Contacts of the helix formed by residues 207 - 220 (chain A) in PDB entry 1PKD
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 SER 207 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A LEU* 3.5 11.3 - - - +
206A ASP* 1.3 78.2 - - - +
208A GLU* 1.3 62.0 + - - +
209A ILE* 3.6 12.5 - - - +
210A ASP* 3.1 22.8 + - - +
211A GLN* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A HIS* 4.2 20.9 + - - -
166A LEU* 4.3 3.1 - - + +
169A ARG* 3.9 26.9 + - - +
174A LEU* 3.7 35.3 - - + +
207A SER* 1.3 75.7 - - - +
209A ILE* 1.3 57.4 + - - +
211A GLN* 3.3 2.6 + - - +
212A LEU* 2.9 29.9 + - - +
235A ASP* 5.3 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A SER* 3.6 13.0 - - - +
208A GLU* 1.3 75.5 - - - +
210A ASP* 1.3 66.5 + - + +
212A LEU* 3.3 11.8 + - + +
213A PHE* 2.8 69.3 + - + -
237A LYS* 4.4 14.4 - - + +
240A PHE* 3.8 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A GLY* 3.3 6.8 - - - -
206A ASP* 2.6 35.6 + - + +
207A SER* 3.1 23.1 - - - +
209A ILE* 1.3 82.1 - - + +
211A GLN* 1.3 62.4 - - - +
213A PHE* 3.3 7.0 + - - +
214A ARG* 2.9 43.3 + - - +
217A ARG* 5.0 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A LEU* 3.3 34.5 + - + +
167A TRP* 3.4 14.5 + - - -
169A ARG 4.7 1.9 + - - +
174A LEU* 3.8 18.8 - - + -
203A PHE* 2.6 42.7 + - - +
205A GLY* 2.7 32.0 + - - -
207A SER 2.9 19.0 + - - +
208A GLU 3.4 4.9 - - - +
210A ASP* 1.3 74.1 - - - +
212A LEU* 1.3 63.0 + - - +
214A ARG* 3.3 4.9 + - - +
215A ILE* 3.1 32.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A PRO* 4.6 9.2 - - + -
174A LEU* 4.0 33.2 - - + +
175A LEU* 3.7 30.7 - - + -
208A GLU 2.9 15.4 + - - +
209A ILE* 3.4 19.5 - - + +
211A GLN* 1.3 77.0 - - - +
213A PHE* 1.3 62.4 + - + +
215A ILE* 3.1 8.4 + - + +
216A PHE* 2.9 59.2 + - + -
235A ASP* 5.3 0.4 - - + +
240A PHE* 3.7 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ILE* 2.8 55.8 + - + +
210A ASP* 3.9 7.2 - - - +
212A LEU* 1.3 76.8 - - + +
214A ARG* 1.3 57.1 + - - +
216A PHE* 3.5 12.8 + + - +
217A ARG* 3.0 54.1 + - - +
240A PHE* 3.8 22.9 - + - -
241A PRO* 3.7 26.0 - - + -
243A TRP* 4.0 19.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A LEU 5.6 0.2 - - - +
203A PHE* 3.7 14.6 - - + -
204A PRO* 3.4 46.1 + - + +
205A GLY* 3.6 28.4 - - - +
206A ASP* 5.0 5.1 + - - -
210A ASP* 2.9 31.5 + - - +
211A GLN* 3.7 4.7 - - - +
212A LEU 3.2 0.2 - - - -
213A PHE* 1.3 75.8 - - - +
215A ILE* 1.3 61.9 + - - +
217A ARG* 3.6 24.0 + - - +
218A THR* 3.1 25.6 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
169A ARG 4.2 7.0 - - - +
171A PRO* 4.7 7.0 - - + -
174A LEU* 3.8 25.6 - - + -
187A TRP* 3.6 37.2 - - + -
203A PHE* 3.7 30.5 - - + -
211A GLN* 3.1 19.8 + - + +
212A LEU* 3.1 9.4 + - + +
214A ARG* 1.3 76.0 - - - +
216A PHE* 1.3 61.5 + - + +
218A THR* 2.9 6.6 + - - -
219A LEU* 2.9 30.4 + - + +
269A TYR* 3.5 20.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A PRO* 5.5 0.4 - - + -
175A LEU* 4.9 7.0 - - + -
212A LEU* 2.9 49.2 + - + +
213A PHE* 3.7 22.2 - + - +
215A ILE* 1.3 71.5 - - + +
217A ARG* 1.3 55.4 + - - +
220A GLY* 2.6 34.1 + - - -
221A THR* 3.6 22.8 + - + +
222A PRO* 3.3 28.5 - - + -
236A TYR* 5.7 0.4 - + - -
240A PHE* 3.6 39.0 - + - -
241A PRO 4.5 2.0 - - - -
243A TRP* 3.7 19.3 - + + +
269A TYR* 3.5 22.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ASP* 5.0 4.8 + - - -
213A PHE* 3.0 40.1 + - - +
214A ARG* 3.8 35.5 - - - +
215A ILE 3.2 0.4 - - - -
216A PHE* 1.3 75.5 - - - +
218A THR* 1.3 59.6 + - - +
220A GLY 4.5 0.4 - - - -
243A TRP* 3.2 58.2 - - + +
244A ALA 4.4 4.4 - - - +
246A GLN* 3.9 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A LEU* 4.8 4.1 + - + +
203A PHE* 3.6 24.7 - - + -
214A ARG 3.1 11.5 + - - -
215A ILE 2.9 7.9 + - - -
217A ARG* 1.3 80.6 - - - +
219A LEU* 1.3 67.6 + - + +
220A GLY 3.5 0.7 - - - -
245A ARG* 4.8 0.5 - - - +
246A GLN* 3.5 32.3 + - - +
248A PHE* 5.6 0.9 - - - -
251A VAL* 3.7 38.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A TRP* 3.5 25.8 - - + -
203A PHE* 4.4 7.6 - - + -
215A ILE* 2.9 13.1 + - + +
218A THR* 1.3 88.4 - - + +
220A GLY* 1.3 61.3 + - - +
245A ARG* 3.1 39.4 + - - +
248A PHE* 3.7 33.2 - - + -
251A VAL* 5.7 0.4 - - + -
267A LEU* 3.4 36.6 - - + +
269A TYR* 3.4 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A PHE 2.6 21.1 + - - -
218A THR 3.5 1.6 - - - -
219A LEU* 1.3 74.9 - - - +
221A THR* 1.3 63.1 + - - -
243A TRP 3.3 13.2 - - - -
244A ALA 3.8 1.5 + - - -
245A ARG* 3.6 16.8 - - - +
269A TYR* 2.6 32.4 + - - -
----------------------------------------------------------
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