Contacts of the helix formed by residues 209 - 225 (chain A) in PDB entry 7CE1
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 ALA 209 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ILE* 3.0 19.0 + - + +
145A GLU 4.2 8.5 - - - -
146A PRO* 4.1 14.1 - - + +
165A GLY* 6.1 0.2 - - - -
166A ARG 3.4 27.6 - - - +
167A SER* 5.3 0.2 - - - -
168A ASP 6.0 0.4 - - - +
207A ARG 4.0 0.6 + - - -
208A PHE* 1.3 72.6 - - - +
210A PHE* 1.3 63.2 + - + +
211A HIS 3.1 1.6 + - - -
212A ASP* 3.3 17.1 + - - +
213A HIS* 3.7 22.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LYS* 6.5 0.7 - - - -
144A ILE 5.5 0.4 - - - -
177A ASP* 5.1 6.7 - - - +
180A ASN* 3.4 27.5 - - - +
204A PRO* 3.4 31.6 - - + -
205A PRO* 4.8 4.0 - - + -
208A PHE* 3.4 33.0 - + + -
209A ALA* 1.3 76.0 - - + +
211A HIS* 1.3 60.4 + - - +
212A ASP 3.2 0.2 - - - -
213A HIS* 3.2 22.7 + - + +
214A ALA* 2.8 32.1 + - - +
237A ILE* 6.0 0.9 - - + -
238A GLU* 5.6 3.1 - - - -
264A ILE* 3.8 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A VAL* 3.2 26.2 - - + +
204A PRO* 2.5 37.8 + - + +
205A PRO 3.1 24.1 + - - +
206A SER* 4.0 22.2 - - - -
208A PHE 3.4 9.5 + - - +
209A ALA 3.1 0.4 - - - -
210A PHE* 1.3 81.8 - - - +
212A ASP* 1.3 80.5 + - - +
214A ALA* 3.4 4.0 + - - +
215A ARG* 3.1 32.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A PRO* 4.8 9.7 - - - +
206A SER 4.6 5.0 - - - +
208A PHE 4.3 6.1 - - - +
209A ALA 3.3 10.6 + - - +
210A PHE 3.2 0.2 - - - -
211A HIS* 1.3 92.7 + - - +
213A HIS* 1.3 68.9 + - + +
215A ARG* 4.0 5.1 - - - +
216A LYS* 3.1 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ARG* 3.9 49.8 + - + +
177A ASP* 3.9 11.0 + - - -
178A PHE 5.6 0.8 + - - -
180A ASN* 4.7 4.7 - - + +
181A GLU* 3.3 41.6 - - + +
209A ALA* 3.9 22.0 + - + +
210A PHE* 3.1 29.2 + - + +
212A ASP* 1.3 82.3 - - + +
214A ALA* 1.3 61.7 + - - +
216A LYS* 3.5 2.8 + - - +
217A GLY 3.5 8.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ASN* 4.3 14.1 - - + +
184A ALA* 3.4 8.7 - - - +
201A ILE* 4.1 8.5 - - + +
203A VAL* 5.0 0.9 - - + -
204A PRO* 4.2 10.1 - - + -
210A PHE 2.8 18.7 + - - +
211A HIS 3.6 4.9 - - - +
213A HIS* 1.3 74.3 - - - +
215A ARG* 1.3 56.7 + - - +
217A GLY 3.4 1.9 + - - -
218A PHE* 3.1 26.3 + - - +
264A ILE* 3.9 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ILE* 3.4 29.1 - - - +
203A VAL* 4.7 19.5 - - + +
211A HIS* 3.1 24.5 + - + +
212A ASP* 3.4 7.8 + - - +
213A HIS 3.3 0.2 - - - -
214A ALA* 1.3 76.4 - - - +
216A LYS* 1.3 56.1 + - - +
218A PHE* 3.9 9.4 - - - +
219A THR* 2.6 50.6 + - - +
229A GLU* 2.6 40.0 + - - -
231A PRO* 5.5 1.4 - - - +
232A LEU 5.6 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A GLU* 4.3 18.2 - - + +
