Contacts of the helix formed by residues 185 - 201 (chain G) in PDB entry 3TDK
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 THR 185 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183G ASP* 3.0 19.8 + - + +
184G GLU* 1.3 86.0 - - - +
186G PRO* 1.3 74.2 - - - +
187G GLU* 3.0 23.0 + - - +
188G GLY* 3.3 10.6 - - - -
189G GLN* 3.1 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 186 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184G GLU 4.9 0.2 - - - +
185G THR* 1.3 87.8 - - - +
187G GLU* 1.3 58.5 + - + +
189G GLN* 3.6 9.9 - - + +
190G ARG* 3.4 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 187 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G TYR* 4.0 6.6 + - - -
153G ASN* 4.1 17.7 + - - +
155G GLN* 3.4 36.5 + - - +
185G THR* 3.6 14.7 + - - +
186G PRO* 1.3 80.9 - - + +
188G GLY* 1.3 53.7 + - - +
190G ARG* 4.0 7.6 - - - +
191G ALA 3.8 11.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 188 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155G GLN* 3.5 9.7 + - - -
157G LEU* 4.6 2.6 - - - +
183G ASP* 3.5 18.9 + - - +
185G THR* 3.3 16.6 - - - -
187G GLU* 1.3 75.1 + - - +
189G GLN* 1.3 60.6 + - - -
190G ARG 3.1 2.5 - - - -
191G ALA* 3.4 7.6 + - - +
192G VAL* 3.3 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 189 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182G GLY 4.2 5.7 + - - -
183G ASP 2.8 29.9 + - - -
184G GLU* 3.6 16.3 - - - +
185G THR 3.1 14.9 + - - +
186G PRO* 3.6 7.0 - - + +
188G GLY* 1.3 72.0 + - - -
190G ARG* 1.3 58.5 + - - +
191G ALA 3.4 0.2 - - - -
192G VAL* 3.4 16.2 + - + +
193G GLN* 2.8 38.3 + - + +
210G THR* 5.7 4.2 - - - -
211G THR 5.6 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 190 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G MET* 4.6 4.6 - - - +
2G PHE* 3.5 45.2 - - + +
123G TYR* 3.8 35.9 + - - -
186G PRO 3.4 17.3 + - - +
187G GLU* 4.0 8.3 - - - +
188G GLY 3.1 0.2 - - - -
189G GLN* 1.3 78.4 - - - +
191G ALA* 1.3 63.2 + - - +
193G GLN* 4.1 5.7 - - + +
194G ALA* 3.2 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 191 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G TYR* 3.9 8.5 + - - +
125G ILE* 3.9 12.3 - - + +
155G GLN* 3.8 33.0 - - + +
157G LEU* 3.2 26.9 - - + +
187G GLU 3.8 2.6 + - - -
188G GLY 3.4 16.4 + - - +
190G ARG* 1.3 75.2 - - - +
192G VAL* 1.3 66.1 + - - +
194G ALA* 3.6 3.1 + - - +
195G LEU* 3.6 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 192 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157G LEU* 3.9 11.4 - - + -
180G ILE* 4.2 14.3 - - + +
182G GLY* 3.8 29.8 - - - +
188G GLY 3.3 14.1 + - - +
189G GLN* 3.5 21.3 - - - +
190G ARG 3.3 0.2 - - - -
191G ALA* 1.3 76.4 - - - +
193G GLN* 1.3 63.1 + - + +
195G LEU* 3.1 6.4 + - - +
196G CYS* 2.8 32.6 + - + +
210G THR* 3.7 33.0 - - + -
211G THR 5.2 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 193 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G MET* 6.2 5.4 - - + -
189G GLN* 2.8 31.4 + - + +
190G ARG* 4.1 6.5 - - - +
191G ALA 3.5 0.2 - - - -
192G VAL* 1.3 77.9 - - + +
194G ALA* 1.3 59.0 + - - +
196G CYS* 3.2 21.5 - - - +
197G ALA* 2.9 28.9 + - - +
200G GLU* 5.6 2.2 + - - -
205G ARG* 4.5 18.8 + - - +
