Contacts of the helix formed by residues 195 - 217 (chain C) in PDB entry 4U1D
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 ARG 195 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C THR* 4.8 9.1 + - - +
155C LEU* 3.7 27.0 - - - +
156C ARG* 3.9 25.1 - - - +
189C PHE* 4.2 12.5 - - + -
190C CYS* 3.0 17.8 + - + +
193C TYR* 3.3 33.7 - - + +
194C GLN* 1.3 71.4 - - - +
196C LYS* 1.3 64.1 + - - +
197C ASN 3.4 2.5 - - - -
198C GLU* 2.6 48.8 + - + +
199C PHE* 3.1 21.9 + - - +
250C LEU* 4.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 196 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C GLN* 3.0 43.5 + - - +
195C ARG* 1.3 70.8 - - - +
197C ASN* 1.3 62.8 + - - +
199C PHE* 3.3 5.9 + - - +
200C LYS* 3.1 29.8 + - - +
250C LEU* 3.2 33.4 + - + +
251C GLU* 4.7 9.1 + - - +
252C LEU* 3.8 33.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 197 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C ARG 3.4 0.4 - - - -
196C LYS* 1.3 78.0 - - - +
198C GLU* 1.3 66.2 - - + +
200C LYS* 3.4 17.1 + - - +
201C ARG* 3.4 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 198 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C ARG* 3.4 16.8 + - - +
159C TRP* 3.1 66.3 - - + +
189C PHE* 3.9 4.0 - - - -
190C CYS* 4.8 0.9 - - - -
195C ARG* 2.6 57.1 + - + +
196C LYS 3.3 0.2 - - - -
197C ASN* 1.3 75.5 - - + +
199C PHE* 1.3 61.6 + - - +
201C ARG* 3.2 18.3 + - - +
202C LEU 2.8 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 199 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C MET* 4.5 16.4 - - + -
190C CYS* 3.9 24.6 - - + -
195C ARG 3.1 14.3 + - - +
196C LYS* 3.3 10.1 + - - +
198C GLU* 1.3 77.1 - - - +
200C LYS* 1.3 65.3 + - - +
202C LEU* 3.1 11.8 + - + +
203C ALA* 2.9 23.6 + - + +
243C GLN* 3.4 26.5 - - + -
246C VAL* 3.6 24.0 - - + -
247C SER* 3.2 38.4 - - - -
250C LEU* 4.3 6.1 - - + -
252C LEU* 3.8 17.9 - - + -
255C GLU* 3.9 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 200 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C LYS* 3.1 16.7 + - - +
197C ASN* 3.6 18.8 - - - +
199C PHE* 1.3 80.1 - - - +
201C ARG* 1.3 61.6 + - + +
203C ALA* 3.5 5.1 + - - +
204C GLU* 3.2 20.8 + - - +
207C ARG* 4.8 0.5 + - - -
252C LEU* 4.0 42.5 - - + +
254C HIS* 5.1 5.3 - - - +
255C GLU* 4.0 31.6 - - + +
258C ARG* 4.2 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 201 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C ARG* 3.6 25.1 - - - +
159C TRP* 3.6 29.7 - - + +
163C ARG* 4.1 18.4 - - - +
197C ASN* 3.4 19.0 + - - +
198C GLU* 3.2 25.6 + - - +
199C PHE 3.2 0.4 - - - -
200C LYS* 1.3 76.2 - - + +
202C LEU* 1.3 61.0 + - - +
204C GLU* 3.3 9.3 + - - +
205C MET* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 202 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C TRP* 3.5 18.8 - - + -
166C LEU* 3.7 19.1 - - + -
183C VAL* 5.0 1.1 - - + +
186C THR* 3.6 26.0 - - + -
187C MET* 3.7 36.1 - - + +
190C CYS* 4.6 3.4 - - - -
198C GLU 2.8 7.3 + - - +
199C PHE* 3.3 18.6 - - + +
201C ARG* 1.3 77.0 - - - +
