Contacts of the helix formed by residues 207 - 223 (chain B) in PDB entry 3HAD
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 VAL 207 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ALA* 3.5 30.1 - - + +
236A MET* 4.0 14.1 - - + +
239A GLY 4.4 15.9 - - - +
240A ALA 4.8 0.9 - - - +
160B PHE* 3.6 24.0 - - + -
168B LEU* 3.6 17.9 - - + -
170B GLU* 2.9 17.4 + - - +
206B ILE* 1.3 78.7 - - - +
208B ASN* 1.3 62.6 + - - +
210B LEU* 3.2 2.1 + - - +
211B LEU* 2.8 46.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B SER* 4.3 10.2 + - - -
158B HIS* 3.4 34.1 + - - -
160B PHE* 4.4 5.5 - - - -
170B GLU* 4.9 0.2 + - - -
204B GLY* 3.4 17.3 + - - +
205B PHE* 5.9 1.0 - - - -
207B VAL* 1.3 79.9 - - - +
209B ARG* 1.3 66.1 + - - +
211B LEU* 4.2 12.9 - - - +
212B VAL* 2.9 48.7 + - + +
213B PRO* 3.4 0.7 - - - +
261B ILE* 5.2 10.6 - - + +
265B TRP* 3.6 6.6 - - + -
750B NAD 5.8 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLU* 3.0 35.8 + - - +
221A LEU* 4.2 14.1 - - + -
224A ARG* 3.8 30.1 - - - +
202B THR* 6.1 0.2 - - - +
203B PRO* 3.2 26.5 + - - +
204B GLY* 3.0 13.4 + - - +
205B PHE 3.0 25.1 - - - +
206B ILE 3.2 2.9 + - - +
208B ASN* 1.3 77.5 - - - +
210B LEU* 1.3 59.7 + - + +
213B PRO* 2.9 29.2 - - - +
265B TRP* 4.5 12.1 - - - -
272B ASN* 5.6 5.7 - - - +
274B LEU* 5.0 3.7 - - - +
275B HIS* 5.6 11.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A TYR* 3.6 33.5 - - + +
217A GLU* 3.7 42.0 - - + +
218A ALA* 3.8 14.6 - - + +
221A LEU* 4.3 14.4 - - + -
232A ILE* 3.7 29.8 - - + -
236A MET* 4.0 16.7 - - - +
242A TYR* 5.5 0.7 + - - -
206B ILE* 3.0 20.5 + - + +
207B VAL 4.0 1.6 - - - +
209B ARG* 1.3 87.1 - - + +
211B LEU* 1.3 58.4 + - - +
213B PRO* 4.2 4.2 - - - +
214B TYR* 3.9 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A MET* 4.6 6.3 - - + -
239A GLY 5.6 1.1 - - - +
240A ALA* 4.9 12.1 - - + -
242A TYR* 3.6 24.9 - - + +
207B VAL* 2.8 31.3 + - + +
208B ASN* 4.3 10.8 - - - +
210B LEU* 1.3 79.0 - - - +
212B VAL* 1.3 69.3 + - + +
213B PRO 3.4 0.4 - - - -
214B TYR* 3.1 17.8 + - + +
215B LEU* 3.0 33.6 + - + +
249B LEU* 3.9 30.5 - - + -
253B VAL* 5.7 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ASN* 2.9 42.6 + - + +
211B LEU* 1.3 73.3 - - + +
213B PRO* 1.3 68.5 - - + +
215B LEU* 2.9 14.0 + - + +
216B MET* 2.9 20.2 + - + +
258B THR* 4.1 19.1 - - + +
261B ILE* 4.8 12.3 - - + -
262B VAL* 3.6 30.3 - - + -
265B TRP* 3.6 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLU* 5.5 5.4 - - + +
208B ASN 3.4 2.5 - - - +
209B ARG* 2.9 33.4 - - - +
210B LEU* 4.2 6.1 - - - +
212B VAL* 1.3 93.2 - - + +
214B TYR* 1.3 57.3 + - - +
216B MET* 3.3 10.8 + - + +
217B GLU* 2.9 33.7 + - - +
220B ARG* 4.6 0.5 + - - -
265B TRP* 3.9 13.5 - - + -
274B LEU* 4.1 36.5 - - + +
275B HIS* 5.2 3.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A LEU* 3.7 44.4 - - + +
214A TYR* 4.6 15.7 - + + -
242A TYR* 3.9 17.0 - - - -
210B LEU 3.9 12.3 - - - +
211B LEU* 3.1 23.8 + - + +
213B PRO* 1.3 80.6 - - - +
215B LEU* 1.3 77.6 + - + +
217B GLU* 3.1 9.0 + - - +
218B ALA* 3.0 23.4 + - - +
236B MET* 3.5 17.6 - - + +
242B TYR* 3.6 19.3 - + - -
244B MET 5.0 0.2 + - - -
246B PRO* 3.2 34.2 - - + +
249B LEU* 5.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B LEU* 3.0 34.4 + - + +
212B VAL* 2.9 16.9 + - + +
