Contacts of the helix formed by residues 207 - 222 (chain A) in PDB entry 1JPP
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 ASP 207 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ASN* 3.4 33.7 + - - +
205A THR* 3.2 7.2 + - - +
206A ASN* 1.3 82.5 - - - +
208A VAL* 1.3 81.5 + - - +
209A GLU* 4.1 9.4 + - - +
210A THR* 3.6 12.2 + - - +
211A ALA* 3.8 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ASN 4.2 1.1 + - - +
207A ASP* 1.3 80.1 + - - +
209A GLU* 1.3 70.5 + - + +
210A THR 3.2 1.1 - - - -
211A ALA* 2.8 25.9 + - - +
212A ARG* 2.8 15.2 + - + +
248A VAL* 4.6 33.0 - - + -
251A VAL* 4.9 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ASP* 4.1 7.3 + - - +
208A VAL* 1.3 85.1 - - + +
210A THR* 1.3 61.1 + - - +
212A ARG* 3.5 38.4 + - + +
213A CYS* 2.7 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A VAL* 4.7 2.0 - - + +
169A ASN* 2.7 44.3 + - - +
172A ALA* 4.2 17.0 - - + -
173A VAL* 6.2 0.9 - - - -
201A THR* 4.1 24.2 - - + -
205A THR* 3.6 25.4 - - - +
207A ASP* 3.6 8.8 + - - -
208A VAL 3.1 1.2 + - - -
209A GLU* 1.3 76.4 - - - +
211A ALA* 1.3 58.5 + - - +
213A CYS* 4.0 3.7 - - - +
214A THR* 2.9 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A MET* 5.0 4.7 - - - +
205A THR* 4.3 13.7 - - + +
207A ASP 3.8 11.1 + - - +
208A VAL* 2.8 13.8 + - - +
210A THR* 1.3 78.1 - - - +
212A ARG* 1.3 63.2 + - - +
214A THR* 3.1 7.0 + - - -
215A ALA* 3.0 29.3 + - - +
243A MET* 5.3 7.4 - - - -
251A VAL* 4.4 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A HIS* 4.6 11.8 + - - -
208A VAL* 2.8 12.0 + - + +
209A GLU* 3.6 38.7 + - + +
211A ALA* 1.3 78.1 - - - +
213A CYS* 1.3 88.6 + - - +
215A ALA* 4.3 2.7 - - - +
216A GLY* 3.6 14.2 + - - -
248A VAL* 5.2 1.8 - - + -
250A SER* 3.2 34.1 - - - +
251A VAL* 3.8 14.9 - - + +
254A TYR* 4.4 18.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ALA* 4.6 11.9 - - + +
173A VAL* 4.5 24.0 - - + -
176A HIS* 3.7 31.3 + - + -
209A GLU* 2.7 24.6 + - - +
210A THR* 4.0 4.7 - - - +
212A ARG* 1.3 102.2 - - - +
214A THR* 1.3 63.7 + - - +
215A ALA 3.3 1.3 - - - -
216A GLY 3.3 1.2 + - - -
217A THR* 3.0 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ALA* 4.2 19.3 - - + -
198A ILE* 4.5 13.6 - - + +
201A THR* 4.2 21.5 - - + -
202A MET* 3.1 32.2 - - - +
210A THR* 2.9 27.4 + - + +
211A ALA* 3.1 7.6 + - - -
213A CYS* 1.3 71.8 - - - +
215A ALA* 1.3 66.6 + - - +
217A THR* 3.3 16.5 + - - -
218A LEU* 3.4 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A MET* 4.2 18.2 - - + -
211A ALA 3.0 17.2 + - - +
212A ARG 4.3 3.4 - - - +
214A THR* 1.3 78.4 + - - +
216A GLY* 1.3 63.7 + - - +
217A THR 3.4 0.2 + - - -
218A LEU* 3.4 5.5 + - - +
219A HIS* 3.2 21.7 + - - +
240A LEU* 6.4 0.4 - - - -
243A MET* 6.1 1.1 - - + -
