
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 205 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A HIS* 3.2 29.2 + - - +
204A ARG* 1.3 89.9 + - - +
206A ARG* 1.3 57.5 + - - +
207A GLU 3.4 2.7 - - - +
208A LYS* 3.6 41.6 + - + +
209A ARG* 3.0 40.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A GLN* 4.8 12.8 + - - +
203A SER* 4.0 35.0 + - - +
204A ARG 3.3 4.4 + - - -
205A ASP* 1.3 77.5 - - - +
207A GLU* 1.3 60.9 + - - +
209A ARG* 3.8 25.6 - - - +
210A GLU* 3.3 42.5 + - - +
28C PHE* 5.9 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ARG 5.1 0.8 + - - +
205A ASP* 3.4 0.6 - - - +
206A ARG* 1.3 77.4 - - - +
208A LYS* 1.3 62.8 + - - +
210A GLU* 3.8 6.4 + - - +
211A ARG* 3.3 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ASP* 3.5 39.9 + - + +
206A ARG 3.4 0.4 - - - -
207A GLU* 1.3 76.4 - - - +
209A ARG* 1.3 59.4 + - - +
211A ARG* 3.2 36.5 + - - +
212A GLU* 2.8 53.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A MET* 3.0 28.3 - - + +
198A GLN* 3.1 23.8 + - - +
199A HIS* 5.2 1.8 - - - +
200A GLN* 2.7 33.0 + - + +
201A GLY* 3.5 8.8 + - - -
202A HIS 2.9 30.1 + - - +
203A SER* 3.9 11.3 - - - +
205A ASP* 3.0 21.8 + - + +
206A ARG* 3.8 36.3 - - - +
207A GLU 3.4 0.2 - - - -
208A LYS* 1.3 76.0 - - - +
210A GLU* 1.3 53.2 + - - +
212A GLU* 2.9 20.2 + - - +
213A ARG* 2.7 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A GLN* 3.3 34.1 + - - +
206A ARG* 3.3 28.4 + - - +
207A GLU* 4.2 6.4 - - - +
209A ARG* 1.3 77.9 - - - +
211A ARG* 1.3 56.8 + - - +
213A ARG* 4.0 7.2 - - - +
214A GLN* 3.1 33.7 + - + +
257A LEU* 4.1 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A GLU* 3.3 18.2 + - - +
208A LYS* 3.2 47.6 + - - +
209A ARG 3.1 0.4 - - - -
210A GLU* 1.3 76.6 - - - +
212A GLU* 1.3 62.9 + - + +
214A GLN* 3.3 7.6 + - - +
215A GLU* 3.2 36.9 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
59A SER* 4.8 3.6 - - - -
60A PRO* 3.2 38.7 - - + +
197A MET* 5.9 3.1 - - + -
208A LYS* 2.8 38.9 + - + +
209A ARG* 2.9 24.2 + - - +
211A ARG* 1.3 71.4 - - + +
213A ARG* 1.3 65.1 + - + +
215A GLU* 3.3 25.9 + - - +
216A LEU* 3.4 19.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A TRP* 3.0 64.0 + - - +
195A VAL* 3.7 14.9 - - - +
197A MET* 3.8 22.6 - - + +
198A GLN* 2.9 42.5 + - - +
209A ARG* 2.7 22.5 + - + +
210A GLU 4.0 0.2 - - - +
212A GLU* 1.3 73.5 - - + +
214A GLN* 1.3 62.9 + - - +
216A LEU* 3.1 13.1 + - - +
217A ARG 3.2 4.0 + - - -
255A ASP* 2.9 41.4 + - - -
257A LEU* 3.7 28.5 - - + +
258A ALA* 3.9 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A GLU 3.1 22.2 + - - +
211A ARG* 3.5 8.5 - - - +
