Contacts of the helix formed by residues 187 - 205 (chain G) in PDB entry 6CM9
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 187 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G SER* 3.7 27.7 + - - +
155G LYS* 5.6 1.8 - - - +
185G GLU* 3.2 25.7 + - + +
186G LYS* 1.3 81.9 - - - +
188G HIS* 1.3 75.8 + - - +
189G GLY* 3.4 12.2 + - - +
190G VAL* 4.0 12.5 - - + +
191G LEU* 3.4 19.3 + - - +
235G HIS* 5.4 1.9 + - - -
125S GLU* 4.7 5.4 + - - +
130S ILE* 4.3 22.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 188 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186G LYS 4.1 12.4 + - - -
187G ASN* 1.3 80.9 + - - +
189G GLY* 1.3 53.9 + - - +
190G VAL 3.3 0.7 - - - -
191G LEU* 3.5 11.3 - - + +
192G HIS* 2.7 36.0 + - - +
226G LEU* 3.7 16.2 - - + +
235G HIS* 3.1 42.6 + + + -
242G ASP* 3.3 21.7 + - - +
245G LEU* 3.5 19.7 - - + +
126S THR* 4.1 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 189 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155G LYS* 4.0 5.8 - - - -
187G ASN* 3.4 8.9 + - - -
188G HIS* 1.3 78.2 - - - +
190G VAL* 1.3 56.2 + - - +
192G HIS* 3.4 4.8 + - - +
193G THR* 3.0 34.8 + - - +
235G HIS* 5.2 0.4 - - - -
124S GLN 3.7 18.5 - - - +
125S GLU* 4.3 16.8 + - - -
126S THR* 4.5 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 190 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G SER* 3.4 31.9 - - - +
154G ARG* 3.7 34.5 - - + +
155G LYS* 4.1 4.5 - - + +
182G LEU* 5.4 3.6 - - + +
185G GLU* 3.6 35.9 - - + +
187G ASN* 4.0 15.4 - - + +
188G HIS 3.3 0.2 - - - -
189G GLY* 1.3 74.6 - - - +
191G LEU* 1.3 57.5 - - - +
193G THR* 3.1 7.3 + - - -
194G SER* 2.9 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 191 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182G LEU 5.1 1.1 - - - +
183G LEU* 3.8 37.2 - - + +
185G GLU* 4.6 15.0 - - + +
187G ASN 3.4 19.3 + - - +
188G HIS* 3.2 14.8 + - + +
190G VAL* 1.3 80.4 - - - +
192G HIS* 1.3 56.4 + - - +
194G SER* 2.8 19.0 + - - +
195G VAL* 3.0 24.7 + - + +
222G ILE* 3.8 31.0 - - + -
226G LEU* 5.9 0.2 - - + -
245G LEU* 3.7 28.0 - - + -
249G ILE* 5.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 192 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188G HIS 2.7 20.3 + - - +
189G GLY* 3.7 3.8 - - - +
191G LEU* 1.3 74.1 - - - +
193G THR* 1.3 59.9 + - - +
195G VAL* 3.2 4.7 + - - +
196G VAL* 3.0 40.0 + - + +
244G PHE* 3.2 27.4 + - - +
245G LEU* 3.7 14.3 - - + +
248G ARG* 3.3 30.9 + - + +
123S ILE* 3.2 49.9 + - + +
124S GLN* 4.8 1.0 - - - -
126S THR* 3.6 25.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 193 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154G ARG 4.2 0.3 + - - -
155G LYS* 3.2 38.5 - - + +
158G ALA* 3.6 19.5 - - - +
159G LEU* 3.7 16.8 - - + -
189G GLY 3.0 14.2 + - - +
190G VAL* 3.1 9.4 + - - +
192G HIS* 1.3 73.8 - - - +
194G SER* 1.3 62.9 + - - +
196G VAL* 3.2 9.6 + - - +
197G LEU 2.9 22.0 + - - -
123S ILE 3.8 15.0 - - - +
124S GLN* 3.8 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 194 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158G ALA* 4.5 5.8 - - - -
179G THR* 5.2 1.1 + - - -
182G LEU* 3.7 38.8 + - - -
183G LEU* 4.4 6.1 - - - +
190G VAL* 2.9 19.6 + - - -
191G LEU* 2.8 27.9 + - - +
193G THR* 1.3 74.3 + - - +
195G VAL* 1.3 60.0 + - - +
197G LEU* 3.3 9.2 + - - +
198G LEU* 2.9 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 195 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183G LEU* 4.4 19.1 - - + -
191G LEU* 3.0 21.4 + - + +
192G HIS* 3.2 9.8 + - - +
194G SER* 1.3 74.1 - - - +
196G VAL* 1.3 59.5 + - - +
198G LEU* 3.3 7.5 + - + +
199G THR* 2.8 33.3 + - - +
219G LEU* 5.7 2.2 - - + -
245G LEU* 4.6 2.7 - - + -
248G ARG* 3.5 41.5 - - + +
249G ILE* 4.0 22.0 - - + +
252G LEU* 4.2 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 196 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159G LEU* 3.7 25.1 - - + -
