Contacts of the helix formed by residues 202 - 214 (chain B) in PDB entry 1YAA
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 SER 202 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B THR* 1.3 75.6 - - - +
203B GLU* 1.3 60.5 + - - +
205B TRP* 3.5 1.2 + - - -
206B VAL* 3.2 24.0 + - - +
238B TYR* 3.6 40.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B THR* 3.1 9.3 + - - +
202B SER* 1.3 78.2 - - - +
204B GLN* 1.3 67.9 + - - +
206B VAL* 3.2 22.4 + - - +
207B GLN* 3.5 20.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LEU* 4.7 15.6 + - - +
170B LEU* 3.3 37.8 - - + +
199B ASP 4.6 1.4 - - - +
200B PRO* 3.6 13.9 - - + +
201B THR* 3.1 45.1 + - - +
203B GLU* 1.3 78.3 - - + +
205B TRP* 1.3 59.4 + - - +
207B GLN* 3.2 19.0 + - - +
208B ILE* 2.9 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B PHE* 5.8 1.6 - + - -
188B LEU* 4.3 20.4 - - + -
189B HIS 3.6 26.9 - - - -
190B SER 3.7 6.2 + - - -
199B ASP* 4.9 3.5 - - + +
200B PRO* 3.2 44.0 + - + +
201B THR 3.0 23.1 + - - -
202B SER* 3.6 11.7 - - - +
203B GLU 3.3 0.2 - - - -
204B GLN* 1.3 74.2 - - - +
206B VAL* 1.3 59.9 + - - +
208B ILE* 3.6 29.5 - - + +
209B VAL* 2.9 46.1 + - + +
221B PHE* 4.3 11.7 - + - -
238B TYR* 4.4 16.2 - + + -
239B ALA* 3.5 35.8 - - + +
242B LEU* 4.4 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B SER 3.2 17.5 - - - +
203B GLU* 3.3 13.0 - - - +
204B GLN 3.1 0.6 - - - -
205B TRP* 1.3 78.1 - - - +
207B GLN* 1.3 58.0 + - + +
209B VAL* 3.8 0.7 - - - -
210B ASP* 2.9 44.8 + - - +
238B TYR* 3.9 15.3 - - - +
242B LEU* 4.2 11.4 - - + -
243B LYS* 3.3 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU* 4.0 17.0 - - + +
174B LEU* 3.7 30.4 - - + +
203B GLU* 3.9 18.1 - - + +
204B GLN* 3.2 23.6 + - - +
206B VAL* 1.3 79.3 - - + +
208B ILE* 1.3 62.4 + - - +
210B ASP* 3.2 7.6 + - - +
211B ALA* 3.0 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LEU* 5.7 0.2 - - + -
170B LEU* 4.4 5.4 - - + -
173B PHE* 3.5 42.4 - - + -
174B LEU* 3.9 23.3 - - + -
177B ILE* 4.0 6.4 - - + +
188B LEU* 4.5 1.3 - - + -
200B PRO* 3.6 29.4 - - + -
204B GLN 2.9 21.5 + - - +
205B TRP* 3.6 26.2 - - + +
206B VAL 3.3 0.2 - - - -
207B GLN* 1.3 76.2 - - - +
209B VAL* 1.3 62.5 + - + +
211B ALA* 3.5 4.1 + - - +
212B ILE* 3.2 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LEU* 6.2 0.9 - - + -
205B TRP* 2.9 37.9 + - + +
206B VAL 4.0 0.9 - - - +
208B ILE* 1.3 77.3 - - + +
210B ASP* 1.3 60.4 + - - +
211B ALA 3.2 0.2 - - - -
212B ILE* 3.3 9.4 + - + +
213B ALA* 2.9 26.5 + - - +
221B PHE* 5.2 4.5 - - + -
239B ALA 4.8 2.9 - - - +
242B LEU* 3.4 42.0 - - + +
243B LYS* 3.8 14.4 - - + -
244B LEU* 3.5 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B VAL* 2.9 38.5 + - - +
207B GLN* 3.8 7.0 + - - +
209B VAL* 1.3 76.9 - - - +
211B ALA* 1.3 63.0 + - - +
213B ALA* 3.8 7.5 - - - +
214B SER* 3.2 24.1 + - - -
243B LYS* 3.0 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LEU* 4.8 13.7 - - + +
177B ILE* 3.6 32.5 - - + +
178B GLN* 5.6 5.2 - - + -
207B GLN 3.0 17.6 + - - +
208B ILE* 3.6 5.8 - - - +
210B ASP* 1.3 77.3 - - - +
212B ILE* 1.3 62.2 + - - +
214B SER* 2.9 20.9 + - - -
215B LYS* 3.5 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ILE* 4.0 20.2 - - + -
186B PHE* 4.4 13.7 - - + -
188B LEU* 3.9 35.9 - - + -
208B ILE* 3.2 21.2 + - + +
209B VAL* 3.3 12.5 + - + +
211B ALA* 1.3 79.2 - - - +
213B ALA* 1.3 59.2 + - - +
215B LYS 3.6 0.5 + - - -
216B ASN* 3.4 3.1 + - - -
217B HIS* 3.1 52.8 + - + +
218B ILE 5.0 0.2 - - - -
219B ALA* 4.4 11.0 - - + +
244B LEU* 3.9 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B VAL 2.9 15.8 + - - +
210B ASP* 3.8 10.5 - - - +
212B ILE* 1.3 79.6 - - - +
214B SER* 1.3 58.5 + - - +
215B LYS 3.3 0.4 + - - -
216B ASN* 3.7 4.5 + - - +
243B LYS* 4.3 12.1 - - + +
244B LEU* 3.8 19.1 - - + -
247B VAL* 3.5 29.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B GLU* 4.7 5.0 - - - +
210B ASP 3.2 15.2 + - - -
211B ALA* 2.9 19.9 + - - -
213B ALA* 1.3 76.0 - - - +
215B LYS* 1.3 66.0 + - - +
216B ASN* 3.5 4.4 + - - -
----------------------------------------------------------
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