212A GLU 3.3 0.2 - - - -
213A ARG* 1.3 78.2 - - - +
215A GLU* 1.3 62.6 + - + +
217A ARG* 3.2 65.0 + - - +
257A LEU* 3.2 30.8 - - + +
260A GLU* 6.0 0.2 + - - -
261A TYR* 5.8 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PRO* 3.8 18.6 - - + +
61A LYS* 4.4 27.6 + - + +
211A ARG* 3.2 29.0 + - + +
212A GLU* 3.5 19.8 - - - +
213A ARG 3.3 0.2 - - - -
214A GLN* 1.3 78.6 - - + +
216A LEU* 1.3 63.7 + - + +
217A ARG* 3.5 3.0 + - - +
218A ILE* 4.4 12.3 + - - +
219A LEU* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PRO* 4.2 20.6 - - + +
64A TYR* 5.8 1.1 - - + -
144A LEU* 3.8 9.0 - - + -
147A LEU* 4.2 14.5 - - + +
148A PHE* 3.7 33.7 - - + -
194A TRP* 4.5 4.3 - - - +
197A MET* 3.4 40.8 - - + -
212A GLU 3.4 13.0 + - - +
213A ARG 3.1 8.5 + - - +
215A GLU* 1.3 78.1 - - + +
217A ARG* 1.3 62.0 + - - +
218A ILE 3.2 3.1 - - - -
219A LEU* 3.1 31.7 + - + +
220A VAL* 4.0 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A TRP* 3.6 30.7 - - + -
213A ARG 3.2 3.6 + - - +
214A GLN* 3.2 45.2 + - - +
215A GLU* 3.4 3.0 + - - +
216A LEU* 1.3 75.9 - - - +
218A ILE* 1.3 67.2 + - + +
220A VAL* 3.3 4.4 + - - +
221A GLY 3.1 17.3 + - - -
257A LEU* 5.8 0.2 - - - -
261A TYR* 3.2 46.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TYR* 6.6 0.2 - - + -
215A GLU 4.4 11.6 + - - +
217A ARG* 1.3 85.5 - - + +
219A LEU* 1.3 70.1 + - + +
222A THR* 2.6 46.9 + - - +
261A TYR* 3.9 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TYR* 5.5 6.7 - - + -
147A LEU* 4.0 28.5 - - + +
148A PHE* 3.7 47.8 - - + -
151A ASN* 4.2 23.5 + - + +
154A LEU* 5.0 0.7 - - - +
190A MET* 3.4 23.7 - - + +
215A GLU 5.5 0.2 - - - +
216A LEU* 3.1 25.5 + - + +
218A ILE* 1.3 93.2 - - + +
220A VAL* 1.3 61.3 + - - +
222A THR* 3.8 11.8 + - - -
223A ASN* 3.7 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LEU* 3.9 16.8 - - + -
187A PHE* 3.8 28.3 - - + -
190A MET* 4.0 7.0 - - - +
191A ASN* 3.9 20.4 - - + +
194A TRP* 3.6 44.4 - - + -
216A LEU 4.0 3.1 + - - +
217A ARG 3.3 8.2 + - - +
218A ILE 3.3 0.4 - - - -
219A LEU* 1.3 75.9 - - - +
221A GLY* 1.3 62.4 + - - +
223A ASN* 3.1 28.5 + - - +
224A LEU 4.4 0.2 + - - -
262A LEU* 4.0 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ARG 3.1 10.1 + - - -
218A ILE* 3.3 1.3 + - - -
220A VAL* 1.3 74.2 - - - +
222A THR* 1.3 57.7 + - - +
223A ASN 3.1 2.9 - - - -
224A LEU* 3.0 26.9 + - - +
225A VAL* 3.1 17.2 + - - +
261A TYR* 3.6 26.6 - - - -
262A LEU* 5.1 1.3 - - - -
265A CYS* 4.1 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ASN* 4.8 5.7 + - - +
154A LEU* 3.8 11.7 - - + -
155A GLN* 3.3 26.5 - - - +
218A ILE* 2.6 31.3 + - - +