162G VAL* 3.8 10.8 - - + -
192G HIS* 3.0 39.9 + - + +
193G THR* 3.4 11.0 - - - +
195G VAL* 1.3 77.9 - - - +
197G LEU* 1.3 61.6 + - - +
199G THR* 3.2 8.6 + - - -
200G GLU* 3.0 22.3 + - - +
248G ARG* 4.2 21.5 - - - +
122S GLU* 3.7 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146G LEU* 4.3 22.9 - - + -
158G ALA* 4.3 10.3 - - + +
161G ALA* 4.3 7.9 - - + -
162G VAL* 3.6 28.0 - - + +
165G ILE* 3.8 28.3 - - + -
175G PHE* 5.1 5.8 - - + -
179G THR* 4.3 26.2 - - + +
182G LEU* 5.9 2.2 - - + -
193G THR 2.9 13.6 + - - +
194G SER* 3.6 9.6 - - - +
195G VAL 3.3 0.2 - - - -
196G VAL* 1.3 77.0 - - - +
198G LEU* 1.3 57.6 + - + +
200G GLU* 3.3 2.2 + - + +
201G MET* 2.9 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 198 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179G THR* 4.2 15.7 - - + +
183G LEU* 3.7 34.5 - - + -
194G SER* 2.9 22.2 + - - +
195G VAL* 3.3 5.6 + - - +
197G LEU* 1.3 73.9 - - + +
199G THR* 1.3 60.5 + - - +
201G MET* 4.3 1.8 - - + -
202G CYS* 2.9 35.8 + - - -
212G PHE* 3.6 43.7 - - + -
215G LEU* 3.9 16.8 - - + -
252G LEU* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 199 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195G VAL* 2.8 22.0 + - - +
196G VAL* 3.5 12.4 - - - -
198G LEU* 1.3 77.2 - - - +
200G GLU* 1.3 57.7 + - - +
203G GLU* 2.9 39.6 + - - +
248G ARG* 4.5 14.3 + - - +
251G ARG* 4.7 20.1 - - + +
252G LEU* 4.1 15.8 - - - +
255G ILE* 3.6 24.7 - - + +
74S GLN* 6.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 200 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162G VAL* 4.2 19.7 - - + +
165G ILE* 4.0 22.2 - - + -
166G ARG* 2.9 34.4 + - - +
196G VAL 3.0 15.3 + - - +
197G LEU* 3.8 5.6 - - + +
199G THR* 1.3 78.3 - - - +
201G MET* 1.3 56.8 + - - +
203G GLU* 3.2 15.0 + - - +
204G ARG* 2.6 76.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 201 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165G ILE* 3.8 12.1 - - + -
172G MET* 3.4 63.5 - - + +
175G PHE* 4.7 4.7 - - + -
176G LEU* 4.2 12.1 - - + +
179G THR* 5.4 1.3 - - + -
197G LEU* 2.9 35.6 + - + +
198G LEU* 3.9 2.7 - - + +
200G GLU* 1.3 76.6 - - - +
202G CYS* 1.3 60.0 + - - +
205G SER 3.7 12.0 + - - +
208G MET* 3.8 35.6 - - + +
212G PHE* 3.6 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 202 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198G LEU* 2.9 23.7 + - - +
201G MET* 1.3 74.9 - - - +
203G GLU* 1.3 63.8 + - - +
204G ARG 3.4 0.2 - - - -
205G SER 4.5 5.9 + - - +
206G PRO* 5.7 0.9 - - - +
208G MET* 5.4 0.9 - - - -
209G LEU* 3.7 30.9 - - + +
212G PHE* 3.6 36.6 - - - -
252G LEU* 4.4 6.3 - - - -
255G ILE* 3.8 21.1 - - + +
256G LEU* 3.8 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 203 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199G THR* 2.9 26.5 + - + +
200G GLU* 3.2 24.3 + - - +
202G CYS* 1.3 79.2 - - - +
204G ARG* 1.3 79.1 + - + +
206G PRO* 5.7 0.5 - - - +
255G ILE* 4.5 10.1 - - + +
72S GLU* 5.5 1.4 - - - +
74S GLN* 2.8 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 204 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165G ILE* 4.4 12.1 + - + +
166G ARG* 3.7 34.9 + - - +
169G PRO* 5.2 13.8 - - + +
172G MET* 3.7 19.1 - - + -
200G GLU* 2.6 50.5 + - + +
202G CYS 3.4 0.2 - - - -
203G GLU* 1.3 93.5 + - - +
205G SER* 1.3 63.6 + - - +
206G PRO* 4.0 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 205 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169G PRO 5.4 0.7 + - - -
172G MET* 3.9 23.0 - - - -
201G MET 3.7 14.5 + - - +
202G CYS 4.5 5.6 - - - +
203G GLU 3.7 0.4 - - - -
204G ARG* 1.3 83.1 + - - +
206G PRO* 1.3 64.3 - - - +
207G ASP* 3.1 20.9 + - - -
208G MET* 3.3 13.5 + - - +
209G LEU* 4.3 1.7 + - - +
----------------------------------------------------------
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