Contacts of the helix formed by residues 214 - 229 (chain Y) in PDB entry 5A31
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 VAL 214 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213Y SER* 1.3 89.5 - - - +
215Y LYS* 1.3 66.6 + - - +
216Y GLY 3.3 1.8 - - - +
217Y ALA* 3.3 25.2 + - + +
218Y GLU* 3.1 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 215 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210Y LEU* 3.7 22.9 - - + +
213Y SER* 3.3 2.9 - - - -
214Y VAL* 1.3 75.2 - - - +
216Y GLY* 1.3 54.5 + - - +
218Y GLU* 3.0 4.0 + - - +
219Y VAL* 2.8 38.6 + - - +
244Y ALA* 3.3 37.9 - - + +
248Y THR* 6.2 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 216 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214Y VAL* 3.3 1.2 - - - +
215Y LYS* 1.3 77.3 - - - +
217Y ALA* 1.3 56.2 + - - +
219Y VAL* 3.3 10.5 + - - +
220Y ALA* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 217 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214Y VAL* 3.3 31.4 + - + +
216Y GLY* 1.3 74.4 - - - +
218Y GLU* 1.3 62.2 + - - +
220Y ALA* 3.4 8.3 + - - +
221Y SER* 3.3 20.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 218 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193Y LYS* 6.0 0.2 - - - +
196Y LEU* 5.5 0.2 - - + -
206Y ILE* 5.1 5.8 - - + -
209Y LEU* 4.3 28.9 - - + -
210Y LEU* 4.1 18.6 - - + -
214Y VAL 3.1 12.0 + - - +
215Y LYS 3.0 8.2 + - - +
217Y ALA* 1.3 72.3 - - - +
219Y VAL* 1.3 65.1 + - - +
221Y SER* 2.9 22.2 + - - -
222Y MET* 3.0 17.1 + - + +
240Y ILE* 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 219 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215Y LYS* 2.8 39.3 + - + +
216Y GLY* 3.4 9.9 - - - +
218Y GLU* 1.3 71.2 - - - +
220Y ALA* 1.3 53.8 + - - +
222Y MET* 3.3 3.2 + - - +
223Y THR* 2.8 54.1 + - + +
237Y SER* 5.1 4.3 - - - +
240Y ILE* 3.3 38.3 - - + +
241Y LYS* 5.1 15.5 - - + +
244Y ALA* 5.1 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 220 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216Y GLY 3.0 13.3 + - - +
217Y ALA* 3.5 13.0 - - - +
218Y GLU 3.3 0.4 - - - -
219Y VAL* 1.3 76.8 - - - +
221Y SER* 1.3 59.8 + - - +
223Y THR* 2.6 21.9 + - - -
224Y MET* 3.4 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 221 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193Y LYS* 3.2 30.8 + - - -
196Y LEU* 4.6 5.2 - - - +
200Y PRO* 5.3 0.6 - - - +
217Y ALA 3.3 7.9 + - - -
218Y GLU* 2.9 23.7 + - - -
220Y ALA* 1.3 78.7 - - - +
222Y MET* 1.3 65.6 + - - +
224Y MET* 3.3 8.7 + - - +
225Y ASN* 3.2 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 222 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196Y LEU* 4.1 10.3 - - + -
200Y PRO* 3.6 35.0 - - + -
201Y LEU* 4.9 5.4 - - - +
206Y ILE* 3.5 43.3 - - + -
218Y GLU 3.0 16.7 + - - +
219Y VAL 3.6 1.6 - - - +
221Y SER* 1.3 85.4 + - - +
223Y THR* 1.3 55.7 + - - +
225Y ASN* 3.2 6.7 - - + +
226Y VAL* 2.8 33.0 + - - +
236Y LEU* 4.3 19.7 - - + -
240Y ILE* 3.4 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 223 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219Y VAL* 2.8 38.3 + - + +
220Y ALA* 2.6 26.6 + - - -
222Y MET* 1.3 68.7 - - + +
224Y MET* 1.3 64.6 + - - +
226Y VAL* 3.2 18.5 + - + +
227Y ILE* 3.2 21.3 + - - +
237Y SER* 5.0 16.2 - - - -
240Y ILE* 5.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 224 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220Y ALA 4.0 5.8 - - - +
221Y SER* 3.3 12.5 + - - +
222Y MET 3.3 0.4 - - - -
223Y THR* 1.3 81.9 + - - +
225Y ASN* 1.3 63.5 + - - +
227Y ILE* 3.5 7.4 + - - +
228Y GLN* 3.3 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 225 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200Y PRO* 3.2 42.6 - - + -
221Y SER 3.2 8.7 + - - +
222Y MET* 3.2 13.7 - - + +
224Y MET* 1.3 80.1 - - - +
226Y VAL* 1.3 49.5 + - - +
228Y GLN* 3.2 9.6 + - - +
229Y THR* 2.4 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 226 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222Y MET* 2.8 27.5 + - + +
223Y THR* 3.2 12.3 + - + +
225Y ASN* 1.3 69.0 - - - +
227Y ILE* 1.3 69.8 + - + +
229Y THR* 3.0 28.8 + - - +
230Y VAL 4.6 1.7 - - - +
233Y LEU 3.7 20.9 - - - +
234Y ASP* 5.5 3.8 - - - +
236Y LEU* 3.5 36.8 - - + -
237Y SER* 4.9 11.9 - - - +
240Y ILE* 5.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 227 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223Y THR* 3.2 15.2 + - - +
224Y MET* 4.1 7.4 - - - +
226Y VAL* 1.3 79.7 - - + +
228Y GLN* 1.3 63.2 + - - +
229Y THR 3.2 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 228 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40X HIS* 6.1 0.7 - - - -
224Y MET 3.3 10.8 + - - +
225Y ASN* 3.2 15.6 + - - +
227Y ILE* 1.3 80.0 - - - +
229Y THR* 1.3 59.3 + - - +
230Y VAL 4.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 229 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37X VAL* 5.3 0.4 - - + -
40X HIS* 6.0 8.1 - - + +
199Y CYS 5.8 0.2 + - - -
200Y PRO* 5.6 1.9 - - - +
201Y LEU* 4.9 12.3 - - + +
225Y ASN* 2.4 34.9 + - - +
226Y VAL* 3.0 25.2 + - - +
227Y ILE 3.2 6.6 - - - +
228Y GLN* 1.3 79.0 - - - +
230Y VAL* 1.3 84.3 + - + +
231Y PRO* 3.9 2.6 - - - +
233Y LEU* 3.4 35.9 - - + -
236Y LEU* 5.3 3.6 - - + +
----------------------------------------------------------
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