Contacts of the helix formed by residues 219 - 228 (chain D) in PDB entry 2Y05
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 GLY 219 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D ASP* 3.0 17.3 + - - -
218D VAL* 1.3 88.1 - - - +
220D GLY* 1.3 69.7 + - - +
222D PHE* 3.6 3.3 + - - +
223D SER* 3.1 23.4 + - - -
240D GLY 4.6 0.7 - - - -
241D ALA* 4.0 13.1 - - - +
243D SER* 3.5 3.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 220 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D GLY* 1.3 72.1 - - - -
221D GLU* 1.3 62.7 + - - -
223D SER* 3.2 12.4 + - - -
224D ASN* 3.2 20.6 + - - +
243D SER* 3.7 11.0 + - - -
244D THR* 4.6 6.7 - - - +
252D PRO* 3.7 23.1 - - - -
253D PRO 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 221 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D LEU* 5.5 0.4 - - - -
219D GLY 3.7 0.2 + - - -
220D GLY* 1.3 72.1 - - - -
222D PHE* 1.3 62.5 + - - +
224D ASN* 3.2 24.9 + - - +
225D THR* 3.1 26.8 + - - +
243D SER* 5.9 0.4 - - - -
252D PRO* 3.6 12.8 - - + +
253D PRO* 3.4 30.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 222 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D MET* 3.6 20.0 - - + -
148D ASN* 3.6 11.2 - - + -
172D ALA* 3.4 32.8 - - + -
191D PHE* 4.5 1.1 - + - -
193D TYR* 3.9 28.9 - + + -
199D LEU* 3.5 38.4 - - + +
203D LEU* 5.4 0.4 - - + -
214D TYR* 3.5 12.1 - - - -
218D VAL* 4.1 14.4 - - + -
219D GLY 3.6 9.4 + - - +
220D GLY 3.2 0.6 - - - -
221D GLU* 1.3 78.5 - - - +
223D SER* 1.3 57.0 + - - +
225D THR* 3.2 5.9 + - - -
226D VAL* 3.0 42.0 + - + +
701D NAP 5.9 1.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 223 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D TYR* 2.6 30.5 + - - -
216D ASP* 2.7 25.4 + - - -
219D GLY* 3.1 15.1 + - - -
220D GLY 3.2 9.3 + - - -
222D PHE* 1.3 76.7 - - - +
224D ASN* 1.3 60.6 + - - +
226D VAL* 3.2 1.3 + - - +
227D ILE* 2.8 42.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 224 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D GLY 3.2 14.5 + - - +
221D GLU* 3.2 31.8 + - - +
223D SER* 1.3 76.7 - - - +
225D THR* 1.3 61.2 + - - +
227D ILE* 3.5 9.2 + - - +
228D GLY* 3.5 13.9 + - - -
253D PRO* 2.7 28.5 + - - +
254D GLY* 3.5 10.4 + - - -
255D PRO* 3.3 28.5 - - + +
256D PRO* 4.3 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 225 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D LEU* 3.8 20.7 - - + +
200D GLU* 3.7 39.5 - - + +
203D LEU* 4.2 3.8 - - + +
221D GLU* 3.1 12.4 + - - +
222D PHE 3.5 8.1 - - - -
223D SER 3.2 0.2 - - - -
224D ASN* 1.3 75.8 - - - +
226D VAL* 1.3 62.6 + - - +
228D GLY* 3.3 13.7 + - - -
229D GLN* 3.8 10.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 226 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D MET* 3.7 17.7 - - + -
203D LEU* 3.8 21.5 - - + -
211D TYR* 5.4 4.7 - - + -
214D TYR* 3.6 43.7 - - + -
222D PHE* 3.0 47.3 + - + +
223D SER 3.2 1.3 + - - +
225D THR* 1.3 71.9 - - - +
227D ILE* 1.3 66.9 + - - +
229D GLN* 2.9 15.9 + - - +
230D MET* 3.4 18.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D TYR* 5.2 3.4 - - + -
223D SER* 2.8 25.1 + - - +
224D ASN* 3.7 7.2 - - - +
225D THR 3.2 0.4 - - - -
226D VAL* 1.3 76.1 - - - +
228D GLY* 1.3 56.9 + - - +
229D GLN 3.0 5.2 + - - -
230D MET* 3.2 22.6 + - - +
236D ILE* 3.8 20.6 - - + -
255D PRO* 3.3 35.0 - - + -
256D PRO* 4.5 5.2 - - + -
259D ILE* 3.7 17.5 - - + +
260D VAL* 4.0 15.7 - - + -
263D GLN* 5.4 0.3 - - - +
265D LEU* 3.8 17.7 - - + +
267D MET* 3.8 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D ASN 3.5 6.0 + - - -
225D THR* 3.3 9.5 + - - -
226D VAL 3.2 1.2 - - - -
227D ILE* 1.3 77.4 - - - +
229D GLN* 1.3 63.5 + - - +
230D MET 3.6 1.0 - - - +
259D ILE* 4.0 27.9 - - - +
----------------------------------------------------------
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