Contacts of the helix formed by residues 211 - 221 (chain B) in PDB entry 1YDY
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 ASP 211 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B PRO* 3.4 34.7 - - + +
176B TRP* 3.8 22.0 + - - +
209B CYS* 3.2 5.6 - - - -
210B PHE* 1.3 75.6 - - - +
212B ALA* 1.3 62.0 + - - +
213B ASP* 3.1 13.9 + - - +
214B GLU* 3.0 25.8 + - + +
215B LEU* 3.0 25.7 + - - +
234B GLN* 4.4 0.9 - - - -
244B THR* 3.9 21.0 - - + +
245B GLN 4.3 2.2 - - - +
253B TRP* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B PHE 3.3 6.8 + - - +
211B ASP* 1.3 69.1 + - - +
213B ASP* 1.3 69.3 + - - +
215B LEU* 3.2 3.9 + - - +
216B LYS* 3.0 33.8 + - - +
234B GLN* 3.3 27.8 - - - +
244B THR* 5.4 0.8 - - - +
256B TYR* 4.0 30.2 - - + +
260B TRP* 5.6 0.9 - - + -
261B MET* 4.4 2.5 - - + -
273B TYR* 3.7 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ASP* 3.1 9.8 + - - +
212B ALA* 1.3 80.0 - - - +
214B GLU* 1.3 58.9 + - - +
216B LYS* 3.3 21.3 + - - +
217B ARG* 3.0 26.5 + - - +
246B GLN* 2.9 42.4 + - - +
256B TYR* 4.6 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ILE* 5.3 1.3 - - + -
175B PRO* 3.7 21.8 - - + +
179B HIS* 3.0 27.3 + - - -
184B ASP* 4.4 0.3 - - - +
186B ALA* 3.4 20.8 + - + +
209B CYS* 4.5 4.3 - - - -
211B ASP* 3.0 31.7 + - + +
212B ALA 3.2 0.2 - - - -
213B ASP* 1.3 74.0 - - - +
215B LEU* 1.3 61.1 + - - +
217B ARG* 2.8 42.9 + - - +
218B ILE* 2.8 37.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B LEU* 4.5 7.0 - - + +
208B GLN 4.9 0.4 - - - -
209B CYS* 3.5 32.1 - - + +
211B ASP 3.0 13.8 + - - +
212B ALA 3.2 6.5 + - - +
214B GLU* 1.3 75.3 - - - +
216B LYS* 1.3 59.1 + - - +
218B ILE* 3.2 16.8 + - + +
219B LYS* 2.9 30.1 + - - +
232B LEU* 4.1 25.1 - - + +
233B VAL 3.5 8.5 - - - +
234B GLN* 3.5 45.5 - - + +
273B TYR* 3.9 17.7 - - + -
274B ALA* 5.3 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ALA* 3.0 22.2 + - - +
213B ASP* 3.6 21.6 + - - +
215B LEU* 1.3 76.5 - - - +
217B ARG* 1.3 56.3 - - - +
219B LYS* 4.5 3.6 - - - -
220B ASN* 2.9 46.9 + - - +
260B TRP* 6.3 1.4 - - - -
273B TYR* 3.6 44.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
179B HIS* 3.6 13.6 - - - -
184B ASP* 2.8 41.8 + - - -
213B ASP 3.0 14.3 + - - +
214B GLU* 2.8 46.2 + - - +
216B LYS* 1.3 76.0 - - - +
218B ILE* 1.3 65.2 - - - +
221B GLU* 2.9 55.8 + - - +
222B LEU* 3.1 38.6 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
172B ILE* 3.8 29.6 - - + -
186B ALA* 3.8 20.9 - - + -
190B LEU* 4.1 11.4 - - + -
207B LEU* 4.4 9.9 - - + -
209B CYS* 5.6 0.9 - - + -
214B GLU* 2.8 27.7 + - + +
215B LEU* 3.6 19.3 - - + +
217B ARG* 1.3 77.4 - - - +
219B LYS* 1.3 60.7 + - - +
222B LEU* 4.2 12.1 - - + -
223B GLU* 2.8 55.6 + - + +
232B LEU* 4.2 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU 2.9 17.1 + - - +
216B LYS 3.9 3.1 - - - +
218B ILE* 1.3 79.3 - - - +
220B ASN* 1.3 72.0 + - - +
223B GLU* 3.7 15.7 - - - +
224B PRO* 3.3 21.1 - - - +
232B LEU* 3.9 11.9 - - + -
271B ALA 5.2 0.8 + - - -
272B GLU 2.7 25.0 + - - +
273B TYR* 3.6 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B LYS* 2.9 33.5 + - - +
219B LYS* 1.3 97.9 + - - +
221B GLU* 1.3 67.0 + - + +
224B PRO* 3.9 12.0 - - - +
273B TYR* 5.4 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ARG* 2.9 43.5 + - + +
219B LYS 3.6 0.4 - - - -
220B ASN* 1.3 88.3 - - + +
222B LEU* 1.3 69.1 + - + +
223B GLU 3.6 1.1 - - - -
224B PRO* 3.5 4.6 - - - +
225B LYS* 3.3 23.5 + - - +
----------------------------------------------------------
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