Contacts of the helix formed by residues 208 - 225 (chain A) in PDB entry 4EC9
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 208 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A HIS* 3.5 37.5 - - + +
146A LEU* 3.7 14.8 - - + -
174A PHE* 3.7 36.1 - - + -
207A GLY* 1.3 80.7 - - - +
209A PRO* 1.3 66.6 - - + +
210A ILE* 5.1 0.2 - - + -
211A ASP* 2.8 27.3 + - + +
212A LEU* 3.4 9.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A GLU* 4.1 7.0 - - - +
207A GLY* 3.1 10.1 - - - +
208A PRO* 1.3 96.3 - - + +
210A ILE* 1.3 61.1 + - - +
212A LEU* 2.9 27.7 + - + +
213A TRP 3.0 4.5 + - - -
300A PRO* 3.9 28.7 - - + +
301A ALA* 5.9 0.7 - - - -
303A ARG* 2.9 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU* 5.0 3.1 - - + -
148A ARG* 3.9 31.0 - - + -
150A MET* 5.0 1.7 - - - +
189A VAL* 5.4 0.7 - - + -
190A VAL* 5.0 6.6 - - + +
194A TYR 4.9 0.7 - - - +
196A PRO* 3.6 29.3 - - + +
198A GLU* 3.3 19.3 - - - +
199A LEU* 4.4 16.8 - - + -
206A TYR* 3.9 33.4 - - + -
207A GLY 3.3 18.1 + - - +
208A PRO* 2.9 1.6 + - + -
209A PRO* 1.3 75.5 - - - +
211A ASP* 1.3 82.3 + - - +
213A TRP* 3.5 13.5 - - - +
214A GLY* 3.6 4.7 + - - -
303A ARG* 4.3 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 4.0 9.1 - - + +
140A ILE* 4.3 1.6 - - - +
141A HIS* 3.4 25.0 + - + +
146A LEU* 3.7 4.1 - - - +
147A HIS* 2.8 34.4 + - - +
148A ARG* 3.0 25.3 + - - -
150A MET* 3.4 31.1 - - + +
208A PRO* 2.8 11.3 + - - +
210A ILE* 1.3 91.2 - - - +
212A LEU* 1.3 61.3 + - - +
214A GLY 3.5 0.3 + - - -
215A ALA* 3.4 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU* 4.1 17.7 - - + -
137A LEU* 4.6 5.2 - - + -
141A HIS* 4.4 12.3 - - + +
208A PRO* 3.4 7.8 + - + +
209A PRO* 2.9 28.1 + - + +
211A ASP* 1.3 77.5 - - - +
213A TRP* 1.3 64.6 + - - +
215A ALA* 3.2 8.5 - - - +
216A GLY* 3.1 16.5 + - - -
295A LEU* 3.9 18.1 - - + +
303A ARG* 4.5 7.0 - - - +
304A ILE 3.5 23.1 - - - +
305A ASP* 3.5 18.4 - - + -
306A SER* 3.6 30.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A TRP 5.1 0.4 + - - -
194A TYR 3.0 27.7 + - - -
195A ARG 3.6 9.3 + - - -
196A PRO* 3.5 16.8 - - + -
197A PRO* 3.8 20.2 - - + -
209A PRO 3.0 4.8 + - - -
210A ILE 3.5 9.0 - - - +
212A LEU* 1.3 75.3 - - - +
214A GLY* 1.3 57.5 + - - +
216A GLY* 2.8 23.4 + - - -
217A CYS* 3.2 14.4 + - - -
229A MET* 4.4 14.9 - - + +
241A ILE* 4.1 23.1 - - + -
245A CYS* 4.4 19.7 - - - -
295A LEU 4.2 6.3 - - - -
296A LEU* 3.5 33.0 - - + +
297A VAL 3.6 18.2 - - - -
298A LEU* 4.8 3.4 - - + -
303A ARG* 3.5 36.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A MET* 4.0 21.5 - - - -
194A TYR* 3.9 23.4 + - - -
210A ILE 3.6 4.2 + - - -
211A ASP 3.5 6.5 + - - -
212A LEU 3.3 0.6 - - - -
213A TRP* 1.3 78.1 - - - +
215A ALA* 1.3 54.9 + - - +
217A CYS* 2.8 25.6 + - - +
218A ILE* 2.9 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A MET* 4.4 5.9 - - + +
133A LEU* 4.2 24.0 - - + -
134A LEU* 4.7 7.4 - - + -
137A LEU* 4.2 4.3 - - + -
150A MET* 3.8 10.0 - - + +
211A ASP 3.4 11.6 + - - +
212A LEU* 3.2 15.0 + - - +
214A GLY* 1.3 75.7 - - - +
216A GLY* 1.3 67.1 + - - +
218A ILE* 3.2 6.1 + - - +
219A MET* 2.9 20.8 + - - +
295A LEU* 4.2 10.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A LEU 3.1 7.1 + - - -
213A TRP 2.8 11.5 + - - -
215A ALA* 1.3 74.7 - - - +
217A CYS* 1.3 56.1 + - - -
219A MET* 2.8 22.4 + - - +
220A ALA* 3.2 11.1 + - - +
292A ILE* 4.6 3.2 - - - +
295A LEU* 3.7 23.4 - - - +
