Contacts of the helix formed by residues 187 - 205 (chain G) in PDB entry 3TKR
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 SER 187 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C GLU* 3.6 29.5 + - - -
193C ARG* 3.6 13.6 - - - +
211C GLY* 4.4 7.6 - - - +
94G PHE* 4.7 2.5 - - - -
186G ARG* 1.3 77.2 - - - +
188G VAL* 1.3 61.4 + - - +
189G ASP* 3.2 10.6 + - - +
190G GLU* 2.9 23.3 + - - +
191G THR* 2.8 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 188 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C ALA* 5.5 2.0 - - + -
211C GLY* 5.4 2.6 - - - +
93G ALA* 3.7 40.4 - - + +
94G PHE* 3.8 25.1 - - + +
97G ARG* 3.8 35.9 - - + +
101G PHE* 3.8 27.4 - - + -
186G ARG 4.2 1.2 + - - -
187G SER* 1.3 69.0 - - - +
189G ASP* 1.3 64.6 + - - +
191G THR* 3.3 1.2 + - - -
192G LEU* 3.0 25.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 189 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C LYS* 4.9 11.1 + - - -
97G ARG* 2.9 34.4 + - - +
187G SER* 3.2 7.2 + - - +
188G VAL* 1.3 79.0 - - - +
190G GLU* 1.3 62.5 + - - +
192G LEU* 3.4 6.2 + - - +
193G ARG* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 190 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C THR* 6.1 0.9 - - - +
186C ARG* 5.3 0.5 - - - -
187C SER* 3.7 20.0 + - - -
190C GLU* 3.8 27.2 - - + +
187G SER* 2.9 25.0 + - - +
189G ASP* 1.3 76.0 - - - +
191G THR* 1.3 63.1 + - - +
193G ARG* 2.9 47.8 + - - +
194G LEU* 3.0 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 191 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G VAL* 3.8 40.6 - - + -
94G PHE* 3.6 21.1 - - + -
101G PHE* 4.1 3.1 - - + -
165G LEU* 3.7 19.3 - - + +
167G ILE* 4.5 4.5 - - + -
186G ARG* 5.6 0.7 - - - +
187G SER 2.8 22.9 + - - -
188G VAL 3.7 4.5 - - - -
189G ASP 3.3 0.2 - - - -
190G GLU* 1.3 76.7 - - - +
192G LEU* 1.3 61.4 + - - +
194G LEU* 3.3 10.5 + - - +
195G VAL* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G ARG* 3.5 17.0 - - - +
100G GLU* 3.3 46.4 - - + +
101G PHE* 3.4 39.0 - - + -
104G ILE* 4.2 10.3 - - + -
188G VAL* 3.0 25.5 + - + +
189G ASP* 3.6 6.1 - - - +
191G THR* 1.3 75.1 - - - +
193G ARG* 1.3 65.6 + - - +
195G VAL* 3.3 3.2 + - - +
196G GLN* 2.9 40.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 193 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C VAL* 5.1 0.6 - - - +
185C GLY 3.1 27.1 + - - +
186C ARG* 3.7 11.5 - - - +
187C SER* 3.7 9.4 - - - -
189G ASP 3.0 15.5 + - - +
190G GLU* 2.9 45.4 + - - +
192G LEU* 1.3 75.2 - - - +
194G LEU* 1.3 71.9 + - - +
196G GLN* 3.4 13.9 + - - +
197G ALA* 2.8 32.7 + - - +
209G PRO 4.7 0.2 + - - -
211G GLY* 3.7 7.0 - - - -
212G TRP* 2.9 55.0 + - + +
213G LYS* 3.9 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 194 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C THR* 6.1 1.1 - - + -
180C ASN* 3.7 26.2 - - - +
184C VAL* 4.0 10.5 - - + -
165G LEU* 6.1 0.4 - - + -
167G ILE* 3.6 18.8 - - + -
176G GLN* 3.8 31.6 - - + +
178G THR* 4.8 3.8 - - - +
190G GLU* 3.0 41.7 + - + +
191G THR* 3.6 2.9 - - - +
193G ARG* 1.3 94.9 - - - +
195G VAL* 1.3 67.6 + - - +
197G ALA* 3.2 3.7 + - - +
198G PHE* 2.9 33.6 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
73G TYR* 4.1 8.3 - - + -
75G VAL* 3.8 28.3 - - + -
101G PHE* 4.6 3.8 - - + -
104G ILE* 3.9 13.9 - - + -
106G THR* 3.3 29.2 - - + +
167G ILE* 4.2 19.5 - - + +
191G THR* 3.0 22.4 + - + +
192G LEU* 3.8 4.3 - - - +
194G LEU* 1.3 74.7 - - - +
196G GLN* 1.3 64.3 - - - +
198G PHE* 3.2 5.1 + - - +