203C ALA* 1.3 63.1 + - - +
205C MET* 3.0 30.1 + - + +
206C LEU* 3.0 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 203 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C MET* 5.8 0.4 - - - -
199C PHE* 2.9 15.2 + - + +
200C LYS* 3.6 9.2 - - - +
202C LEU* 1.3 78.8 - - - +
204C GLU* 1.3 62.2 + - - +
206C LEU* 3.4 4.4 + - - +
207C ARG* 3.1 29.9 + - - +
243C GLN* 3.8 30.8 - - + +
255C GLU* 3.5 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 204 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C LYS 3.2 11.3 + - - +
201C ARG* 3.6 10.8 - - - +
202C LEU 3.2 0.6 - - - -
203C ALA* 1.3 79.0 - - - +
205C MET* 1.3 62.7 + - - +
207C ARG* 3.1 31.2 + - - +
208C GLN* 3.1 44.8 + - + +
258C ARG* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 205 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B LYS* 4.8 11.0 - - - +
159C TRP* 5.1 2.2 - - + -
163C ARG* 4.2 38.6 - - + +
166C LEU* 3.8 20.4 - - + -
167C ASP* 4.1 13.9 - - - +
201C ARG 2.9 13.1 + - - +
202C LEU* 3.0 35.2 + - + +
204C GLU* 1.3 77.6 - - - +
206C LEU* 1.3 58.3 + - + +
208C GLN* 3.2 9.0 + - - +
209C HIS* 2.9 53.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 206 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C LEU* 4.3 12.1 - - + -
179C TYR* 3.8 20.2 - - - +
183C VAL* 3.7 18.8 - - + -
187C MET* 3.7 29.6 - - + -
202C LEU* 3.0 35.2 + - + +
203C ALA 3.7 8.3 - - - +
204C GLU 3.3 0.2 - - - -
205C MET* 1.3 80.1 - - + +
207C ARG* 1.3 62.3 + - + +
209C HIS* 3.5 8.7 + - - +
210C LEU* 3.2 12.3 + - - +
239C GLN* 4.4 1.1 - - + +
240C ARG* 3.2 42.2 + - - +
243C GLN* 4.0 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 207 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C LYS 4.8 0.4 + - - -
203C ALA* 3.1 29.8 + - - +
204C GLU* 3.3 37.3 + - - +
206C LEU* 1.3 75.6 - - + +
208C GLN* 1.3 64.9 + - - +
210C LEU* 3.2 6.7 + - - +
211C ASP* 3.0 33.6 + - - +
240C ARG* 5.2 2.7 - - - +
243C GLN* 3.8 5.4 - - - +
255C GLU* 2.6 33.7 + - - -
258C ARG* 3.3 30.8 + - - +
259C SER* 3.9 1.8 + - - -
262C ASP* 2.8 40.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 208 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B LYS* 3.1 35.7 - - + +
471B GLN* 4.5 23.6 + - - +
204C GLU* 3.1 37.7 + - - +
205C MET* 3.7 7.9 - - - +
207C ARG* 1.3 75.6 - - - +
209C HIS* 1.3 64.6 + - + +
211C ASP* 3.3 12.4 + - - +
212C ALA* 3.1 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 209 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B LYS* 5.6 2.9 - - - -
166C LEU* 3.6 24.9 - - + -
167C ASP* 3.1 23.7 + - - -
170C ARG* 3.7 28.0 - - + +
171C ASN* 3.1 25.5 + - - +
179C TYR* 2.8 31.2 + + + +
205C MET* 2.9 39.3 + - + +
206C LEU* 3.5 10.5 - - + +
207C ARG 3.2 0.2 - - - -
208C GLN* 1.3 81.2 - - + +
210C LEU* 1.3 57.6 + - - +
212C ALA* 3.2 1.9 + - - -
213C ALA 3.1 21.0 + - - -
240C ARG* 5.4 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 210 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C LEU 3.2 9.7 + - - +
207C ARG* 3.2 10.1 + - - +
209C HIS* 1.3 77.7 - - - +
