Contacts of the helix formed by residues 187 - 205 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C PHE* 4.8 1.8 - - - -
186C ARG* 1.3 78.8 - - - +
188C VAL* 1.3 61.4 + - - +
189C ASP* 3.3 10.4 + - - +
190C GLU* 3.0 22.1 + - - +
191C THR* 2.9 27.5 + - - -
190G GLU* 3.7 30.4 + - - -
193G ARG* 3.7 11.5 + - - +
211G GLY* 4.4 9.0 - - - +
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Residues in contact with VAL 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ALA* 3.6 39.9 - - + +
94C PHE* 3.9 25.8 - - + +
97C ARG* 3.6 33.2 - - + +
101C PHE* 3.8 18.3 - - + -
186C ARG 4.2 0.8 + - - -
187C SER* 1.3 73.1 + - - +
189C ASP* 1.3 57.3 + - - +
191C THR* 3.2 2.8 + - - -
192C LEU* 2.9 42.8 + - + +
210G ALA* 5.4 3.1 - - + +
211G GLY* 5.4 2.2 - - - +
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Residues in contact with ASP 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ARG* 2.8 38.8 + - - -
187C SER* 3.3 7.3 + - - +
188C VAL* 1.3 76.9 + - - +
190C GLU* 1.3 62.1 + - - +
192C LEU* 3.4 8.7 + - - +
193C ARG* 3.0 22.9 + - - +
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Residues in contact with GLU 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C SER* 3.0 25.5 + - - +
189C ASP* 1.3 75.0 - - - +
191C THR* 1.3 63.3 + - - +
193C ARG* 2.8 48.8 + - - +
194C LEU* 2.9 41.5 + - + +
178G THR* 6.1 1.0 - - - +
186G ARG* 5.3 0.5 - - - -
187G SER* 3.6 20.2 + - - -
190G GLU* 3.8 25.7 - - + +
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Residues in contact with THR 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C VAL* 3.8 40.4 - - + -
94C PHE* 3.7 13.9 - - + -
101C PHE* 4.1 2.7 - - + -
165C LEU* 3.6 22.1 - - + +
167C ILE* 4.1 10.3 - - + +
186C ARG* 5.5 0.3 - - - +
187C SER 2.9 19.7 + - - -
188C VAL 3.2 8.5 + - - -
190C GLU* 1.3 77.6 - - - +
192C LEU* 1.3 55.0 + - - +
194C LEU* 3.3 10.8 + - - +
195C VAL* 2.9 27.8 + - - +
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Residues in contact with LEU 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ARG* 3.6 25.8 - - - +
100C GLU* 3.6 34.1 - - + +
101C PHE* 3.3 34.1 - - + -
104C ILE* 4.2 10.3 - - + -
188C VAL* 2.9 32.7 + - + +
189C ASP* 3.5 8.7 - - - +
191C THR* 1.3 74.1 - - - +
193C ARG* 1.3 66.5 + - - +
195C VAL* 3.3 3.1 + - + +
196C GLN* 2.9 41.7 + - - +
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Residues in contact with ARG 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C ASP 3.0 14.2 + - - +
190C GLU* 2.8 45.6 + - - +
192C LEU* 1.3 75.6 - - - +
194C LEU* 1.3 70.3 + - - +
196C GLN* 3.4 12.8 + - - +
197C ALA* 2.9 30.2 + - - +
209C PRO 4.7 0.2 + - - -
211C GLY* 3.6 5.8 - - - +
212C TRP* 2.9 55.5 + - - +
213C LYS* 4.0 30.1 - - + +
184G VAL* 5.1 4.2 - - - +
185G GLY 3.1 26.9 + - - -
186G ARG* 3.6 3.4 - - - +
187G SER* 3.6 19.5 - - - -
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Residues in contact with LEU 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C LEU* 6.1 0.7 - - + -
167C ILE* 3.6 18.6 - - + -
176C GLN* 3.7 31.4 - - + +
178C THR* 4.7 3.4 - - - +
190C GLU* 2.9 41.7 + - + +
191C THR* 3.6 2.7 - - - +
193C ARG* 1.3 94.7 - - - +
195C VAL* 1.3 65.6 + - - +
197C ALA* 3.2 3.7 + - - +
198C PHE* 2.9 34.6 + - + -
178G THR* 5.9 1.6 - - + -
180G ASN* 3.8 25.8 - - - +
184G VAL* 4.0 11.0 - - + -
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Residues in contact with VAL 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C TYR* 4.4 6.9 - - + -
75C VAL* 4.0 26.9 - - + -
101C PHE* 4.5 5.6 - - + -
104C ILE* 3.9 13.2 - - + -
106C THR* 3.4 28.0 - - + +
167C ILE* 4.2 20.2 - - + -
191C THR* 2.9 22.6 + - + +
192C LEU* 3.7 5.8 - - - +
194C LEU* 1.3 75.7 - - - +
196C GLN* 1.3 62.2 + - - +
198C PHE* 3.3 5.0 + - - +
199C GLN* 3.0 36.7 + - + +
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Residues in contact with GLN 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C GLU 5.8 0.2 + - - -
