Contacts of the helix formed by residues 214 - 231 (chain B) in PDB entry 3RK6
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 214 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B LEU* 4.8 4.3 - - + -
199B TYR* 3.9 9.6 + - - +
202B LEU* 4.4 15.4 + - + -
204B ILE* 3.8 24.4 - - + +
213B ARG* 1.3 71.9 - - - +
215B ASP* 1.3 65.0 + - - +
216B ILE* 3.3 9.2 - - + -
217B LEU* 3.1 41.7 + - + +
218B GLN 3.3 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ARG 3.3 6.8 + - - +
214B ALA* 1.3 71.2 - - - +
216B ILE* 1.3 63.7 + - - +
218B GLN* 3.2 27.0 + - - +
219B VAL* 3.1 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B LEU* 4.2 34.5 - - + -
168B ARG* 3.6 36.5 + - + +
214B ALA* 4.5 4.5 - - + -
215B ASP* 1.3 81.3 + - - +
217B LEU* 1.3 63.5 + - + +
219B VAL* 3.5 15.8 + - + +
220B GLY* 2.9 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B LEU* 4.1 20.4 - - + -
167B CYS* 5.6 1.8 - - + -
168B ARG* 4.2 13.2 - - - +
195B LEU* 4.1 29.1 - - + +
198B LEU* 3.8 23.3 - - + +
199B TYR* 3.5 42.2 - - + +
202B LEU* 4.6 2.0 - - + -
214B ALA* 3.1 27.8 + - + +
216B ILE* 1.3 75.4 - - + +
218B GLN* 1.3 62.8 + - - +
219B VAL 3.2 0.2 - - - -
220B GLY* 4.2 1.8 - - - +
221B LEU* 2.8 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B TYR* 3.8 31.6 + - + +
214B ALA 3.3 4.4 + - - +
215B ASP* 3.2 27.5 + - - +
217B LEU* 1.3 80.9 - - - +
219B VAL* 1.3 65.3 + - - +
221B LEU* 3.6 2.4 + - - +
222B ARG* 3.5 17.5 + - - +
251B LEU* 3.8 19.2 - - + +
254B ALA* 3.6 21.8 - - + +
255B TRP* 3.9 19.7 + - + +
258B LYS* 5.5 4.4 - - - +
260B LYS* 3.8 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ARG* 5.9 0.7 - - - +
171B TYR* 4.9 3.1 - - - +
215B ASP* 3.1 31.3 + - - +
216B ILE* 3.7 18.8 - - + +
217B LEU 3.2 0.2 - - - -
218B GLN* 1.3 80.2 - - - +
220B GLY* 1.3 66.7 + - - +
222B ARG* 3.4 13.5 + - - +
223B GLU* 3.4 23.7 + - + +
260B LYS* 5.0 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ARG* 4.4 6.5 - - - -
171B TYR* 3.5 28.8 - - - -
195B LEU* 5.5 0.9 - - - -
216B ILE 2.9 16.3 + - - -
217B LEU* 3.2 3.5 + - - -
219B VAL* 1.3 77.9 - - - +
221B LEU* 1.3 57.0 + - - +
223B GLU 3.2 2.8 + - - -
224B LEU* 2.9 36.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
192B VAL 4.5 0.9 - - - +
195B LEU* 4.0 16.8 - - + +
196B GLY* 3.9 22.0 - - - +
199B TYR* 3.5 41.1 - - + -
217B LEU* 2.8 22.3 + - + +
218B GLN 4.1 4.3 - - - +
219B VAL 3.3 0.4 - - - -
220B GLY* 1.3 75.1 - - - +
222B ARG* 1.3 57.8 + - - +
224B LEU* 3.3 13.8 + - + +
225B LEU* 2.9 35.3 + - + +
243B LEU* 4.2 15.5 - - + +
247B THR* 4.1 22.4 - - + +
251B LEU* 4.3 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B GLN 3.5 6.3 + - - +
219B VAL* 3.4 10.7 + - - +
220B GLY 3.2 0.4 - - - -
221B LEU* 1.3 79.1 - - - +
223B GLU* 1.3 70.9 + - - +
225B LEU* 3.3 8.5 + - - +
226B ASN* 3.0 55.2 + - - +
255B TRP* 4.1 18.9 - - + +
262B ASP* 3.0 35.3 + - - +
265B GLU* 2.7 43.5 + - - +
266B ILE* 3.4 23.8 - - - +
269B ARG* 3.5 26.7 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