214B TYR* 1.3 100.3 - - + +
216B MET* 1.3 62.1 + - + +
218B ALA* 3.2 7.4 + - - +
219B ILE* 3.1 27.0 + - - +
246B PRO* 3.7 31.9 - - + +
249B LEU* 4.1 20.0 - - + -
250B LEU* 3.9 27.8 - - + +
253B VAL* 5.0 7.9 - - + -
258B THR* 5.3 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B VAL* 2.9 18.6 + - + +
213B PRO* 3.6 6.3 - - + +
214B TYR 3.3 0.2 - - - -
215B LEU* 1.3 73.0 - - - +
217B GLU* 1.3 68.0 + - - +
219B ILE* 3.2 13.9 + - + +
220B ARG* 2.9 45.5 + - + +
258B THR* 4.5 6.3 - - - -
262B VAL* 3.7 36.8 - - + -
265B TRP* 6.4 0.2 - - + -
274B LEU 4.2 8.7 - - - +
276B GLN 3.8 21.5 - - - +
278B SER* 3.9 26.9 - - - +
281B LEU* 3.7 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ARG* 2.8 41.2 + - - +
210A LEU* 3.8 17.6 - - + +
213A PRO* 5.7 5.8 - - + +
274A LEU* 4.1 10.2 - - - +
213B PRO 2.9 18.1 + - - +
214B TYR* 3.1 12.3 + - - +
216B MET* 1.3 78.2 - - - +
218B ALA* 1.3 61.4 + - - +
220B ARG* 2.6 42.0 + - - +
221B LEU* 2.9 22.7 + - - +
224B ARG* 5.1 1.4 + - - -
273B PRO 5.2 0.7 - - - +
274B LEU* 4.1 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A LEU* 3.7 22.1 - - + +
214B TYR* 3.0 12.2 + - + +
215B LEU 3.4 8.7 - - - +
216B MET 3.2 0.2 - - - -
217B GLU* 1.3 76.4 - - - +
219B ILE* 1.3 63.2 + - + +
221B LEU* 3.2 4.9 + - - +
222B TYR 3.1 16.8 + - - -
232B ILE* 4.1 1.9 - - + +
246B PRO* 3.5 37.5 - - + -
247B PHE* 3.5 15.5 - - + -
250B LEU* 5.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU 3.1 12.7 + - - +
216B MET* 3.5 28.9 - - + +
218B ALA* 1.3 76.7 - - - +
220B ARG* 1.3 50.9 + - - +
222B TYR* 3.0 5.9 + - + +
223B GLU* 2.7 46.8 + - + +
247B PHE* 3.9 11.2 - - + -
250B LEU* 3.6 30.5 - - + -
278B SER* 3.1 29.2 - - - +
280B SER* 4.6 4.0 - - - -
281B LEU* 4.3 13.7 - - + -
298B PHE* 4.0 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B PRO 4.6 0.2 + - - -
216B MET* 2.9 47.6 + - + +
217B GLU* 2.6 43.5 + - - +
219B ILE* 1.3 74.0 - - + +
221B LEU* 1.3 64.0 + - - +
223B GLU* 3.2 16.1 + - - +
224B ARG* 2.9 42.7 + - - +
273B PRO 3.3 12.5 + - - -
274B LEU* 2.9 27.9 + - - +
275B HIS 3.8 0.2 - - - -
276B GLN* 2.8 40.6 + - - +
277B PRO 5.5 1.0 + - - -
278B SER* 5.8 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A CYS* 5.4 0.4 - - - -
202A THR* 5.2 2.7 - - - +
205A PHE 3.9 17.5 - - - +
206A ILE* 4.1 24.2 - - + -
209A ARG* 4.1 13.0 - - + -
210A LEU* 4.5 11.0 - - + -
217B GLU 2.9 13.3 + - - +
218B ALA* 3.2 9.4 + - - +
220B ARG* 1.3 74.5 - - - +
222B TYR* 1.3 62.6 + - - +
224B ARG* 3.3 34.0 + - - +
226B ASP* 3.2 39.8 + - + +
227B ALA* 4.2 5.4 - - + -
232B ILE* 3.4 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B ALA 3.1 1.4 + - - -
219B ILE* 3.0 10.5 + - + +
221B LEU* 1.3 81.1 - - - +
223B GLU* 1.3 65.6 + - + +
225B GLY* 2.9 22.9 + - - -
227B ALA 3.5 22.5 - - - +
228B SER* 4.5 3.1 - - - -
229B LYS* 3.1 55.3 + - + +
232B ILE* 4.1 4.4 - - + +
247B PHE* 3.6 24.2 - + + -
280B SER* 4.9 10.1 - - - -
298B PHE* 5.1 8.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B ILE* 2.7 30.8 + - + +
220B ARG* 3.8 14.8 - - - +
222B TYR* 1.3 75.9 - - + +
224B ARG* 1.3 60.6 + - - +
225B GLY 3.2 0.2 - - - -
278B SER* 2.5 31.0 + - - -
279B PRO* 3.1 19.5 - - - +
280B SER* 2.9 40.5 + - - +
----------------------------------------------------------
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