Contacts of the helix formed by residues 187 - 205 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E PHE* 4.7 2.2 - - - -
186E ARG* 1.3 78.3 - - - +
188E VAL* 1.3 54.2 + - - +
189E ASP* 3.3 9.5 + - - +
190E GLU* 3.0 22.1 + - - +
191E THR* 2.7 35.9 + - - -
190J GLU* 3.7 20.0 + - - -
193J ARG* 3.7 21.9 + - - +
211J GLY* 4.5 7.3 - - - +
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Residues in contact with VAL 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E ALA* 3.7 40.4 - - + +
94E PHE* 3.8 24.9 - - + +
97E ARG* 3.7 36.6 - - + +
100E GLU* 6.1 0.2 - - - -
101E PHE* 3.8 26.2 - - + -
186E ARG 4.2 0.8 + - - -
187E SER* 1.3 69.8 + - - +
189E ASP* 1.3 60.6 + - - +
191E THR* 3.7 1.0 - - - -
192E LEU* 2.9 29.0 + - + +
210J ALA* 5.4 2.9 - - + +
211J GLY* 5.4 2.4 - - - +
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Residues in contact with ASP 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E ARG* 2.8 35.1 + - - +
187E SER* 3.3 7.0 + - - +
188E VAL* 1.3 77.3 - - - +
190E GLU* 1.3 62.2 + - - +
192E LEU* 3.3 8.0 + - - +
193E ARG* 2.9 22.6 + - - +
213J LYS* 5.4 6.8 + - - -
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Residues in contact with GLU 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187E SER* 3.0 19.0 + - - +
189E ASP* 1.3 77.1 - - - +
191E THR* 1.3 62.8 + - - +
193E ARG* 3.0 48.7 + - - +
194E LEU* 2.9 41.0 + - + +
186J ARG* 5.3 0.3 - - - -
187J SER* 3.6 14.0 + - - -
190J GLU* 3.7 37.9 - - + +
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Residues in contact with THR 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E VAL* 3.9 33.4 - - + -
94E PHE* 3.5 26.5 - - + -
101E PHE* 4.2 3.1 - - + -
165E LEU* 3.7 14.5 - - + +
167E ILE* 4.3 10.5 - - + +
186E ARG* 5.6 0.3 - - - +
187E SER 2.7 23.6 + - - -
188E VAL 3.7 4.5 - - - -
189E ASP 3.3 0.2 - - - -
190E GLU* 1.3 77.7 - - - +
192E LEU* 1.3 62.0 + - - +
194E LEU* 3.4 9.8 + - - +
195E VAL* 3.0 28.1 + - - +
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Residues in contact with LEU 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E ARG* 4.4 7.4 - - - +
100E GLU* 3.8 38.6 - - + +
101E PHE* 4.3 20.3 - - + -
104E ILE* 3.5 31.9 - - + -
188E VAL* 2.9 18.4 + - + +
189E ASP* 3.6 6.1 - - - +
191E THR* 1.3 74.5 - - - +
193E ARG* 1.3 65.9 + - - +
195E VAL* 3.2 3.3 + - - +
196E GLN* 3.0 49.3 + - - +
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Residues in contact with ARG 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189E ASP 2.9 13.8 + - - +
190E GLU* 3.0 46.9 + - - +
192E LEU* 1.3 76.2 - - - +
194E LEU* 1.3 72.0 + - - +
196E GLN* 3.2 13.3 + - - +
197E ALA* 2.8 29.3 + - - +
211E GLY* 3.7 6.6 - - - -
212E TRP* 2.9 55.1 + - - +
213E LYS* 4.1 28.9 - - + +
184J VAL* 5.1 4.2 - - - +
185J GLY 3.1 26.9 + - - +
186J ARG* 3.7 12.3 - - - +
187J SER* 3.7 9.3 - - - -
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Residues in contact with LEU 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165E LEU* 6.2 0.7 - - + -
167E ILE* 3.7 14.6 - - + -
176E GLN* 3.8 30.7 - - + +
178E THR* 4.8 4.0 - - - +
190E GLU* 2.9 41.2 + - + +
191E THR* 3.7 6.1 - - - +
193E ARG* 1.3 96.4 - - - +
195E VAL* 1.3 66.0 + - - +
197E ALA* 3.2 4.0 + - - +
198E PHE* 2.9 33.5 + - + -
180J ASN* 3.7 25.4 - - - +
184J VAL* 4.0 10.3 - - + -
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Residues in contact with VAL 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E TYR* 4.2 11.4 - - + -
75E VAL* 4.0 26.5 - - + -
101E PHE* 4.5 6.7 - - + -
104E ILE* 4.0 12.1 - - + -
106E THR* 3.4 26.5 - - + +
167E ILE* 4.3 19.5 - - + +
191E THR* 3.0 21.7 + - + +
192E LEU* 3.7 5.8 - - - +
194E LEU* 1.3 74.7 - - - +
196E GLN* 1.3 63.3 + - - +
198E PHE* 3.4 3.0 + - - +
199E GLN* 3.0 37.6 + - - +
