Contacts of the helix formed by residues 210 - 225 (chain A) in PDB entry 4OQZ
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 210 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLU* 3.0 16.4 + - - -
207A ASN 3.3 5.4 + - - -
208A PHE 3.3 0.6 - - - -
209A ALA* 1.3 74.1 - - - +
211A MET* 1.3 61.6 + - - +
212A GLY 3.4 2.0 + - - -
213A GLN* 3.6 18.0 - - - +
214A PHE* 3.6 19.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ASN* 3.3 39.6 + - - +
208A PHE* 3.2 35.8 + - + +
210A GLY* 1.3 74.8 - - - +
212A GLY* 1.3 57.1 + - - +
214A PHE* 2.9 44.3 + - + +
215A ILE* 3.0 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A PHE 4.5 1.4 + - - -
209A ALA 4.4 5.1 + - - -
210A GLY 3.4 1.0 - - - -
211A MET* 1.3 76.7 - - - +
213A GLN* 1.3 59.1 + - - +
215A ILE* 3.5 15.7 - - - +
216A ASP* 3.1 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A GLY* 3.6 18.0 + - - +
211A MET 3.2 0.2 - - - -
212A GLY* 1.3 75.6 - - - +
214A PHE* 1.4 61.7 + - + +
216A ASP* 3.9 6.9 + - - +
217A PHE* 3.2 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ASN* 6.2 0.2 - - - -
210A GLY 3.6 19.5 - - - -
211A MET* 2.9 26.0 + - + +
213A GLN* 1.4 81.1 - - + +
215A ILE* 1.4 60.2 + - + +
217A PHE* 3.3 6.3 + + + +
218A TYR* 2.9 55.7 + + + -
278A PHE* 6.3 1.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A MET* 3.0 34.2 + - + +
212A GLY* 3.5 19.0 + - - +
214A PHE* 1.4 77.4 - - + +
216A ASP* 1.4 67.9 + - - +
218A TYR* 4.3 3.0 - - - +
219A ALA* 2.8 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A GLY* 3.1 23.7 + - - +
213A GLN* 3.9 8.0 + - - +
215A ILE* 1.4 82.0 - - - +
217A PHE* 1.4 66.0 + - - +
219A ALA* 3.5 6.3 + - - +
220A ALA* 3.5 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A GLN 3.2 15.4 + - - +
214A PHE* 3.6 7.4 - + - +
216A ASP* 1.4 78.4 - - - +
218A TYR* 1.3 92.3 + + - +
220A ALA* 3.9 4.7 + - - +
221A ARG* 3.3 49.4 + - + +
230A ASP* 5.8 1.1 - - - -
231A VAL* 3.8 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A PHE* 2.9 49.1 + + + +
215A ILE* 4.3 3.4 - - - +
217A PHE* 1.3 97.4 - + - +
219A ALA* 1.3 63.8 + - - +
221A ARG* 3.2 36.5 + - - +
222A ILE* 3.0 37.1 + - + +
231A VAL* 5.0 4.0 - - - +
232A ASP* 2.5 36.9 + - - +
277A SER* 3.7 5.8 - - - -
278A PHE* 3.8 22.7 - + - -
279A SER* 4.3 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A ILE* 2.8 26.4 + - + +
216A ASP* 3.8 9.2 - - - +
217A PHE 3.5 0.2 - - - -
218A TYR* 1.3 72.1 - - - +
220A ALA* 1.4 61.3 + - - +
222A ILE* 3.5 9.3 + - - +
223A ASP* 3.1 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ASP 3.5 12.3 + - - +
217A PHE* 4.1 5.8 - - - +
218A TYR 3.3 0.4 - - - -
219A ALA* 1.4 78.3 - - - +
221A ARG* 1.3 62.1 + - + +
223A ASP* 3.9 4.8 + - - +
224A ALA* 3.4 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A PHE* 3.3 51.4 - - + +
218A TYR* 3.2 32.1 + - - +
220A ALA* 1.3 76.8 - - + +
222A ILE* 1.4 57.1 + - + +
224A ALA* 3.4 2.0 + - - +
225A GLY 3.0 7.3 + - - -
226A ASN* 2.7 69.4 + - + +
227A HIS* 4.0 2.6 - - - +
228A ALA* 3.2 38.8 - - - +
229A GLY 4.6 0.8 - - - +
230A ASP* 4.9 7.7 + - - +
231A VAL* 5.6 2.8 - - - +
232A ASP* 5.3 1.7 + - - -
277A SER* 4.1 11.1 + - - -
279A SER* 4.7 3.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A TYR* 3.0 36.3 + - + +
219A ALA* 4.0 7.9 - - - +
221A ARG* 1.4 72.6 - - + +
223A ASP* 1.3 67.0 + - - +
225A GLY* 3.0 20.1 + - - +
226A ASN 4.5 2.9 - - - +
227A HIS* 4.3 14.0 - - + +
279A SER* 3.4 22.0 - - - +
282A ILE* 3.7 35.2 - - + -
286A LYS* 5.3 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ALA* 3.1 24.3 + - - +
220A ALA* 4.3 5.5 - - - +
222A ILE* 1.3 80.9 - - - +
224A ALA* 1.3 58.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ALA 3.4 16.6 + - - +
221A ARG* 3.8 6.5 - - - +
222A ILE 3.1 0.6 - - - -
223A ASP* 1.3 77.5 - - - +
225A GLY* 1.3 58.9 + - - +
226A ASN* 4.5 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ARG 3.0 0.2 + - - -
222A ILE 3.0 15.6 + - - -
223A ASP 3.5 0.2 - - - -
224A ALA* 1.3 77.4 - - - +
226A ASN* 1.3 59.2 + - - +
227A HIS* 3.9 16.2 + - - +
----------------------------------------------------------
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