211C ASP* 1.3 63.6 + - - +
213C ALA* 3.2 4.4 + - + +
214C ASN* 2.9 44.3 + - - +
227C LEU* 4.1 15.0 - - + -
236C TYR* 3.9 35.0 - - + -
240C ARG* 3.8 17.5 - - - +
266C LEU* 3.5 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 211 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B VAL* 3.9 26.6 - - + +
207C ARG* 3.0 21.2 + - - +
208C GLN* 3.6 13.8 - - - +
209C HIS 3.3 0.4 - - - -
210C LEU* 1.3 81.9 - - - +
212C ALA* 1.3 55.9 + - - +
214C ASN* 3.6 9.5 + - - +
215C TYR* 3.2 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 212 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B LEU* 4.1 28.9 - - + -
474B VAL* 4.8 5.1 - - + +
171C ASN* 3.4 20.6 - - - +
208C GLN 3.1 12.3 + - - +
209C HIS* 3.5 3.1 - - - +
211C ASP* 1.3 73.4 - - - +
213C ALA* 1.3 66.8 + - - +
215C TYR* 3.2 6.6 + - - +
216C GLN* 3.0 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 213 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C ASN* 3.7 22.6 - - - +
209C HIS 3.1 7.8 + - - +
210C LEU* 3.2 17.2 + - + +
212C ALA* 1.3 76.3 - - - +
214C ASN* 1.3 63.2 + - - +
216C GLN* 3.0 8.4 + - - +
217C GLN* 3.0 28.0 + - - +
225C VAL* 4.6 11.4 - - + -
227C LEU* 3.9 22.9 - - + -
236C TYR* 5.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 214 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C LEU* 2.9 35.8 + - - +
211C ASP* 3.8 10.0 - - - +
212C ALA 3.3 0.2 - - - -
213C ALA* 1.3 77.6 - - - +
215C TYR* 1.3 61.2 + - - +
217C GLN* 3.5 21.3 + - - +
218C SER* 4.6 2.8 + - - -
227C LEU* 3.4 18.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 215 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B LEU* 4.6 13.0 - - + -
473B ALA* 3.4 43.0 - - + +
474B VAL* 4.0 17.0 - - + -
476B ASP* 4.9 4.7 - - - -
478B VAL 5.0 0.2 - - - -
479B SER* 3.4 15.7 + - - -
480B ILE* 2.9 48.5 + - + -
211C ASP 3.2 17.0 + - - +
212C ALA* 3.7 5.6 - - - +
213C ALA 3.2 0.4 - - - -
214C ASN* 1.3 77.9 - - - +
216C GLN* 1.3 66.5 + - + +
217C GLN 3.5 0.3 + - - -
218C SER* 3.8 8.8 + - - -
219C LYS* 3.8 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 216 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B GLU* 5.5 0.6 + - - -
470B LEU* 4.0 22.8 - - + +
482B ILE* 4.0 24.7 - - + +
484B HIS* 4.2 8.7 + - - -
171C ASN* 4.0 20.2 - - - +
212C ALA 3.0 19.9 + - - +
213C ALA* 3.0 6.2 + - - +
215C TYR* 1.3 84.8 - - + +
217C GLN* 1.3 65.8 + - - +
218C SER 3.2 2.5 - - - -
219C LYS* 3.2 27.3 + - + +
220C SER 4.3 0.9 + - - -
224C LEU* 3.3 44.0 - - + +
225C VAL* 5.5 2.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 217 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C ALA 3.0 23.9 + - - +
214C ASN* 3.5 15.9 - - - +
215C TYR 3.3 0.8 - - - -
216C GLN* 1.3 78.4 - - - +
218C SER* 1.3 57.7 + - - +
219C LYS 3.1 5.0 + - - -
220C SER* 4.1 5.4 + - - -
225C VAL* 2.5 30.8 + - - +
226C ASP* 3.8 9.7 - - - +
227C LEU* 3.0 49.6 + - + +
228C SER* 4.0 5.7 + - - -
----------------------------------------------------------
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