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Residues in contact with GLN 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E ILE* 4.1 21.2 - - + +
192E LEU* 3.0 47.0 + - - +
193E ARG* 3.4 14.5 - - - +
195E VAL* 1.3 75.4 - - - +
197E ALA* 1.3 58.3 + - - +
199E GLN* 3.3 9.9 + - - +
200E TYR* 2.8 30.8 + - - +
212E TRP* 3.8 14.0 - - + -
214E PRO* 3.3 33.0 - - + +
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Residues in contact with ALA 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193E ARG* 2.8 16.7 + - - +
194E LEU* 3.2 8.7 + - - +
196E GLN* 1.3 75.9 - - - +
198E PHE* 1.3 58.2 + - - +
200E TYR* 3.1 4.2 + - - +
201E THR* 2.9 31.5 + - - +
208E CYS* 4.0 8.7 - - + -
212E TRP* 3.5 24.1 - - + -
184J VAL* 3.6 31.2 - - + -
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Residues in contact with PHE 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E TYR* 3.3 23.6 - - + +
167E ILE* 4.9 6.5 - - + -
175E ARG* 3.3 53.2 - - + -
176E GLN* 3.9 21.1 - - + -
194E LEU* 2.9 36.4 + - + +
195E VAL 4.1 0.4 - - - +
197E ALA* 1.3 72.7 - - - +
199E GLN* 1.3 58.0 + - - +
201E THR* 3.2 4.5 + - - -
202E ASP* 2.9 35.3 + - - +
180J ASN* 4.7 1.8 - - + -
181J ASP* 3.5 31.4 - - + -
183J PRO* 4.3 3.8 - - + -
184J VAL* 3.5 34.8 - - + -
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Residues in contact with GLN 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E TYR* 3.6 32.5 - - + +
104E ILE* 2.8 44.8 + - - +
105E ASN* 4.6 6.7 - - - +
106E THR* 3.5 10.3 + - - -
195E VAL* 3.0 26.5 + - + +
196E GLN* 3.6 7.1 - - - +
198E PHE* 1.3 74.1 - - - +
200E TYR* 1.3 64.5 + - - +
202E ASP* 3.3 8.3 + - - +
203E LYS* 3.2 23.2 + - - +
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Residues in contact with TYR 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196E GLN 2.8 13.5 + - - +
197E ALA* 3.4 8.3 - - - +
199E GLN* 1.3 76.5 - - - +
201E THR* 1.3 61.4 + - + +
203E LYS* 3.0 3.7 + - - -
204E HIS* 2.9 71.7 + + + +
206E GLU* 4.9 7.2 + - + -
208E CYS* 4.4 6.5 - - - -
212E TRP* 4.0 26.5 - + + -
215E GLY 6.2 0.7 - - - -
216E SER 5.8 0.8 + - - -
218E THR* 3.7 37.4 + - + +
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Residues in contact with THR 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E ARG* 4.7 0.5 + - - -
197E ALA 2.9 14.0 + - - +
198E PHE* 3.2 15.6 + - - -
200E TYR* 1.3 69.9 - - + +
202E ASP* 1.3 69.2 + - - +
205E GLY* 3.1 21.5 + - - +
206E GLU 3.2 26.0 - - - +
207E VAL* 3.9 1.1 - - - -
208E CYS* 3.4 27.8 - - - -
183J PRO* 3.6 39.3 - - + +
184J VAL* 4.2 2.3 - - + +
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Residues in contact with ASP 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E TYR* 2.7 30.2 + - - -
169E ASP* 4.5 2.5 - - - +
170E ASP* 4.2 6.6 - - - +
175E ARG* 3.0 27.4 + - - -
198E PHE 2.9 21.7 + - - +
199E GLN* 3.4 7.4 - - - +
200E TYR 3.2 0.2 - - - -
201E THR* 1.3 78.2 + - - +
203E LYS* 1.3 61.6 + - + +
205E GLY 4.7 0.7 + - - -
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Residues in contact with LYS 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E GLN 3.2 12.7 + - - +
200E TYR* 3.0 5.2 + - - +
202E ASP* 1.3 81.6 - - - +
204E HIS* 1.3 92.8 + - + +
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Residues in contact with HIS 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200E TYR* 2.9 73.8 + + + +
203E LYS* 1.3 113.5 + - + +
205E GLY* 1.3 62.8 + - - +
206E GLU* 3.1 17.2 + - + +
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Residues in contact with GLY 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E THR 3.1 19.7 + - - -
202E ASP 4.7 1.0 + - - -
203E LYS 3.7 0.8 - - - -
204E HIS* 1.3 77.3 - - - +
206E GLU* 1.3 61.2 + - - +
207E VAL* 4.9 0.8 - - - +
221E PRO* 3.4 23.2 - - - +
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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