Contacts of the helix formed by residues 215 - 232 (chain C) in PDB entry 2PJ7
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 ASN 215 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C PRO* 3.8 1.2 - - - +
214C GLU* 1.3 73.8 - - + +
216C ASN* 1.3 57.6 + - - +
217C ALA 3.2 2.9 - - - -
218C GLU* 3.0 33.7 + - + +
219C LEU* 2.9 38.5 + - - +
259C TYR* 2.6 37.2 + - - -
264C LYS* 3.2 29.7 - - + +
265C TYR* 4.6 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 216 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C TYR* 4.2 9.4 + - + +
212C LEU* 4.0 28.4 - - + +
213C PRO* 2.8 47.3 + - + +
214C GLU* 3.3 8.7 + - - +
215C ASN* 1.3 76.6 - - - +
217C ALA* 1.3 72.0 + - - +
219C LEU* 3.7 4.8 - - - +
220C ASN* 2.8 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 217 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C GLU 5.0 0.2 + - - -
215C ASN 3.2 0.8 - - - -
216C ASN* 1.3 85.7 + - - +
218C GLU* 1.3 62.8 + - - +
220C ASN* 3.9 6.0 - - - +
221C ASN* 2.5 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 218 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C ASN* 3.0 35.5 + - + +
217C ALA* 1.3 80.0 - - - +
219C LEU* 1.3 62.4 + - - +
221C ASN* 3.4 7.1 + - - +
222C LEU* 3.0 23.4 + - + +
264C LYS* 5.3 3.3 + - - -
265C TYR* 2.6 36.7 + - + -
303C TYR* 2.5 35.7 + - + +
307C HIS* 4.5 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C TYR* 3.9 28.7 - - + -
205C PRO* 4.3 3.8 - - + -
213C PRO* 3.8 21.5 - - + -
215C ASN* 2.9 39.4 + - - +
216C ASN 3.8 4.5 - - - +
218C GLU* 1.3 77.5 - - - +
220C ASN* 1.3 59.3 + - - +
222C LEU* 3.3 5.1 + - + +
223C ALA* 2.9 30.7 + - - +
259C TYR* 4.3 9.0 - - + -
264C LYS 3.7 17.5 - - - +
265C TYR* 4.2 14.1 - - + -
266C SER 4.8 1.8 - - - +
267C PHE* 3.7 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 220 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C TYR* 2.9 27.9 + - - +
216C ASN 2.8 20.0 + - - +
217C ALA* 3.9 6.1 - - - +
219C LEU* 1.3 77.0 - - - +
221C ASN* 1.3 62.7 + - - +
223C ALA* 3.4 0.5 + - - +
224C LYS* 2.9 36.6 + - - +
240C TYR* 3.5 30.1 + - - -
241C GLY* 4.6 3.0 - - - -
242C PRO* 5.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 221 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C ALA* 2.5 31.9 + - - +
218C GLU* 3.8 6.7 - - - +
220C ASN* 1.3 78.1 - - - +
222C LEU* 1.3 60.9 + - - +
224C LYS* 3.4 21.5 + - + +
225C ALA* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 222 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C GLU 3.0 16.6 + - - +
219C LEU* 3.6 6.5 - - + +
221C ASN* 1.3 74.3 - - - +
223C ALA* 1.3 60.1 + - - +
225C ALA* 3.2 3.5 + - - +
226C ALA* 2.8 31.2 + - - +
265C TYR* 4.3 11.9 - - + -
267C PHE* 3.9 26.9 - - + -
299C TYR* 3.5 33.2 - - + -
300C VAL* 4.1 20.4 - - + -
303C TYR* 3.6 46.0 - - + -
304C VAL* 5.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 223 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C ILE* 4.0 19.7 - - + -
204C TYR* 4.5 9.6 - - + -
219C LEU 2.9 17.6 + - - +
220C ASN 3.8 3.6 - - - +
222C LEU* 1.3 76.1 - - - +
224C LYS* 1.3 58.8 + - - +
226C ALA* 3.2 6.8 + - - +
227C VAL* 2.9 36.9 + - - +
240C TYR* 3.9 26.5 - - + -
267C PHE* 4.5 4.2 - - + -
