Contacts of the helix formed by residues 213 - 223 (chain B) in PDB entry 1SQ0
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 ILE 213 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B TYR 4.2 7.2 - - - +
186B THR* 4.1 25.5 + - - +
187B ILE 4.4 1.1 - - - +
207B TRP* 4.3 8.5 - - + -
208B LEU 3.7 12.6 - - - +
209B CYS* 3.8 9.0 - - + -
210B ASN* 2.8 27.2 + - - +
212B GLU* 1.3 76.7 - - - +
214B LEU* 1.3 59.6 - - - +
215B TYR 3.3 1.1 - - - -
216B PHE* 3.1 31.3 + - + -
217B ARG* 2.9 24.8 + - + +
256B VAL* 3.5 22.2 - - + -
259B TYR* 3.5 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B CYS* 3.2 19.5 - - - +
212B GLU 3.1 1.6 - - - -
213B ILE* 1.3 75.2 - - - +
215B TYR* 1.3 66.2 + - - +
217B ARG* 3.3 40.9 + - - +
218B ARG* 3.1 23.6 + - - +
259B TYR* 4.1 20.9 - - + -
260B PRO 4.5 4.3 - - - +
261B GLY* 4.6 2.9 - - - +
264B CYS* 3.3 31.6 - - + +
265B PRO 4.2 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ILE* 3.4 35.2 - - + +
188B PRO 3.6 5.8 - - - -
189B LYS* 3.8 21.1 - - + -
190B GLY* 3.3 30.9 - - - -
191B PHE 3.5 5.3 + - - -
192B PHE* 2.9 43.0 + + - +
193B GLY 3.6 6.2 + - - -
212B GLU 4.1 8.5 + - - +
213B ILE 3.3 0.8 - - - -
214B LEU* 1.3 78.6 - - - +
216B PHE* 1.3 63.5 + - - +
218B ARG* 3.3 20.5 + - - +
219B TRP* 3.1 26.8 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ILE* 4.2 16.8 + - + +
192B PHE* 4.1 14.6 - + - -
202B LEU* 3.6 34.1 - - + -
207B TRP* 3.8 32.8 - + - -
212B GLU 5.0 0.2 + - - -
213B ILE* 3.1 38.7 + - + +
215B TYR* 1.3 84.5 - - - +
217B ARG* 1.3 57.3 + - - +
219B TRP* 3.1 22.9 + + - +
220B LEU* 2.8 36.0 + - + +
246B VAL* 3.5 28.7 - - + -
256B VAL* 4.0 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ILE* 2.9 15.1 + - + +
214B LEU* 3.4 37.7 - - + +
215B TYR 3.3 0.2 - - - -
216B PHE* 1.3 77.4 - - - +
218B ARG* 1.3 69.3 + - - +
220B LEU* 3.2 12.6 + - - +
221B GLN* 3.0 51.2 + - - +
256B VAL* 3.3 26.4 - - + +
257B TYR 3.8 12.8 - - - +
258B LYS* 4.4 0.4 - - - +
259B TYR* 2.5 32.7 + - - +
260B PRO* 3.5 14.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B LEU 3.1 15.6 + - - +
215B TYR* 3.8 22.0 - - - +
217B ARG* 1.3 81.1 - - - +
219B TRP* 1.3 62.2 + - - +
221B GLN* 3.4 15.2 + - - +
222B ASP* 3.2 46.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B PHE* 3.4 59.6 - + + +
193B GLY 5.3 4.2 + - - -
195B HIS 5.6 3.4 + - - -
197B LEU* 4.7 11.9 - - + +
200B ALA* 3.9 23.6 - - + -
202B LEU* 3.5 22.7 - - + -
215B TYR* 3.1 22.3 + + + +
216B PHE* 3.1 21.9 + + - +
218B ARG* 1.3 79.3 - - - +
220B LEU* 1.3 83.5 + - + +
222B ASP* 3.2 3.9 + - - -
223B ASN* 2.8 69.3 + - + +
226B ASN* 5.5 1.3 - - + -
227B VAL* 3.9 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B LEU* 4.5 0.2 - - + -
216B PHE* 2.8 31.9 + - + +
217B ARG* 3.4 6.5 - - - +
219B TRP* 1.3 102.4 - - + +
221B GLN* 1.3 57.0 - - - +
223B ASN* 3.4 1.5 - - - +
224B ALA* 2.8 32.7 + - - +
227B VAL* 3.9 14.1 - - + -
243B VAL* 3.8 11.0 - - + +
246B VAL* 3.9 20.2 - - + -
256B VAL* 3.7 24.2 - - + -
257B TYR* 3.6 35.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ARG* 3.0 43.6 + - - +
218B ARG* 3.8 13.6 - - + +
219B TRP 3.3 0.2 - - - -
220B LEU* 1.3 77.3 - - - +
222B ASP* 1.3 66.1 + - - +
223B ASN 3.5 0.2 + - - -
224B ALA* 3.9 12.4 + - - +
257B TYR* 2.8 37.6 + - + +
258B LYS* 4.8 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B ARG* 3.2 32.1 + - - +
219B TRP* 3.2 6.7 + - - +
221B GLN* 1.3 81.9 - - - +
223B ASN* 1.3 70.4 + - - +
224B ALA 3.7 0.4 - - - -
225B GLU* 5.8 1.2 - - - +
226B ASN* 5.2 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B HIS 5.7 0.3 - - - +
196B LEU* 4.7 8.3 - - - +
197B LEU* 5.2 4.7 + - - +
219B TRP* 2.8 72.7 + - + +
220B LEU 3.4 3.1 - - - +
221B GLN 3.2 0.2 - - - -
222B ASP* 1.3 89.9 - - - +
224B ALA* 1.3 55.2 + - - +
225B GLU* 3.0 4.9 - - - -
226B ASN* 2.7 52.1 + - + +
227B VAL* 3.4 9.6 + - - +
----------------------------------------------------------
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