Contacts of the helix formed by residues 215 - 228 (chain B) in PDB entry 3ROT
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 THR 215 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ASP* 5.9 1.3 - - - -
157B PRO* 3.3 12.2 - - + +
164B LEU* 3.7 31.6 - - + -
213B CYS* 3.2 6.6 - - - +
214B LEU* 1.3 83.8 - - - +
216B SER* 1.3 63.5 + - - +
217B GLN* 3.0 37.7 + - - +
218B ALA* 3.1 13.0 + - - +
219B LEU 3.3 7.1 + - - -
242B SER* 4.1 2.9 - - - -
243B PHE* 4.0 11.0 - - - -
244B ASP* 4.5 1.3 - - - -
317B GOL 4.2 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ASP* 2.9 33.3 + - - -
35B PRO* 4.6 1.4 - - - +
215B THR* 1.3 71.6 - - - +
217B GLN* 1.3 64.5 + - - +
218B ALA 3.1 0.2 - - - -
219B LEU* 3.5 10.5 - - - -
220B ASP* 2.9 34.5 + - - +
242B SER* 4.5 0.7 - - - -
243B PHE 3.6 12.2 + - - -
244B ASP* 4.4 3.1 + - - -
246B THR* 3.6 31.1 - - - +
249B THR* 4.1 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ASP* 3.4 29.8 + - - +
37B TRP* 5.4 5.0 - - - +
63B ALA* 3.1 36.8 + - - +
157B PRO* 3.9 16.5 - - + +
158B GLN* 5.8 1.7 - - - +
188B GLY 5.6 0.2 - - - -
189B THR* 4.2 23.3 - - + +
194B VAL* 4.6 4.9 - - - +
215B THR* 3.0 27.0 + - - +
216B SER* 1.3 79.8 + - - +
218B ALA* 1.3 54.7 + - - +
220B ASP* 5.3 1.6 - - - -
221B PRO* 3.2 22.6 - - - +
317B GOL 6.1 0.7 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
155B LEU* 4.1 28.5 - - + +
157B PRO* 4.4 8.5 - - + +
187B VAL* 4.2 14.8 - - + -
194B VAL* 3.8 14.1 - - + +
213B CYS* 4.1 14.9 - - + -
215B THR* 3.1 9.6 + - - +
216B SER 3.1 0.4 - - - -
217B GLN* 1.3 80.7 - - - +
219B LEU* 1.3 64.1 + - - +
220B ASP 3.5 0.2 - - - -
221B PRO* 3.4 8.5 - - - +
222B LEU* 3.6 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B CYS* 3.8 9.1 - - - -
215B THR 3.3 2.8 + - - -
216B SER* 3.1 10.6 + - - +
218B ALA* 1.3 77.9 - - - +
220B ASP* 1.3 58.2 + - - +
222B LEU* 2.9 9.2 + - + +
223B GLY* 2.6 35.6 + - - +
226B LEU* 5.2 1.3 - - + -
240B VAL* 4.1 19.1 - - + -
242B SER* 3.6 30.1 - - - +
249B THR* 3.7 37.0 - - + +
252B LEU* 3.9 26.0 - - + -
258B VAL* 4.0 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PRO* 6.1 1.0 - - + +
247A PRO* 5.9 0.7 - - - +
35B PRO* 5.7 6.8 - - - +
216B SER* 2.9 29.2 + - - +
217B GLN* 4.8 1.3 - - - +
219B LEU* 1.3 79.8 - - - +
221B PRO* 1.3 70.6 - - + +
223B GLY* 3.2 8.6 + - - +
224B GLN* 3.2 13.5 + - - +
246B THR* 4.4 4.3 + - - -
248B ASN* 3.7 36.3 - - - +
249B THR* 4.7 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B THR 5.4 0.4 - - - +
191B PRO* 3.6 50.5 - - + +
194B VAL* 3.8 16.8 - - + -
195B GLN* 2.9 32.7 + - + +
217B GLN 3.2 24.5 - - - +
218B ALA 3.4 6.3 - - - +
220B ASP* 1.3 94.0 - - + +
