Contacts of the helix formed by residues 209 - 219 (chain A) in PDB entry 3P9K
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 209 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLY 3.0 6.1 + - - -
207A GLY 3.0 6.3 - - - -
208A VAL* 1.3 78.2 - - - +
210A ALA* 1.3 64.3 + - - +
211A THR* 3.1 3.5 + - - -
212A VAL* 3.5 6.9 - - - +
213A ALA* 3.1 23.7 + - - +
226A ASN* 3.3 30.1 - - - -
239A PHE* 3.8 5.5 - - - -
244A HIS* 4.3 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LYS* 3.8 35.0 - - + +
181A SER* 5.2 2.9 - - - -
182A ILE* 4.1 20.6 - - + +
206A GLY 4.5 0.8 + - - -
208A VAL* 3.4 6.4 + - + +
209A GLY* 1.3 77.4 - - - +
211A THR* 1.3 57.1 + - - +
213A ALA* 3.7 6.6 - - - +
214A ALA* 3.1 27.5 + - - +
239A PHE* 4.3 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A SER* 3.2 29.3 + - - -
185A THR* 3.4 21.6 + - + +
188A LEU* 5.8 2.5 - - + -
203A ASP* 3.7 19.1 - - - +
206A GLY* 5.2 4.7 + - - -
209A GLY* 3.1 1.5 - - - -
210A ALA* 1.3 74.1 - - - +
212A VAL* 1.3 67.8 + - - +
213A ALA 3.1 1.3 - - - -
214A ALA* 3.1 13.8 + - - +
215A ILE* 3.1 19.6 + - + +
260A LEU* 3.8 18.2 - - + -
262A LYS* 4.6 11.6 - - + +
401A SAH 4.4 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LEU* 4.0 23.6 - - + +
203A ASP* 4.1 16.0 + - + -
209A GLY* 3.5 12.9 + - - +
211A THR* 1.3 80.6 - - - +
213A ALA* 1.3 59.9 + - - +
215A ILE* 3.9 7.5 - - - +
216A ALA* 2.9 30.2 + - + +
222A ILE* 5.9 0.4 - - + -
224A GLY* 3.8 26.7 - - - -
225A VAL 3.9 9.0 - - - +
226A ASN* 4.0 18.2 - - + +
242A VAL* 3.9 23.1 - - + +
260A LEU* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A GLY 3.1 19.6 + - - +
210A ALA* 3.7 7.2 - - - +
211A THR 3.1 0.6 - - - -
212A VAL* 1.3 76.2 - - - +
214A ALA* 1.3 59.7 + - - +
216A ALA* 3.2 2.5 + - - +
217A ALA* 2.8 30.9 + - - +
239A PHE* 3.5 38.4 - - + -
240A PRO* 4.9 2.8 - - + +
242A VAL* 3.5 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ILE* 6.2 3.1 - - + +
185A THR* 3.6 22.2 - - + -
189A LEU* 3.9 7.0 - - + +
210A ALA 3.1 10.7 + - - +
211A THR 3.1 10.0 + - - +
213A ALA* 1.3 80.0 - - - +
215A ILE* 1.3 62.8 + - - +
217A ALA* 3.3 7.6 + - - +
218A HIS* 3.1 22.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
185A THR* 3.9 14.8 - - + -
188A LEU* 4.7 2.2 - - + -
189A LEU* 4.1 14.8 - - + -
195A PHE* 3.9 29.2 - - + -
201A LEU* 3.7 26.2 - - + -
211A THR* 3.1 21.7 + - + +
212A VAL* 4.0 4.0 - - - +
214A ALA* 1.3 76.7 - - - +
216A ALA* 1.3 58.9 + - - +
218A HIS* 3.2 3.1 + - - +
219A TYR* 2.9 44.5 + - + +
222A ILE* 5.6 3.8 - - + -
260A LEU* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A VAL 2.9 20.4 + - - +
213A ALA* 3.6 5.8 - - - +
215A ILE* 1.3 78.7 - - - +
217A ALA* 1.3 59.5 + - - +
219A TYR 3.3 22.8 - - - +
220A PRO* 3.7 5.7 - - - +
222A ILE* 4.7 18.4 - - + +
224A GLY* 5.0 2.0 - - - +
240A PRO 4.1 17.9 - - - +
241A GLY* 4.2 17.0 - - - +
242A VAL* 4.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ALA 2.8 17.2 + - - +
214A ALA* 3.6 8.5 - - - +
215A ILE 3.2 0.2 - - - -
216A ALA* 1.3 77.2 - - - +
218A HIS* 1.3 61.0 + - - +
220A PRO* 4.6 5.2 - - - +
240A PRO* 5.2 3.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LEU* 3.7 41.6 + - + +
214A ALA 3.1 12.8 + - - +
215A ILE 3.2 7.6 + - - +
217A ALA* 1.3 80.6 - - - +
219A TYR* 1.3 91.8 + + + +
220A PRO* 3.4 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LEU* 3.9 21.6 + - + +
192A TYR 4.5 11.1 + - - -
193A HIS* 5.0 0.2 - - - -
195A PHE* 4.0 22.4 - + + +
196A GLU* 3.6 41.1 + - + +
197A GLY 5.6 0.9 - - - -
215A ILE* 2.9 26.8 + - + +
216A ALA* 3.3 9.2 - - - +
218A HIS* 1.3 105.8 + + + +
220A PRO* 1.3 62.8 - - - +
221A THR* 3.1 3.8 - - - +
222A ILE* 2.9 46.1 + - + +
----------------------------------------------------------
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