Contacts of the helix formed by residues 187 - 205 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A GLU* 3.6 20.5 + - - -
193A ARG* 3.6 21.8 - - - +
211A GLY* 4.4 8.7 - - - +
94I PHE* 4.5 2.5 - - - -
186I ARG* 1.3 77.1 - - - +
188I VAL* 1.3 61.5 + - - +
189I ASP* 3.2 10.0 + - - +
190I GLU* 2.9 23.1 + - - +
191I THR* 2.8 27.7 + - - -
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Residues in contact with VAL 188 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ALA* 5.3 2.2 - - + -
211A GLY* 5.4 2.4 - - - +
93I ALA* 3.7 40.6 - - + +
94I PHE* 3.8 23.6 - - + +
97I ARG* 3.7 39.3 - - + +
101I PHE* 4.0 24.6 - - + -
186I ARG 4.2 0.8 + - - -
187I SER* 1.3 71.3 + - - +
189I ASP* 1.3 59.5 + - - +
191I THR* 3.2 3.1 + - - -
192I LEU* 2.9 31.2 + - + +
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Residues in contact with ASP 189 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A GLY* 6.2 0.3 - - - -
97I ARG* 2.8 40.9 + - - +
187I SER* 3.2 7.4 + - - +
188I VAL* 1.3 78.2 + - - +
190I GLU* 1.3 56.5 + - - +
192I LEU* 3.5 7.4 + - - +
193I ARG* 3.0 27.9 + - - +
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Residues in contact with GLU 190 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ARG* 5.4 0.3 - - - -
187A SER* 3.6 20.2 + - - -
190A GLU* 3.9 32.4 - - + +
187I SER* 2.9 19.8 + - - +
189I ASP* 1.3 73.4 - - - +
191I THR* 1.3 66.1 + - - +
193I ARG* 2.9 45.5 + - - +
194I LEU* 3.0 41.3 + - + +
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Residues in contact with THR 191 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75I VAL* 3.8 39.5 - - + -
94I PHE* 3.6 19.1 - - + -
101I PHE* 4.1 4.0 - - + -
165I LEU* 3.7 14.1 - - + +
167I ILE* 4.2 11.4 - - + -
186I ARG* 5.6 0.5 - - - +
187I SER 2.8 20.3 + - - -
188I VAL 3.5 7.0 - - - -
190I GLU* 1.3 77.8 - - - +
192I LEU* 1.3 57.2 + - - +
194I LEU* 3.3 9.8 + - - +
195I VAL* 2.9 29.2 + - - +
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Residues in contact with LEU 192 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97I ARG* 3.5 16.6 - - - +
100I GLU* 3.4 55.6 - - + +
101I PHE* 3.5 30.5 - - + -
104I ILE* 4.3 9.2 - - + -
188I VAL* 2.9 27.3 + - + +
189I ASP* 3.7 6.5 - - - +
191I THR* 1.3 73.0 - - - +
193I ARG* 1.3 64.8 + - - +
195I VAL* 3.3 2.9 + - - +
196I GLN* 2.9 42.6 + - - +
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Residues in contact with ARG 193 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A VAL* 5.2 0.4 - - - +
185A GLY 3.1 26.5 + - - -
186A ARG* 3.7 11.7 - - - +
187A SER* 3.7 10.3 - - - -
189I ASP 3.0 14.9 + - - +
190I GLU* 2.9 45.5 + - - +
192I LEU* 1.3 75.6 - - - +
194I LEU* 1.3 71.8 + - - +
196I GLN* 3.4 13.3 + - - +
197I ALA* 2.8 34.4 + - - +
209I PRO 4.7 0.2 + - - -
211I GLY* 3.6 6.5 - - - -
212I TRP* 2.9 56.9 + - - +
213I LYS* 4.0 30.1 - - + +
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Residues in contact with LEU 194 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A THR* 6.1 0.9 - - + -
180A ASN* 3.8 25.1 - - - +
184A VAL* 4.0 10.3 - - + -
165I LEU* 6.1 0.9 - - + -
167I ILE* 3.6 14.4 - - + -
176I GLN* 3.7 32.1 - - + +
178I THR* 4.7 4.0 - - - +
190I GLU* 3.0 40.1 + - + +
191I THR* 3.6 6.1 - - - +
193I ARG* 1.3 95.8 - - - +
195I VAL* 1.3 65.7 + - - +
197I ALA* 3.2 3.5 + - - +
198I PHE* 2.9 35.1 + - + -
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Residues in contact with VAL 195 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I TYR* 4.3 6.9 - - + -
75I VAL* 4.0 26.0 - - + -
101I PHE* 4.6 4.0 - - + -
104I ILE* 3.8 17.0 - - + -
106I THR* 3.3 30.1 - - + +
167I ILE* 4.1 21.5 - - + -
191I THR* 2.9 26.1 + - + +
192I LEU* 3.8 5.2 - - - +
194I LEU* 1.3 71.1 - - - +
196I GLN* 1.3 63.5 + - - +
198I PHE* 3.4 4.8 + - - +
199I GLN* 3.0 32.1 + - - +
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Residues in contact with GLN 196 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100I GLU 5.7 0.4 + - - -