210G THR* 5.3 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 194 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G PHE* 3.8 28.4 - - + +
4G ILE* 3.8 13.9 + - + +
125G ILE* 3.8 24.2 - - + -
190G ARG 3.2 17.3 + - - +
191G ALA 3.9 0.4 - - - +
192G VAL 3.1 0.8 - - - -
193G GLN* 1.3 77.6 - - - +
195G LEU* 1.3 59.1 + - - +
197G ALA* 3.4 15.3 + - - +
198G VAL* 3.4 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G ILE* 4.2 7.9 - - + -
84G LEU* 3.7 32.1 - - + -
86G PHE* 4.1 10.8 - - + -
125G ILE* 5.6 0.4 - - + -
127G THR* 4.0 15.9 - - + +
157G LEU* 3.9 13.7 - - + -
159G ASN* 4.2 4.9 - - + -
180G ILE* 3.7 35.2 - - + -
191G ALA 3.6 8.8 + - - +
192G VAL 3.1 7.6 + - - +
194G ALA* 1.3 75.2 - - - +
196G CYS* 1.3 65.2 + - - +
197G ALA 3.2 0.2 - - - -
198G VAL* 3.0 17.8 + - + +
199G TYR* 3.1 42.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 196 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180G ILE* 4.1 9.7 - - + +
192G VAL 2.8 13.2 + - - +
193G GLN* 3.2 31.9 - - - +
195G LEU* 1.3 75.2 - - - +
197G ALA* 1.3 56.3 + - - +
199G TYR* 3.2 6.5 + - - +
200G GLU* 2.9 43.2 + - - +
205G ARG* 5.1 9.4 - - - -
208G ILE* 3.7 32.4 - - - +
210G THR* 4.3 14.8 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
2G PHE 5.9 1.3 - - - +
3G GLU* 6.5 1.3 - - + -
193G GLN 2.9 13.3 + - - +
194G ALA* 3.6 11.2 - - - +
195G LEU 3.2 0.4 - - - -
196G CYS* 1.3 75.9 - - - +
198G VAL* 1.3 62.8 + - + +
200G GLU* 3.4 24.3 + - - +
201G HIS* 3.4 20.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 198 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G ILE* 3.9 34.5 - - + +
7G ILE* 4.5 7.6 - - + -
23G ILE* 4.4 28.5 - - + -
27G CYS* 3.9 6.4 - - - -
30G ILE* 4.5 9.0 - - + -
84G LEU* 5.7 0.2 - - + -
194G ALA 3.4 13.4 + - - +
195G LEU* 3.0 16.6 + - + +
197G ALA* 1.3 77.8 - - + +
199G TYR* 1.3 69.1 + - + +
201G HIS* 3.3 28.9 + - + +
202G TRP* 3.7 8.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 199 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G THR* 5.1 2.1 - - + +
23G ILE* 5.0 7.4 - - + +
86G PHE* 4.3 6.7 - + - -
129G LYS* 2.6 19.5 + - - +
159G ASN* 2.4 39.1 + - - -
161G GLU* 5.8 0.2 - - - -
172G LEU* 6.3 2.7 - - + -
178G VAL* 3.7 30.5 - - + -
180G ILE* 4.2 7.4 - - + -
195G LEU* 3.1 47.3 + - + -
196G CYS* 3.7 6.7 - - - +
198G VAL* 1.3 80.6 - - + +
200G GLU* 1.3 59.5 + - - +
201G HIS 3.1 0.2 - - - -
202G TRP* 3.0 36.2 + + - -
203G VAL* 2.9 33.2 + - + +
208G ILE* 4.2 13.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
193G GLN* 5.6 2.4 + - - -
196G CYS* 2.9 33.7 + - - +
197G ALA* 3.6 19.5 - - - +
198G VAL 3.3 1.0 - - - -
199G TYR* 1.3 73.3 - - - +
201G HIS* 1.3 64.3 + - - +
202G TRP* 3.2 1.5 + - - -
203G VAL 3.4 16.7 + - - +
205G ARG* 3.1 36.3 + - + +
208G ILE* 3.7 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 201 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G MET* 3.9 13.3 - - - +
27G CYS* 3.5 22.3 - - + -
28G PRO* 5.8 0.7 - - + -
29G GLU* 3.4 36.2 + - - -
30G ILE* 5.2 2.7 - - + -
197G ALA* 3.4 15.6 + - + -
198G VAL* 3.3 26.8 + - + +
199G TYR 3.1 0.2 + - - -
200G GLU* 1.3 78.2 - - - +
202G TRP* 1.3 61.6 + - + +
----------------------------------------------------------
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