Contacts of the helix formed by residues 209 - 226 (chain B) in PDB entry 3TQI
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 209 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B PRO 4.3 7.6 + - - -
207B ASN* 2.8 10.1 + - - -
208B TRP* 1.3 74.9 - - - +
210B THR* 1.3 78.9 + - + +
211B LYS* 3.7 20.9 - - + +
212B HIS* 3.4 25.7 + - + -
213B ILE* 3.1 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B THR* 1.3 77.7 - - + +
211B LYS* 1.3 68.4 + - - +
213B ILE* 3.2 8.1 + - + +
214B ILE* 3.0 27.6 + - - +
382B GLU* 5.6 1.1 - - + +
385B LYS* 4.0 40.5 + - + +
386B LEU* 3.8 18.6 - - - +
389B GLU* 4.3 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B THR* 3.3 13.3 - - + +
210B THR* 1.3 85.6 + - - +
212B HIS* 1.3 66.3 + - + +
214B ILE* 3.4 11.9 + - + +
215B GLU* 3.2 32.8 + - - +
389B GLU* 3.7 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 4.2 15.5 - - + +
207B ASN* 3.3 42.1 + - + +
209B THR* 3.4 24.6 + - + +
210B THR 3.3 0.6 - - - -
211B LYS* 1.3 78.4 - - + +
213B ILE* 1.3 60.4 + - - +
215B GLU* 3.3 14.5 + - - +
216B ASP* 2.9 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 5.8 2.2 - - + -
208B TRP* 3.4 56.1 - - + +
209B THR 3.1 20.0 + - - +
210B THR* 3.2 11.9 + - + +
212B HIS* 1.3 78.1 - - + +
214B ILE* 1.3 61.2 + - - +
216B ASP* 4.1 4.3 - - - +
217B SER* 2.9 32.7 + - - -
374B PRO 5.9 1.1 - - - +
378B LEU* 4.0 23.6 - - + -
382B GLU* 4.5 5.6 - - + +
386B LEU* 4.0 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B THR 3.0 21.0 + - - +
211B LYS* 3.6 10.8 - - + +
212B HIS 3.3 0.2 - - - -
213B ILE* 1.3 76.1 - - - +
215B GLU* 1.3 61.6 + - + +
217B SER* 3.8 3.8 - - - -
218B ILE* 3.0 44.1 + - + +
246B LEU* 4.3 6.5 - - + +
249B LYS* 5.7 0.7 - - + -
386B LEU* 3.8 22.4 - - + -
389B GLU* 3.9 33.7 - - + -
390B LEU* 3.8 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B LYS* 3.2 23.4 + - - +
212B HIS* 3.3 14.3 + - - +
213B ILE 3.2 0.4 - - - -
214B ILE* 1.3 78.2 - - + +
216B ASP* 1.3 64.6 + - - +
218B ILE* 3.4 9.6 + - + +
219B ARG* 3.1 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 3.2 37.6 - - + +
6B HIS* 3.5 19.9 + - - -
212B HIS 2.9 16.6 + - - +
213B ILE* 4.1 4.3 - - - +
215B GLU* 1.3 76.5 - - - +
217B SER* 1.3 58.2 + - - +
219B ARG* 3.5 6.7 + - - +
220B ASP* 2.9 30.7 + - - +
377B GLU* 5.4 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ILE* 2.9 26.1 + - - -
214B ILE* 3.8 4.3 - - - -
216B ASP* 1.3 79.0 - - - +
218B ILE* 1.3 63.6 + - - +
220B ASP* 3.3 7.2 + - - +
221B ILE* 3.1 29.2 + - - +
246B LEU* 3.3 27.7 - - - +
374B PRO* 3.6 20.8 + - - +
386B LEU* 5.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ILE* 3.0 39.0 + - + +
215B GLU* 3.9 9.6 - - + +
217B SER* 1.3 74.2 - - - +
219B ARG* 1.3 62.1 + - - +
221B ILE* 3.4 5.1 + - - +
222B GLN* 3.0 46.6 + - - +
246B LEU* 4.3 20.2 - - + +
249B LYS* 4.3 23.6 - - + +
250B ALA* 3.8 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B GLU 3.1 15.2 + - - +
216B ASP* 3.7 7.4 - - - +
218B ILE* 1.3 77.9 - - - +
220B ASP* 1.3 59.0 + - - +
222B GLN* 3.3 18.8 + - - +
223B GLU* 2.9 49.2 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
216B ASP* 2.9 22.9 + - - +
217B SER* 3.3 8.7 + - - +
219B ARG* 1.3 77.3 - - - +
221B ILE* 1.3 62.1 + - + +
223B GLU* 3.5 16.7 + - - +
224B LYS* 3.0 59.4 + - - +
372B ILE* 4.1 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B SER 3.1 20.1 + - - +
218B ILE 3.6 5.4 - - - +
219B ARG 3.2 0.2 - - - -
220B ASP* 1.3 74.1 - - + +
222B GLN* 1.3 61.1 + - - +
224B LYS* 3.2 4.5 + - - +
225B VAL* 2.9 37.2 + - + +
230B VAL* 5.7 2.0 - - + -
246B LEU* 4.0 25.8 - - + +
247B VAL* 4.0 32.5 - - + +
250B ALA* 3.8 16.8 - - + -
251B ILE* 4.1 13.0 - - + -
372B ILE* 4.6 22.7 - - + -
374B PRO* 4.4 12.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
218B ILE* 3.0 37.0 + - - +
219B ARG* 3.3 20.6 + - + +
221B ILE* 1.3 78.9 - - - +
223B GLU* 1.3 62.3 + - + +
225B VAL* 4.7 3.6 - - - -
226B GLY* 3.0 26.5 + - - +
249B LYS 4.9 1.8 + - - -
250B ALA* 3.1 30.9 + - + +
251B ILE* 4.8 3.1 - - + -
----------------------------------------------------------
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 ARG* 2.9 34.9 + - + +
220B ASP* 3.7 18.5 - - - +
221B ILE 3.3 0.2 - - - -
222B GLN* 1.3 77.0 - - + +
224B LYS* 1.3 64.1 + - + +
226B GLY* 4.5 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ASP* 3.0 44.0 + - - +
221B ILE* 3.8 3.6 - - - +
223B GLU* 1.3 82.6 - - + +
225B VAL* 1.3 62.4 + - + +
228B GLU* 5.2 0.9 - - - +
330B TRP* 3.4 34.7 - - + -
371B LEU 5.9 0.2 - - - +
372B ILE* 3.4 30.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ILE* 2.9 25.9 + - + +
222B GLN* 4.6 0.7 - - - +
224B LYS* 1.3 75.4 - - + +
226B GLY* 1.3 79.3 + - - +
227B LYS 3.2 0.2 + - - -
228B GLU* 3.1 39.2 + - - +
230B VAL* 3.3 28.0 - - + -
251B ILE* 3.7 26.2 - - + -
330B TRP* 3.4 29.8 - - + +
372B ILE* 6.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B GLN* 3.0 19.9 + - - -
223B GLU 4.5 1.9 + - - -
224B LYS 3.6 1.2 - - - -
225B VAL* 1.3 81.4 - - - +
227B LYS* 1.3 58.8 + - - -
251B ILE* 4.6 2.6 - - - +
254B GLN* 2.8 20.3 + - - +
----------------------------------------------------------
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