171B TYR* 3.1 29.4 - - - +
174B LYS* 3.9 17.9 - - - +
175B ASP* 5.2 0.3 - - - +
219B VAL* 3.5 17.3 - - + +
220B GLY 3.2 2.1 + - - +
222B ARG* 1.3 95.9 - - - +
224B LEU* 1.3 60.1 + - - +
226B ASN* 3.3 20.5 + - - +
227B ALA* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B TYR* 3.8 10.1 - - + -
174B LYS* 3.8 23.3 - - + -
188B PHE* 3.7 27.0 - - + -
191B PHE* 4.2 7.0 - - + -
192B VAL* 4.2 28.5 - - + -
195B LEU* 3.7 29.4 - - + -
220B GLY 2.9 24.0 + - - +
221B LEU* 3.3 16.1 + - + +
223B GLU* 1.3 70.9 - - - +
225B LEU* 1.3 67.5 + - - +
227B ALA* 3.2 6.0 + - - +
228B LEU* 2.9 28.6 + - - +
243B LEU* 5.1 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B LEU 2.9 22.7 + - - +
222B ARG* 3.3 9.2 + - - +
224B LEU* 1.3 77.4 - - - +
226B ASN* 1.3 61.4 + - - +
228B LEU* 3.1 5.5 + - + +
229B PHE* 2.9 33.8 + - + -
240B ALA* 3.7 31.0 - - + -
243B LEU* 3.8 25.6 - - + -
244B LEU* 3.8 39.7 - - + -
251B LEU* 4.8 9.6 - - + -
255B TRP* 5.1 2.0 - - + -
266B ILE* 3.9 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ARG* 3.0 53.6 + - - +
223B GLU* 3.5 32.2 + - - +
224B LEU 3.3 0.2 - - - -
225B LEU* 1.3 74.1 - - - +
227B ALA* 1.3 58.0 + - - +
229B PHE* 3.4 2.0 + - - -
230B SER* 3.0 34.3 + - - -
266B ILE* 4.0 2.6 - - - +
269B ARG* 3.3 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LYS* 4.0 23.1 - - + +
175B ASP* 3.9 21.3 - - - +
178B ALA* 3.5 9.1 - - + +
188B PHE* 4.5 5.4 - - + -
223B GLU 3.0 14.4 + - - +
224B LEU* 3.2 10.3 + - - +
226B ASN* 1.3 78.3 - - - +
228B LEU* 1.3 60.5 + - - +
230B SER* 3.6 4.8 + - - -
231B ASN* 2.7 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ALA* 4.9 0.2 - - - -
188B PHE* 3.6 25.6 - - + -
189B HIS* 4.0 7.4 - - + -
192B VAL* 4.1 15.7 - - + -
224B LEU 2.9 21.5 + - - +
225B LEU* 3.1 10.5 + - + +
227B ALA* 1.3 76.5 - - - +
229B PHE* 1.3 63.4 + - - +
231B ASN 3.3 23.2 + - - +
232B PRO* 3.9 2.1 - - - +
236B ASN* 3.6 46.4 - - - +
237B LEU* 4.4 1.9 - - - +
239B CYS* 3.8 12.1 - - - -
240B ALA* 3.8 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B LEU* 2.9 36.0 + - + +
226B ASN* 4.1 5.4 - - - +
228B LEU* 1.3 75.3 - - - +
230B SER* 1.3 60.8 + - - +
231B ASN 3.4 0.7 + - - -
232B PRO* 3.5 18.2 - - - +
237B LEU* 3.7 19.5 - - + -
240B ALA* 3.6 27.4 - - + -
244B LEU* 4.1 9.0 - - + -
266B ILE* 4.1 20.9 - - + -
269B ARG* 4.2 27.8 - - + +
270B ILE* 3.4 35.4 - - + -
273B VAL* 3.9 19.6 - - + +
287B LEU* 4.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ASN 3.0 18.9 + - - -
227B ALA* 3.8 2.5 - - - -
228B LEU 3.2 0.4 - - - -
229B PHE* 1.3 75.4 - - - +
231B ASN* 1.3 76.2 + - - +
232B PRO* 3.5 7.5 - - - +
269B ARG* 3.9 14.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ASP* 4.6 5.7 + - - +
178B ALA* 3.5 31.2 - - - +
179B LYS* 2.5 37.0 + - + +
227B ALA* 2.7 25.4 + - - +
228B LEU 3.3 6.8 + - - +
230B SER* 1.3 92.3 - - - +
232B PRO* 1.4 52.0 - - - +
233B MET* 2.7 25.4 + - - +
236B ASN* 2.9 20.6 - - - +
----------------------------------------------------------
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