296A LEU* 3.5 21.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A TRP 4.0 11.9 - - - +
194A TYR* 3.7 16.6 - - + -
213A TRP* 3.8 28.5 - - - -
214A GLY* 2.8 14.1 + - - +
216A GLY* 1.3 71.4 - - - -
218A ILE* 1.3 57.5 + - - +
220A ALA* 3.7 4.2 + - - +
221A GLU* 3.1 27.5 + - - +
227A PRO* 6.5 0.4 - - + -
228A ILE* 3.8 21.4 - - + +
229A MET* 3.7 28.7 - - - -
296A LEU* 3.7 4.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
110A LEU* 4.2 25.4 - - + -
114A LEU* 5.6 0.2 - - + -
129A VAL* 6.3 0.2 - - + -
130A MET* 5.0 4.3 - - - -
133A LEU* 4.5 14.4 - - + -
150A MET* 3.4 33.0 - - + -
151A LYS* 3.9 24.7 - - - +
152A ALA* 4.0 10.1 - - + +
155A VAL* 4.7 6.5 - - + -
194A TYR* 3.4 19.3 - - + +
214A GLY 2.9 10.7 + - - +
215A ALA* 3.7 6.7 - - - +
217A CYS* 1.3 74.7 - - - +
219A MET* 1.3 60.7 + - - +
221A GLU* 2.7 29.5 + - + +
222A MET* 3.0 13.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A MET* 3.3 50.0 - - + -
134A LEU* 4.8 2.0 - - + -
215A ALA 2.9 10.8 + - - +
216A GLY* 2.8 11.9 + - - +
218A ILE* 1.3 75.6 - - - +
220A ALA* 1.3 64.3 + - - +
222A MET* 2.8 27.7 + - + +
223A TRP* 3.2 20.8 - - + -
288A ALA* 4.2 5.4 - - - +
291A LEU* 3.4 39.7 - - + -
292A ILE* 3.2 32.5 - - + -
295A LEU* 3.8 10.3 - - + -
314A PHE* 4.7 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A GLY 3.2 4.9 + - - +
217A CYS 3.8 4.7 - - - +
219A MET* 1.3 78.9 - - - +
221A GLU* 1.3 57.9 + - - +
223A TRP* 2.9 23.3 + - - +
224A THR* 3.0 17.6 + - - +
228A ILE* 3.5 31.2 - - + -
279A LEU* 3.8 25.8 - - + -
283A VAL* 6.3 0.2 - - - -
292A ILE* 3.5 14.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ALA* 5.8 0.7 - - - +
114A LEU* 3.3 25.3 - - + +
152A ALA* 3.8 13.4 - - - +
194A TYR* 2.8 32.8 + - - -
217A CYS 3.1 15.3 + - - +
218A ILE* 2.7 18.6 + - - +
220A ALA* 1.3 72.2 - - - +
222A MET* 1.3 57.5 - - - +
223A TRP 3.0 0.2 - - - -
224A THR* 3.6 8.5 - - - -
225A ARG* 2.9 25.4 + - - -
226A SER* 3.7 16.6 - - - +
227A PRO* 3.5 31.7 - - - +
228A ILE* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 3.9 28.0 - - + -
114A LEU* 3.9 15.3 - - - +
121A PHE* 4.0 33.3 - - + -
126A ILE* 3.9 47.2 - - + +
129A VAL* 4.2 21.8 - - + -
130A MET* 4.8 8.1 - - - -
218A ILE* 3.5 8.7 - - - +
219A MET* 2.8 21.5 + - - +
221A GLU* 1.3 78.9 - - - +
223A TRP* 1.3 66.2 + - + +
225A ARG* 3.9 15.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 4.1 20.0 - - + +
126A ILE* 3.8 38.1 - - + +
219A MET* 3.2 46.7 - - + -
220A ALA* 2.9 7.8 + - - +
222A MET* 1.3 86.5 - - + +
224A THR* 1.3 62.1 + - + +
225A ARG* 3.0 17.4 + - - +
282A TYR* 3.5 44.3 - - + +
283A VAL* 3.5 36.4 - - + +
284A ARG 4.7 3.0 - - - +
285A ASP* 5.9 0.4 - - + -
288A ALA* 4.1 13.0 - - + -
292A ILE* 4.4 3.8 - - + -
314A PHE* 4.9 3.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ALA 3.0 15.1 + - - +
221A GLU* 3.6 1.6 - - - -
223A TRP* 1.3 75.2 - - - +
225A ARG* 1.3 67.9 + - - +
226A SER* 2.6 38.0 + - - -
228A ILE* 3.5 12.9 - - + +
279A LEU* 3.8 22.7 - - + -
282A TYR* 3.8 38.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU 3.4 14.6 + - - -
114A LEU* 3.1 38.9 + - - +
115A SER* 5.0 2.4 - - - -
116A ASN 3.1 23.0 + - - -
117A VAL* 4.3 6.7 + - - +
119A VAL* 2.8 32.7 + - - +
120A LYS* 4.3 4.8 - - - +
121A PHE* 4.1 19.7 - - - +
221A GLU* 2.9 17.7 + - - -
222A MET 3.9 16.9 + - - -
223A TRP 3.2 13.2 - - - +
224A THR* 1.3 77.5 - - - +
226A SER* 1.3 59.9 + - - +
----------------------------------------------------------
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