300C VAL* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 224 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C ASN* 2.9 25.7 + - - +
221C ASN* 3.5 20.6 + - - +
223C ALA* 1.3 76.7 - - - +
225C ALA* 1.3 60.6 + - + +
227C VAL* 2.9 22.1 - - + +
228C LYS* 3.2 8.3 + - - +
240C TYR* 3.4 32.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 225 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C ASN 3.0 17.6 + - - +
222C LEU 3.8 0.2 - - - +
224C LYS* 1.3 79.2 - - + +
226C ALA* 1.3 57.6 + - - +
228C LYS* 3.3 11.0 + - - +
229C GLU* 3.0 27.5 + - - +
299C TYR* 3.3 40.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 226 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C ILE* 3.8 17.3 - - + -
222C LEU 2.8 16.8 + - - +
223C ALA* 3.2 5.6 + - - +
225C ALA* 1.3 78.4 - - - +
227C VAL* 1.3 56.8 + - - +
229C GLU* 3.3 8.4 + - - +
230C LEU* 3.0 27.4 + - - +
296C ALA* 3.8 26.2 - - + +
299C TYR* 4.3 8.2 - - + -
300C VAL* 4.2 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 227 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C ILE* 3.8 20.2 - - + -
223C ALA 2.9 17.8 + - - +
224C LYS* 2.9 26.2 - - + +
226C ALA* 1.3 73.2 - - - +
228C LYS* 1.3 66.1 + - - +
230C LEU* 3.3 8.6 + - - +
231C ALA* 3.1 24.3 + - - +
236C THR 4.9 1.0 - - - +
238C TYR* 3.7 37.1 + - + +
240C TYR* 3.8 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 228 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C LYS* 3.2 9.1 + - + +
225C ALA* 3.4 13.7 - - - +
226C ALA 3.2 0.2 - - - -
227C VAL* 1.3 84.3 - - + +
229C GLU* 1.3 62.0 + - - +
231C ALA* 3.3 12.8 + - - +
232C THR* 3.3 21.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 229 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C ALA 3.0 12.7 + - - +
226C ALA* 3.3 12.1 + - - +
228C LYS* 1.3 78.3 - - - +
230C LEU* 1.3 59.3 + - - +
232C THR* 2.8 34.8 + - - +
295C LEU* 3.4 50.1 - - + +
299C TYR* 4.5 18.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 230 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C ILE* 5.8 0.7 - - + -
226C ALA 3.0 16.1 + - - +
227C VAL* 3.6 7.6 - - - +
228C LYS 3.3 0.2 - - - -
229C GLU* 1.3 76.5 - - - +
231C ALA* 1.3 63.0 + - - +
232C THR 3.2 0.7 + - - -
233C LEU* 3.6 9.2 + - - +
234C TYR 4.5 0.9 + - - -
236C THR* 3.7 17.7 + - - +
238C TYR* 3.6 51.6 - - + +
269C PHE* 5.5 1.8 - - + -
292C GLU* 3.4 59.0 - - + +
293C THR* 4.1 13.5 - - + +
295C LEU* 4.5 2.0 - - - +
296C ALA* 4.2 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 231 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C VAL 3.1 15.1 + - - +
228C LYS* 3.8 8.3 - - - +
229C GLU 3.2 0.6 - - - -
230C LEU* 1.3 76.0 - - - +
232C THR* 1.3 58.3 + - - +
233C LEU 3.2 0.4 - - - -
235C GLY* 2.9 31.6 + - - -
236C THR 3.5 27.4 - - - +
237C LYS* 5.3 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 232 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C LYS* 3.3 22.2 - - + +
229C GLU* 2.8 27.4 + - - +
231C ALA* 1.3 76.6 - - - +
233C LEU* 1.3 62.9 + - - +
235C GLY 4.7 0.2 - - - -
295C LEU* 3.7 10.6 - - - +
----------------------------------------------------------
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