104I ILE* 4.0 25.1 - - + +
192I LEU* 2.9 36.6 + - - +
193I ARG* 3.6 13.0 - - - +
195I VAL* 1.3 76.7 - - - +
197I ALA* 1.3 57.7 + - - +
199I GLN* 3.4 8.0 + - - +
200I TYR* 2.9 30.8 + - - +
212I TRP* 3.6 14.1 - - + -
214I PRO* 3.3 31.0 - - + +
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Residues in contact with ALA 197 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A VAL* 3.6 30.5 - - + -
193I ARG* 2.8 21.2 + - - +
194I LEU* 3.2 5.6 + - - +
196I GLN* 1.3 76.1 - - - +
198I PHE* 1.3 58.0 + - - +
200I TYR* 3.3 2.6 + - - +
201I THR* 3.0 31.2 + - - +
208I CYS* 3.8 8.9 - - + -
212I TRP* 3.3 24.0 - - + -
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Residues in contact with PHE 198 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ASN* 4.8 1.3 - - + -
181A ASP* 3.6 29.2 - - + -
183A PRO* 4.3 2.9 - - + -
184A VAL* 3.6 34.3 - - + -
73I TYR* 3.3 25.1 - - + +
167I ILE* 4.8 7.4 - - + -
175I ARG* 3.3 51.6 - - + -
176I GLN* 3.9 26.2 - - + -
194I LEU* 2.9 33.5 + - + +
195I VAL 4.0 0.2 - - - +
197I ALA* 1.3 77.2 - - - +
199I GLN* 1.3 58.4 + - - +
201I THR* 3.3 4.2 - - + +
202I ASP* 2.9 35.2 + - - +
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Residues in contact with GLN 199 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I TYR* 3.5 32.1 - - + +
104I ILE* 2.8 43.4 + - - +
105I ASN* 4.4 7.3 + - - +
106I THR* 3.5 11.5 + - - -
195I VAL* 3.0 24.1 + - - +
196I GLN* 3.8 6.4 - - - +
198I PHE* 1.3 76.3 - - - +
200I TYR* 1.3 64.0 + - - +
202I ASP* 3.3 8.2 + - - +
203I LYS* 3.1 24.8 + - - +
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Residues in contact with TYR 200 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196I GLN 2.9 18.3 + - - +
197I ALA 3.3 4.0 + - - +
199I GLN* 1.3 77.0 - - - +
201I THR* 1.3 59.3 + - - +
203I LYS* 3.2 2.3 + - - -
204I HIS* 2.9 77.3 + + + +
206I GLU* 4.8 7.6 + - + -
208I CYS* 4.3 7.6 - - - -
212I TRP* 3.9 24.2 - + + -
215I GLY 6.3 0.9 - - - -
216I SER 5.6 1.1 + - - -
218I THR* 3.6 38.9 + - + +
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Residues in contact with THR 201 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A PRO* 3.3 42.2 - - + +
184A VAL* 4.0 5.2 - - + -
175I ARG* 4.9 0.9 - - - +
197I ALA 3.0 16.3 + - - +
198I PHE* 3.3 20.2 - - + +
200I TYR* 1.3 75.0 - - - +
202I ASP* 1.3 71.6 + - - +
205I GLY* 3.1 21.6 + - - +
206I GLU 2.8 26.8 + - - -
207I VAL* 4.1 1.7 - - - +
208I CYS* 4.5 5.2 - - - -
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Residues in contact with ASP 202 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I TYR* 2.6 30.6 + - - -
169I ASP* 4.5 2.1 - - - +
170I ASP* 4.1 7.4 - - - +
171I LYS* 6.4 0.4 - - - -
175I ARG* 3.0 27.5 + - - -
198I PHE 2.9 22.8 + - - +
199I GLN* 3.4 7.1 - - - +
200I TYR 3.3 0.2 - - - -
201I THR* 1.3 79.3 - - - +
203I LYS* 1.3 61.7 + - + +
205I GLY* 4.7 1.2 + - - -
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Residues in contact with LYS 203 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199I GLN 3.1 16.0 + - - +
200I TYR* 3.8 3.4 - - - +
201I THR 3.2 0.2 - - - -
202I ASP* 1.3 80.3 - - - +
204I HIS* 1.3 90.6 + - + +
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Residues in contact with HIS 204 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200I TYR* 2.9 70.4 + + + +
203I LYS* 1.3 117.9 + - + +
205I GLY* 1.3 65.7 + - - +
206I GLU* 3.2 13.8 + - + +
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Residues in contact with GLY 205 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201I THR* 3.1 20.2 + - - -
202I ASP 4.7 1.2 + - - -
203I LYS 3.8 0.6 - - - -
204I HIS* 1.3 78.1 - - - +
206I GLU* 1.3 61.2 + - - +
207I VAL* 5.4 0.9 - - - -
221I PRO* 3.5 21.6 - - - +
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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
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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