222B LEU* 1.3 60.5 + - - +
224B GLN* 3.4 7.6 + - + +
225B MSE 3.6 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B LEU* 4.6 5.2 - - + -
194B VAL* 4.9 3.5 - - + +
198B VAL* 4.5 6.5 - - + -
211B ILE* 4.0 24.0 - - + -
213B CYS* 4.0 15.3 - - - -
218B ALA 3.6 10.5 + - - +
219B LEU* 2.9 10.8 + - + +
221B PRO* 1.3 76.5 - - - +
223B GLY* 1.3 64.7 + - - +
225B MSE 3.0 28.8 + - + +
226B LEU* 3.0 22.5 + - + +
234B PHE* 3.9 29.8 - - + -
240B VAL* 3.9 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A PRO* 5.8 0.2 - - - -
219B LEU* 2.6 19.0 + - - +
220B ASP 3.2 3.1 + - - -
222B LEU* 1.3 73.0 - - - +
224B GLN* 1.3 56.6 + - - +
226B LEU* 3.0 12.9 + - - +
227B LEU* 2.8 39.4 + - - +
248B ASN* 5.3 1.3 - - - -
252B LEU* 3.8 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PRO* 3.2 31.9 + - - +
38A THR* 2.5 22.1 + - - +
39A SER* 4.3 7.3 - - - -
246A THR* 5.8 0.2 - - - +
247A PRO* 4.2 22.0 - - + +
195B GLN* 3.3 13.2 + - - +
220B ASP 3.2 10.8 + - - +
221B PRO* 3.6 10.9 - - - +
222B LEU 3.2 0.2 - - - -
223B GLY* 1.3 76.0 - - - +
225B MSE 1.3 62.6 + - - +
227B LEU* 3.3 12.7 + - - +
228B HIS* 3.1 29.8 + - + +
232B TYR* 3.2 27.0 + - + +
248B ASN* 5.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B VAL* 6.2 0.2 - - + -
195B GLN* 3.6 53.4 - - + +
198B VAL* 4.1 15.5 - - + -
199B LYS* 3.7 31.9 - - + -
221B PRO 3.6 1.5 + - - +
222B LEU* 3.0 31.9 + - + +
224B GLN* 1.3 76.6 - - - +
226B LEU* 1.3 58.7 + - - +
229B PRO* 3.0 32.7 - - - +
232B TYR* 3.6 28.0 - - + -
234B PHE* 4.1 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B LEU* 5.2 0.9 - - + -
222B LEU* 3.0 34.3 + - + +
223B GLY* 3.0 14.3 + - - +
225B MSE 1.3 77.6 - - - +
227B LEU* 1.3 59.1 + - - +
229B PRO* 3.5 12.8 - - - +
234B PHE* 4.2 17.9 - - + +
237B GLN* 5.2 5.2 - - - +
238B PRO* 4.2 28.9 - - + +
240B VAL* 4.1 11.0 - - + -
252B LEU* 5.3 0.7 - - + -
257B LEU* 3.9 55.3 - - + +
258B VAL* 5.0 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A PRO* 3.8 35.4 - - + -
223B GLY 2.8 20.3 + - - +
224B GLN 3.7 4.9 - - - +
225B MSE 3.2 0.2 - - - -
226B LEU* 1.3 79.5 - - - +
228B HIS* 1.3 79.5 + - + +
229B PRO* 3.4 6.0 - - - +
248B ASN* 5.0 2.2 - - - +
251B SER* 6.1 0.9 - - - +
252B LEU* 4.0 17.0 - - + -
255B LYS* 3.5 37.9 - - + -
257B LEU* 3.7 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LYS 6.0 0.2 + - - -
247A PRO* 5.7 4.3 - - + +
224B GLN* 3.1 26.6 + - + +
225B MSE 3.3 3.6 - - - -
227B LEU* 1.3 97.2 + - + +
229B PRO* 1.3 66.9 - - - +
230B ASP 3.2 4.1 + - - -
231B ARG* 3.2 43.6 + - + +
232B TYR* 3.2 29.6 - + + -
----------------------------------------------------------
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