219A LEU* 3.9 9.6 + - - -
220A VAL 3.3 0.4 - - - -
221A GLY* 1.3 74.9 - - - +
223A ASN* 1.3 56.6 + - - +
225A VAL* 3.3 16.3 + - + +
226A ARG* 2.8 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 3.4 18.3 - - - +
183A VAL* 3.2 20.5 - - + +
186A ASN* 3.0 24.3 + - - +
187A PHE* 3.6 37.6 + - + +
190A MET* 3.2 28.9 - - - +
219A LEU 3.7 3.6 + - - -
220A VAL* 3.1 22.5 + - - +
221A GLY 3.1 0.4 - - - -
222A THR* 1.3 78.4 - - - +
224A LEU* 1.3 58.8 + - - +
226A ARG* 3.4 0.9 + - - -
227A LEU* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A PHE* 3.9 28.9 - - + -
221A GLY* 3.0 13.0 + - - +
223A ASN* 1.3 74.3 - - - +
225A VAL* 1.3 66.2 + - - +
227A LEU* 3.2 19.9 + - + +
228A SER 3.2 9.4 + - - -
246A ILE* 3.6 33.7 - - + -
262A LEU* 4.1 22.4 - - + +
265A CYS* 4.0 28.3 - - + -
266A ILE* 4.2 17.3 - - + +
269A VAL* 3.4 11.2 - - + +
270A PHE* 3.9 11.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A GLY 3.1 11.9 + - - +
222A THR* 3.4 18.8 - - + +
224A LEU* 1.3 77.8 - - - +
226A ARG* 1.3 60.2 + - - +
228A SER* 2.8 20.5 + - - +
229A GLN* 3.3 31.1 - - + +
265A CYS* 5.3 1.3 - - - -
269A VAL* 3.7 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 4.0 30.3 + - + -
158A ARG* 2.7 46.9 + - - +
159A ASN 5.3 0.2 - - - -
161A LEU* 3.6 29.0 + - + +
163A ASP* 5.3 2.0 + - - -
183A VAL* 4.1 13.2 - - + -
222A THR* 2.8 19.3 + - + +
223A ASN 3.5 7.2 - - - +
224A LEU 3.2 0.2 - - - -
225A VAL* 1.3 78.8 - - - +
227A LEU* 1.3 60.8 + - - +
229A GLN* 3.3 38.7 + - - +
230A LEU* 3.6 24.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A MET* 4.4 22.2 - - + +
183A VAL* 3.7 25.6 - - + +
184A LEU* 4.1 20.6 - - + +
187A PHE* 5.6 1.1 - - + -
223A ASN* 3.1 20.2 + - + +
224A LEU* 3.2 17.4 + - + +
226A ARG* 1.3 78.3 - - - +
228A SER* 1.3 60.1 + - - +
230A LEU* 3.5 14.9 + - + +
233A VAL* 3.5 28.2 - - + +
242A VAL* 4.0 37.5 - - + -
246A ILE* 4.2 6.5 - - + -
270A PHE* 4.2 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A LEU 3.2 3.4 + - - -
225A VAL* 2.8 19.9 + - - +
227A LEU* 1.3 78.1 - - - +
229A GLN* 1.3 63.4 + - - +
230A LEU 3.2 6.5 + - - +
233A VAL* 5.6 2.1 - - - +
269A VAL* 3.3 39.7 + - - +
270A PHE* 3.9 19.0 - - - -
271A PRO* 5.5 3.4 - - - -
274A PHE* 6.2 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ARG* 4.7 12.3 - - - +
163A ASP* 4.2 4.0 - - - +
225A VAL* 3.3 32.4 + - + +
226A ARG* 3.6 39.5 + - - +
227A LEU 3.3 0.6 - - - -
228A SER* 1.3 78.4 + - - +
230A LEU* 1.3 61.8 + - - +
231A GLU* 3.2 6.1 + - - +
----------------------------------------------------------
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