Contacts of the helix formed by residues 173 - 189 (chain G) in PDB entry 5JLH
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 HIS 173 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135G TYR* 3.4 33.2 - + - +
137G TYR* 3.5 7.9 + - - -
142G CYS* 4.1 4.3 - - - -
153G ILE* 3.5 18.3 - - + +
154G TYR* 3.2 33.5 - + - -
158G ILE* 4.7 0.4 - - + -
162G TYR* 3.2 33.6 - + + +
171G PRO 3.3 3.1 + - - +
172G PRO* 1.3 76.4 - - - +
174G VAL* 1.3 80.3 + - + +
175G TYR* 3.0 43.9 + + - +
176G ALA* 3.3 17.2 - - + +
177G VAL* 3.5 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 174 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135G TYR* 3.3 36.1 - - + +
142G CYS* 4.9 3.6 - - - -
154G TYR* 5.6 0.4 - - + -
173G HIS* 1.3 78.5 + - + +
175G TYR* 1.3 55.4 + - + +
176G ALA 2.9 4.5 - - - -
177G VAL* 2.8 24.2 + - + +
178G THR* 2.8 35.9 + - + +
207G ASN* 3.3 20.6 - - - +
210G LYS* 6.6 0.2 - - + -
211G VAL* 3.3 34.3 - - + -
693G VAL* 5.3 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 175 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154G TYR* 3.2 44.0 + + - +
155G THR 4.8 0.6 + - - -
158G ILE* 4.3 4.0 - - + -
159G VAL* 4.2 20.4 - - + -
162G TYR* 3.2 34.3 - + + -
173G HIS* 3.0 25.1 + + - +
174G VAL* 1.3 80.0 - - + +
176G ALA* 1.3 55.9 + - - +
178G THR* 3.4 8.8 - - + +
179G GLU* 2.9 29.9 + - - +
210G LYS* 3.1 36.3 + - + +
211G VAL* 4.4 0.9 - - - -
213G GLN* 4.0 11.3 + - - +
214G TYR* 3.3 33.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 176 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137G TYR* 3.0 26.7 - - - +
162G TYR* 4.8 2.3 - - + -
165G LYS 5.6 0.3 - - - +
166G LYS 5.6 0.7 - - - +
167G ARG* 4.6 13.2 - - + +
170G VAL* 4.4 21.8 - - + -
171G PRO 4.7 0.2 - - - +
173G HIS* 3.3 13.4 + - + +
174G VAL 2.9 1.4 + - - -
175G TYR* 1.3 77.1 - - - +
177G VAL* 1.3 57.8 + - - +
179G GLU* 3.1 13.9 + - - +
180G GLY* 2.8 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 177 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137G TYR* 3.7 30.1 - - + +
140G LEU 5.9 2.2 - - - +
142G CYS* 3.7 17.0 - - + -
167G ARG* 5.6 8.3 - - - +
173G HIS 3.5 1.1 + - - +
174G VAL* 2.8 41.1 + - + +
176G ALA* 1.3 73.1 - - - +
178G THR* 1.3 58.9 + - - +
180G GLY* 3.0 17.0 + - - +
181G ALA* 3.0 11.4 + - - +
194G ILE* 5.2 3.8 - - + -
691G SER* 4.1 20.9 + - - +
692G PHE 5.1 1.8 - - - +
693G VAL* 4.2 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 178 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174G VAL* 2.8 24.2 + - - +
175G TYR* 3.4 17.5 - - + +
177G VAL* 1.3 74.4 - - - +
179G GLU* 1.3 65.3 + - - +
181G ALA* 3.1 7.1 + - - +
182G TYR* 2.9 28.9 + - - +
194G ILE* 4.7 7.8 - - - +
211G VAL* 3.5 29.0 - - + +
214G TYR* 3.6 25.3 - - + -
215G LEU* 4.8 3.5 - - - +
474G LEU* 4.3 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 179 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162G TYR* 2.6 34.6 - - - +
164G GLY* 2.5 13.9 + - - +
165G LYS 2.5 45.5 + - - +
170G VAL* 5.7 1.2 - - - +
175G TYR 2.9 19.5 + - - +
176G ALA* 3.1 10.8 + - - +
178G THR* 1.3 75.3 - - - +
180G GLY* 1.3 64.6 + - - +
182G TYR* 3.9 1.7 - - - +
183G ARG* 2.9 37.7 + - + +
214G TYR* 3.0 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 180 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176G ALA 2.8 14.4 + - - -
177G VAL* 3.0 6.9 + - - -
179G GLU* 1.3 76.9 - - - +