251A VAL* 4.6 16.4 - - + +
254A TYR* 4.4 23.6 - - + +
255A ALA* 5.3 3.1 - - + +
258A THR* 4.8 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A HIS* 4.3 13.4 - - - -
212A ARG 3.6 8.3 + - - -
213A CYS 3.3 7.8 + - - -
214A THR 3.3 0.4 - - - -
215A ALA* 1.3 80.9 - - - +
217A THR* 1.3 59.5 + - - +
219A HIS* 3.5 0.9 + - - +
220A ASN* 3.3 31.0 + - - -
254A TYR* 4.0 25.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ALA 5.0 0.9 + - - -
175A VAL* 4.3 13.2 - - + +
176A HIS* 3.5 21.4 + - - +
179A SER* 4.3 20.6 - - - -
188A ILE* 5.3 2.5 - - + -
198A ILE* 4.0 30.5 - - + -
213A CYS 3.0 15.9 + - - -
214A THR* 3.6 11.6 - - - -
215A ALA 3.2 0.4 - - - -
216A GLY* 1.3 76.3 - - - +
218A LEU* 1.3 62.2 + - + +
220A ASN* 3.6 1.9 + - - +
221A LEU* 2.9 37.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A VAL* 5.2 7.0 - - + +
198A ILE* 4.1 22.9 - - + -
199A VAL* 4.4 23.1 - - + -
202A MET* 3.9 36.6 - - + -
214A THR 3.7 8.3 - - - +
215A ALA* 3.4 7.0 + - - +
216A GLY 3.4 0.2 - - - -
217A THR* 1.3 76.3 - - + +
219A HIS* 1.3 65.8 + - - +
221A LEU* 3.0 20.8 + - + +
222A SER* 3.2 10.6 + - - -
231A ILE* 3.6 33.3 - - + +
236A GLY* 5.6 1.1 - - - +
240A LEU* 4.1 13.2 - - + -
258A THR* 4.6 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A ALA 3.2 15.1 + - - +
216A GLY 3.6 5.8 - - - +
218A LEU* 1.3 79.2 - - - +
220A ASN* 1.3 71.1 + - - +
222A SER* 2.8 23.5 + - - -
223A HIS* 3.6 34.0 + + - -
254A TYR* 3.9 26.5 - + + -
257A THR* 3.1 33.1 + - - +
258A THR* 3.6 20.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A HIS* 4.9 2.4 - - - -
179A SER* 3.5 36.3 + - - +
180A LYS* 4.2 16.5 - - - +
185A ARG* 4.5 13.2 + - - +
189A MET* 5.4 1.4 - - - +
216A GLY* 3.3 16.2 + - - +
217A THR 4.0 5.2 - - - +
218A LEU 3.2 0.6 - - - -
219A HIS* 1.3 96.6 + - - +
221A LEU* 1.3 62.4 - - + +
222A SER 3.2 3.4 + - - -
223A HIS* 3.6 25.3 + - - +
254A TYR* 5.9 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A SER* 4.4 17.3 - - - -
185A ARG* 5.0 9.4 - - + +
188A ILE* 3.8 23.8 - - + -
189A MET* 3.6 42.7 - - + +
195A VAL* 5.2 7.6 - - + -
198A ILE* 6.3 1.1 - - + -
217A THR* 2.9 30.5 - - + +
218A LEU* 3.0 16.2 + - + +
220A ASN* 1.3 78.9 - - + +
222A SER* 1.3 60.0 + - - +
223A HIS 3.4 1.2 + - - -
224A HIS 3.7 2.8 - - - +
227A GLY* 3.2 30.9 - - - +
230A ALA* 5.9 1.1 - - + -
231A ILE* 4.0 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LEU 3.2 8.7 + - - -
219A HIS* 2.8 21.8 + - - -
220A ASN 3.2 0.4 - - - -
221A LEU* 1.3 76.6 - - - +
223A HIS* 1.3 56.0 + - - +
224A HIS 3.1 9.9 + - - -
228A LEU* 3.3 36.3 - - - +
231A ILE* 4.5 2.2 - - - -
258A THR* 4.2 19.8 - - - +
261A ASN* 3.5 30.2 + - - +
----------------------------------------------------------
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