212A ASP 3.1 17.1 + - - +
213A HIS* 3.7 6.5 - - - +
214A ALA 3.2 0.2 - - - -
215A ARG* 1.3 75.6 - - - +
217A GLY* 1.3 59.3 + - - +
219A THR* 3.4 4.9 + - - -
220A ARG* 3.0 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A GLU* 3.3 31.1 - - - +
184A ALA* 3.7 8.1 - - - -
185A TYR* 3.5 13.1 - - - +
213A HIS 3.5 4.8 + - - -
214A ALA 3.4 5.8 + - - -
216A LYS* 1.3 79.3 - - - +
218A PHE* 1.3 52.8 + - - +
220A ARG* 3.8 3.3 - - - -
221A GLY* 2.7 31.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ALA* 3.5 10.0 - - + +
188A VAL* 3.3 33.9 - - + -
199A ILE* 3.4 28.5 - - + -
200A ALA 3.8 3.6 - - - -
201A ILE* 3.5 49.8 - - + -
214A ALA 3.1 16.9 + - - +
215A ARG* 3.9 11.9 - - - +
217A GLY* 1.3 76.6 - - - +
219A THR* 1.3 58.4 + - - +
221A GLY* 3.7 1.2 - - - -
222A ILE* 2.9 40.8 + - + +
229A GLU* 3.8 32.1 - - + -
262A VAL* 3.9 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A ARG* 2.6 39.2 + - - +
216A LYS* 3.9 5.2 - - - -
217A GLY 3.3 0.2 - - - -
218A PHE* 1.3 74.4 - - - +
220A ARG* 1.3 63.7 + - - +
222A ILE* 3.6 5.2 + - - +
223A ARG* 3.2 22.6 + - + +
229A GLU* 5.7 3.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A GLU* 2.3 48.5 + - - +
182A ALA* 6.0 0.6 - - - +
185A TYR* 5.0 10.7 - - + +
216A LYS* 3.0 15.7 + - - +
217A GLY* 4.2 9.8 - - - +
219A THR* 1.3 75.3 - - - +
221A GLY* 1.3 60.0 + - - +
223A ARG* 3.5 28.4 - - - +
224A ASP* 2.9 48.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
185A TYR* 4.5 10.3 - - - +
188A VAL* 4.0 20.8 - - - +
217A GLY 2.7 20.9 + - - -
218A PHE 3.7 1.6 - - - -
219A THR 3.2 0.2 - - - -
220A ARG* 1.3 78.6 - - - +
222A ILE* 1.3 55.4 + - - +
224A ASP* 4.6 2.2 - - - +
225A PHE* 3.2 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A VAL* 4.4 7.6 - - + -
199A ILE* 4.2 19.7 - - + -
218A PHE* 2.9 31.3 + - + +
219A THR* 4.0 5.4 - - - +
221A GLY* 1.3 75.9 - - - +
223A ARG* 1.3 62.3 + - - +
226A GLY* 3.3 12.5 + - - -
227A VAL* 3.0 58.4 + - + +
228A SER* 4.3 1.1 - - - +
229A GLU* 3.8 42.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A THR* 3.2 17.2 + - + +
220A ARG* 3.5 28.1 - - - +
222A ILE* 1.3 79.3 - - - +
224A ASP* 1.3 74.9 + - - +
226A GLY* 3.3 12.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ARG* 2.9 34.7 + - - +
221A GLY* 4.6 2.0 - - - +
223A ARG* 1.3 95.7 + - - +
225A PHE* 1.3 58.9 + - - +
226A GLY 3.2 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A VAL* 5.2 5.2 - - + +
189A GLU* 5.2 7.2 - - + -
192A ALA* 4.2 16.9 - - + +
221A GLY 3.2 20.4 + - - +
224A ASP* 1.3 77.4 - - - +
226A GLY* 1.3 63.8 + - - +
227A VAL* 3.1 25.2 + - + +
----------------------------------------------------------
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