181G ALA* 1.3 56.2 + - - +
183G ARG* 3.9 3.6 - - - +
184G SER* 3.0 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 181 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177G VAL 3.0 10.5 + - - +
178G THR* 3.1 10.0 + - - +
180G GLY* 1.3 76.6 - - - +
182G TYR* 1.3 57.6 + - - +
184G SER* 2.5 23.1 + - - -
185G MET* 2.9 12.3 + - - +
192G GLN* 3.2 18.0 - - + +
194G ILE* 4.1 15.0 - - + -
474G LEU* 4.0 28.0 - - + -
691G SER* 5.1 6.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 182 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178G THR* 2.9 16.8 + - - +
179G GLU* 3.9 4.9 - - - +
181G ALA* 1.3 75.4 - - - +
183G ARG* 1.3 85.8 + - + +
185G MET* 3.2 17.5 + - + +
186G LEU* 3.0 66.1 + - + +
214G TYR* 4.9 10.3 - + + -
215G LEU* 4.9 20.2 - - + -
218G VAL* 3.5 36.4 + - + +
219G ALA* 4.4 11.3 - - + +
270G PHE* 5.4 5.2 - + - -
273G ALA 5.2 0.3 + - - -
274G GLY* 3.7 24.3 + - - -
474G LEU* 6.1 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 183 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163G ARG* 4.2 25.7 - - - +
164G GLY* 3.7 36.2 - - - +
165G LYS 5.8 0.9 - - - +
179G GLU* 2.9 33.2 + - + +
180G GLY* 4.1 4.3 - - - +
182G TYR* 1.3 99.7 - - + +
184G SER* 1.3 57.6 + - - +
186G LEU* 4.1 14.1 - - - +
187G GLN* 2.8 35.0 + - - +
214G TYR* 5.8 0.2 + - - -
218G VAL* 5.4 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 184 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180G GLY 3.0 17.3 + - - -
181G ALA* 2.5 21.3 + - - -
183G ARG* 1.3 76.3 - - - +
185G MET* 1.3 53.0 + - - +
187G GLN* 4.2 5.4 - - - -
188G ASP* 2.6 44.2 + - - +
192G GLN* 2.8 31.6 + - - +
689G ASN* 4.8 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 185 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181G ALA 2.9 12.5 + - - +
182G TYR* 3.2 15.9 + - + +
184G SER* 1.3 75.9 + - - +
186G LEU* 1.3 81.4 + - + +
189G ARG* 2.5 34.2 + - - -
190G GLU 3.5 26.9 - - - +
191G ASP* 4.8 0.7 - - - -
192G GLN* 4.2 5.4 - - + -
270G PHE* 3.3 48.9 - - + -
271G ASP 5.2 3.4 - - - +
274G GLY* 5.4 1.6 - - - -
472G SER* 4.1 22.2 - - - -
473G PHE 4.2 10.5 - - - +
474G LEU* 5.4 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 186 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182G TYR* 3.0 70.5 + - + +
183G ARG* 4.1 16.4 - - - +
185G MET* 1.3 87.7 - - + +
187G GLN* 1.3 63.0 + - - +
189G ARG* 4.1 5.6 + - - +
272G VAL 5.4 5.6 - - - +
273G ALA 5.1 7.9 - - - +
274G GLY* 4.7 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 187 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183G ARG* 2.8 22.1 + - + +
184G SER* 3.9 4.7 - - - +
186G LEU* 1.3 81.0 - - - +
188G ASP* 1.3 62.3 + - + +
189G ARG* 5.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 188 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184G SER* 2.6 26.7 + - - +
187G GLN* 1.3 76.2 - - + +
189G ARG* 1.3 71.7 + - - +
190G GLU* 3.0 43.7 + - + +
192G GLN* 5.0 4.5 + - - +
689G ASN* 5.2 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 189 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185G MET* 2.5 28.3 + - - -
186G LEU 4.9 4.3 - - - +
187G GLN 3.4 2.8 - - - +
188G ASP* 1.3 82.6 - - - +
190G GLU* 1.3 61.5 + - + +
191G ASP* 5.4 0.2 - - - +
472G SER* 4.4 11.2 + - - -
----------------------------------------------------------
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