104C ILE* 4.0 25.6 - - + +
192C LEU* 2.9 35.4 + - - +
193C ARG* 3.5 13.1 - - - +
195C VAL* 1.3 74.8 - - - +
197C ALA* 1.3 57.8 + - - +
199C GLN* 3.5 8.3 + - - +
200C TYR* 2.9 30.8 + - - +
212C TRP* 3.7 15.0 - - + -
214C PRO* 3.4 32.0 - - + +
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Residues in contact with ALA 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C ARG* 2.9 22.3 + - - +
194C LEU* 3.5 5.6 - - - +
196C GLN* 1.3 77.2 - - - +
198C PHE* 1.3 57.9 + - - +
200C TYR* 3.2 2.4 + - - +
201C THR* 3.0 33.3 + - - +
208C CYS* 4.1 7.0 - - + -
212C TRP* 3.4 23.5 - - + -
184G VAL* 3.5 31.0 - - + -
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Residues in contact with PHE 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C TYR* 3.3 24.2 - - + +
167C ILE* 4.9 5.4 - - + -
175C ARG* 3.3 57.9 - - + -
176C GLN* 4.0 22.0 - - + -
194C LEU* 2.9 32.5 + - + +
195C VAL 3.9 0.4 - - - +
197C ALA* 1.3 75.4 - - - +
199C GLN* 1.3 57.8 + - - +
201C THR* 3.3 5.8 + - - -
202C ASP* 2.8 34.3 + - - +
180G ASN* 4.8 1.6 - - + -
181G ASP* 3.6 28.9 - - + -
183G PRO* 4.3 3.4 - - + -
184G VAL* 3.6 35.2 - - + -
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Residues in contact with GLN 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C TYR* 3.7 33.1 - - + +
104C ILE* 2.8 43.6 + - - +
105C ASN* 4.4 5.9 + - - +
106C THR* 3.3 12.7 + - - -
195C VAL* 3.0 24.8 + - + +
196C GLN* 3.9 5.6 - - - +
198C PHE* 1.3 75.8 - - - +
200C TYR* 1.3 63.5 + - - +
202C ASP* 3.3 8.0 + - - +
203C LYS* 3.1 25.9 + - - +
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Residues in contact with TYR 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C GLN 2.9 19.3 + - - +
197C ALA* 3.2 4.7 + - - +
199C GLN* 1.3 76.6 - - - +
201C THR* 1.3 61.0 + - + +
203C LYS* 3.2 2.5 + - - -
204C HIS* 2.9 71.4 + + + +
206C GLU* 3.9 14.7 + - + -
208C CYS* 4.4 6.1 - - - -
212C TRP* 3.9 23.8 - + + -
215C GLY 6.3 1.1 - - - -
216C SER 5.6 1.4 + - - -
218C THR* 3.7 35.5 + - + -
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Residues in contact with THR 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C ARG* 4.8 0.3 + - - -
197C ALA 3.0 8.7 + - - +
198C PHE* 3.3 13.7 + - - -
200C TYR* 1.3 72.9 - - + +
202C ASP* 1.3 70.4 + - - +
205C GLY* 3.1 21.7 + - - +
206C GLU 3.2 25.8 - - - +
207C VAL* 3.9 0.2 - - - -
208C CYS* 3.3 31.0 - - - +
183G PRO* 3.7 37.4 - - - +
184G VAL* 4.1 2.5 - - + +
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Residues in contact with ASP 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C TYR* 2.6 31.9 + - - -
169C ASP* 4.4 2.1 - - - +
170C ASP* 4.2 7.1 - - - +
175C ARG* 2.9 27.6 + - - -
198C PHE 2.8 21.0 + - - +
199C GLN* 3.5 6.3 - - - +
200C TYR 3.3 0.2 - - - -
201C THR* 1.3 78.8 + - - +
203C LYS* 1.3 61.1 + - + +
205C GLY* 4.6 1.2 + - - -
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Residues in contact with LYS 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C GLN 3.1 16.3 + - - +
200C TYR* 3.8 4.5 - - - +
202C ASP* 1.3 80.9 - - + +
204C HIS* 1.3 89.6 + - + +
205C GLY 3.7 0.2 - - - -
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Residues in contact with HIS 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C TYR* 2.9 70.4 + + + +
203C LYS* 1.3 115.8 + - + +
205C GLY* 1.3 62.9 + - - +
206C GLU* 3.1 16.9 + - + +
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Residues in contact with GLY 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C THR 3.1 16.6 + - - -
202C ASP 4.6 1.0 + - - -
203C LYS 3.7 1.0 - - - -
204C HIS* 1.3 77.9 - - - +
206C GLU* 1.3 60.9 + - - +
207C VAL* 5.1 1.2 - - - +
221C PRO* 3.5 22.7 - - - +
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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) + - + + + + + -
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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