Contacts of the helix formed by residues 209 - 226 (chain B) in PDB entry 4YP9
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 GLY 209 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ASP* 3.1 17.7 - - - -
137B THR* 4.8 2.2 - - - -
207B SER 3.4 2.8 + - - -
208B GLU* 1.3 76.6 - - - +
210B TYR* 1.3 59.4 + - - -
211B ILE 3.3 2.7 - - - -
212B SER* 3.5 3.8 + - - -
213B ASP* 3.0 39.2 + - - +
236B TYR* 5.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 3.9 9.6 - - + -
28B TYR* 3.8 40.6 - + - +
135B LEU* 3.8 21.5 - - + +
136B ASP* 2.7 16.8 + - - +
159B ASN 5.0 1.3 - - - -
160B ILE* 3.9 20.3 - - + +
161B THR* 4.6 2.1 + - - -
162B THR* 2.4 37.2 + - - +
180B HIS* 3.7 28.7 - + - +
209B GLY* 1.3 69.4 - - - -
211B ILE* 1.3 66.2 + - + +
213B ASP* 3.4 9.4 + - - +
214B VAL* 2.9 49.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU 5.9 0.4 - - - +
136B ASP* 3.0 30.7 + - + +
159B ASN* 3.2 33.9 - - - +
180B HIS* 3.4 20.2 - - + +
206B PHE* 4.2 26.5 - - + -
210B TYR* 1.3 79.0 - - + +
212B SER* 1.3 60.4 + - - +
214B VAL* 5.2 1.1 - - - -
215B ARG* 2.8 70.8 + - + +
264B CYS 4.6 0.7 - - - +
402B A1B 4.1 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B TYR* 3.5 21.2 - - - +
206B PHE* 2.9 29.0 + - - +
207B SER 2.6 28.2 + - - -
209B GLY 3.5 7.5 + - - -
211B ILE* 1.3 78.4 - - - +
213B ASP* 1.3 59.7 + - - +
215B ARG* 4.9 1.1 - - - -
216B GLY* 2.8 33.6 + - - +
236B TYR* 3.8 12.8 - - - -
264B CYS* 5.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B VAL* 3.6 3.6 - - + +
25B LEU* 3.4 40.7 - - + +
205B TYR* 5.2 0.6 - - - -
209B GLY* 3.0 23.5 + - - +
210B TYR* 3.5 5.0 - - - +
212B SER* 1.3 79.4 - - - +
214B VAL* 1.3 58.5 + - - +
217B ASP* 2.9 47.1 + - - +
236B TYR* 4.4 13.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B VAL* 3.7 12.1 - - + -
25B LEU* 4.0 12.6 - - + -
180B HIS* 3.6 12.1 - - + -
181B ALA* 3.4 36.6 - - + +
210B TYR* 2.9 51.0 + - + +
211B ILE 4.3 0.2 - - - +
213B ASP* 1.3 69.0 - - - +
215B ARG* 1.3 68.3 + - - +
218B THR* 2.6 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B HIS* 3.1 36.7 + - + +
184B SER* 3.1 17.6 + - - +
211B ILE* 2.8 30.4 + - + +
214B VAL* 1.3 76.0 - - - +
216B GLY* 1.3 61.8 + - - +
219B PHE 3.7 2.9 + - - -
262B TYR* 3.0 20.8 + - - +
264B CYS* 2.7 46.5 + - + -
265B SER* 3.7 5.1 - - - +
289B TRP* 3.4 50.8 - - + +
310B ARG* 3.5 4.2 - - - +
402B A1B 2.8 54.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B VAL* 4.8 1.1 - - - -
205B TYR* 3.7 8.7 - - - -
212B SER 2.8 21.0 + - - -
215B ARG* 1.3 72.3 - - - +
217B ASP* 1.3 60.9 + - - -
219B PHE* 3.4 4.9 + - - +
220B ILE* 2.9 34.8 + - - +
262B TYR* 4.2 3.9 - - - -
264B CYS* 3.5 18.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B VAL* 3.6 22.8 - - + +
25B LEU* 5.9 0.7 - - - +