199G GLN* 2.9 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 196 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G ILE* 4.2 25.9 - - + +
192G LEU* 2.9 33.6 + - - +
193G ARG* 3.6 12.0 - - - +
195G VAL* 1.3 77.5 - - - +
197G ALA* 1.3 57.4 + - - +
199G GLN* 3.4 8.7 + - - +
200G TYR* 2.9 29.3 + - - +
212G TRP* 3.7 12.8 - - + -
214G PRO* 3.3 31.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 197 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C VAL* 3.7 31.0 - - + -
193G ARG* 2.8 24.6 + - - +
194G LEU* 3.2 2.6 + - - +
196G GLN* 1.3 73.0 - - - +
198G PHE* 1.3 58.1 + - - +
200G TYR* 3.2 2.1 + - - +
201G THR* 2.9 31.0 + - - +
208G CYS* 3.7 11.0 - - + -
212G TRP* 3.4 24.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 198 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C ASN* 4.8 1.3 - - + -
181C ASP* 3.6 29.8 - - + -
183C PRO* 4.3 3.1 - - + -
184C VAL* 3.5 35.4 - - + -
73G TYR* 3.3 21.8 - - + +
167G ILE* 4.9 5.4 - - + -
175G ARG* 3.3 58.3 - - + -
176G GLN* 4.0 21.3 - - + -
194G LEU* 2.9 31.7 + - + +
195G VAL 3.9 2.7 - - - +
197G ALA* 1.3 76.1 - - - +
199G GLN* 1.3 57.9 + - - +
201G THR* 3.2 5.5 - - + +
202G ASP* 2.8 34.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 199 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G TYR* 3.7 29.4 - - + +
104G ILE* 2.8 41.1 + - - +
105G ASN* 4.5 5.6 + - - +
106G THR* 3.3 14.1 + - - -
195G VAL* 2.9 27.6 + - + +
196G GLN* 3.8 6.7 - - - +
198G PHE* 1.3 77.4 - - - +
200G TYR* 1.3 60.9 + - - +
202G ASP* 3.5 8.1 + - - +
203G LYS* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 200 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196G GLN 2.9 18.1 + - - +
197G ALA 3.2 4.5 + - - +
199G GLN* 1.3 77.6 - - - +
201G THR* 1.3 61.4 + - - +
203G LYS* 3.2 2.1 + - - -
204G HIS* 3.0 73.1 + + + +
206G GLU* 4.8 7.8 + - + -
208G CYS* 4.3 5.8 - - - -
212G TRP* 4.0 23.1 - + + -
216G SER 6.0 0.7 - - - -
218G THR* 3.7 40.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 201 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C PRO* 3.4 43.7 - - + +
184C VAL* 4.1 4.0 - - + -
175G ARG* 4.7 0.9 - - - +
197G ALA 2.9 16.2 + - - +
198G PHE* 3.2 19.3 - - + +
200G TYR* 1.3 74.2 - - - +
202G ASP* 1.3 72.2 + - - +
205G GLY* 2.9 23.4 + - - +
206G GLU 2.7 27.6 + - - -
207G VAL* 4.0 1.6 - - - +
208G CYS* 4.5 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 202 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G TYR* 2.6 31.7 + - - -
169G ASP* 4.5 1.6 - - - +
170G ASP* 4.2 7.1 - - - +
175G ARG* 2.9 28.4 + - - -
198G PHE 2.8 20.2 + - - +
199G GLN* 3.5 7.9 - - - +
201G THR* 1.3 79.9 - - - +
203G LYS* 1.3 61.9 + - - +
205G GLY* 4.5 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 203 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199G GLN 3.1 14.0 + - - +
200G TYR* 3.7 4.9 - - - +
201G THR 3.2 0.2 - - - -
202G ASP* 1.3 82.6 - - - +
204G HIS* 1.3 83.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 204 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200G TYR* 3.0 65.1 + + + +
203G LYS* 1.3 97.6 - - + +
205G GLY* 1.3 59.0 + - - +
206G GLU* 3.1 21.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 205 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201G THR* 2.9 21.1 + - - -
202G ASP 4.5 0.8 + - - -
203G LYS 3.7 0.8 - - - -
204G HIS* 1.3 76.3 - - - +
206G GLU* 1.3 62.1 + - - +
207G VAL* 4.3 2.4 - - - +
221G PRO* 3.5 23.5 - - - +
----------------------------------------------------------
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