205B TYR* 2.7 29.1 + - - -
213B ASP* 2.9 34.5 + - - +
216B GLY* 1.3 71.1 - - - -
218B THR* 1.3 58.7 + - - +
220B ILE* 4.0 9.1 - - - +
221B HIS* 2.8 45.1 + - + +
401B CA 2.2 26.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B VAL* 3.6 17.1 - - + +
181B ALA* 3.9 26.1 - - + +
184B SER* 4.0 10.5 - - - -
185B ARG* 4.3 22.9 - - + +
188B ALA* 5.5 0.2 - - - -
214B VAL* 2.6 37.7 + - - +
217B ASP* 1.3 75.7 - - - +
219B PHE* 1.3 58.6 + - - +
221B HIS* 4.0 1.6 - - - +
222B GLN* 3.0 31.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B SER* 4.2 5.1 - - - +
187B LEU 4.2 0.2 - - - -
188B ALA* 3.7 39.7 - - + -
191B PHE* 3.7 20.6 - + + -
201B TYR* 3.9 14.6 - + - -
215B ARG 3.7 3.8 + - - +
216B GLY 3.4 3.1 + - - +
217B ASP 3.3 0.2 - - - -
218B THR* 1.3 80.2 - - - +
220B ILE* 1.3 63.7 + - + +
222B GLN* 3.9 1.0 - - - +
223B VAL* 2.9 44.0 + - + +
260B PHE* 3.6 32.8 - + - -
262B TYR* 3.2 71.3 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B TYR* 3.5 17.9 - - + +
203B VAL* 3.7 36.6 - - + -
205B TYR* 3.7 23.6 - - + +
216B GLY 2.9 24.5 + - - +
217B ASP* 4.0 8.1 - - - +
219B PHE* 1.3 78.4 - - + +
221B HIS* 1.3 67.3 + - + +
224B ASN* 2.8 49.3 + - - +
231B LEU* 4.3 18.6 - - + -
234B ALA* 5.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B MET 4.7 5.1 + - - -
24B VAL* 3.6 30.8 - - + +
217B ASP* 2.8 32.3 + - + +
218B THR* 4.0 3.1 - - - +
220B ILE* 1.3 84.3 - - + +
222B GLN* 1.3 57.1 + - - +
224B ASN* 4.8 0.4 - - - -
225B ARG* 2.9 78.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ARG* 3.2 30.6 - - - +
188B ALA* 3.3 20.8 + - + +
189B THR* 3.1 38.4 + - - +
218B THR* 3.0 18.1 + - + +
221B HIS* 1.3 76.3 - - - +
223B VAL* 1.3 58.6 - - - +
225B ARG* 5.1 0.2 - - - -
226B ASP* 2.8 55.9 + - - +
227B ASN* 3.5 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ALA* 4.3 15.5 - - + +
191B PHE* 4.6 1.1 - - + -
201B TYR* 3.3 36.1 - - + +
219B PHE* 2.9 34.4 + - + +
222B GLN* 1.3 74.6 - - + +
224B ASN* 1.3 67.6 + - - +
227B ASN* 3.4 17.9 + - - +
228B ASN 3.2 6.9 + - - -
229B PHE* 3.1 59.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B TYR* 2.5 41.0 + - - -
220B ILE* 2.8 35.6 + - + +
221B HIS* 4.1 2.0 - - - +
223B VAL* 1.3 73.9 - - - +
225B ARG* 1.3 66.3 + - + +
228B ASN* 3.0 27.5 + - - +
229B PHE 3.7 16.4 + - - +
230B GLU* 5.4 0.2 - - - -
231B LEU* 4.3 11.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B HIS* 2.9 71.2 + - - +
224B ASN* 1.3 81.8 + - - +
226B ASP* 1.3 67.9 - - - +
228B ASN* 4.5 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LYS* 4.6 4.0 - - - -
222B GLN* 2.8 40.4 + - - +
225B ARG* 1.3 84.3 - - - +
227B ASN* 1.3 71.9 + - - +
228B ASN* 3.6 9.2 + - - -
----------------------------------------------------------
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