Contacts of the helix formed by residues 187 - 205 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D PHE* 4.8 2.7 - - - -
186D ARG* 1.3 78.9 - - - +
188D VAL* 1.3 61.1 + - - +
189D ASP* 3.2 10.0 + - - +
190D GLU* 2.9 23.2 + - - +
191D THR* 2.8 27.5 + - - -
190F GLU* 3.6 21.0 + - - -
193F ARG* 3.6 21.5 - - - +
211F GLY* 4.4 8.3 - - - +
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Residues in contact with VAL 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D ALA* 3.7 31.2 - - + +
94D PHE* 3.8 36.1 - - + +
97D ARG* 3.6 37.5 - - + +
101D PHE* 3.9 24.9 - - + -
186D ARG 4.2 1.2 + - - -
187D SER* 1.3 72.7 - - - +
189D ASP* 1.3 57.6 + - - +
191D THR* 3.2 2.3 + - - -
192D LEU* 2.9 31.0 + - + +
210F ALA* 5.5 3.3 - - + +
211F GLY* 5.4 2.2 - - - +
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Residues in contact with ASP 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D ARG* 2.8 40.4 + - - +
187D SER* 3.2 6.9 + - - +
188D VAL* 1.3 77.1 + - - +
190D GLU* 1.3 61.3 + - - +
192D LEU* 3.3 6.3 + - - +
193D ARG* 3.0 22.3 + - - +
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Residues in contact with GLU 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D SER* 2.9 22.5 + - - +
189D ASP* 1.3 72.4 - - - +
191D THR* 1.3 64.5 + - - +
193D ARG* 2.8 48.9 + - - +
194D LEU* 3.0 41.9 + - + +
186F ARG* 5.3 0.3 - - - -
187F SER* 3.6 19.8 + - - -
190F GLU* 3.8 31.9 - - + +
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Residues in contact with THR 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D VAL* 3.8 38.6 - - + -
94D PHE* 3.7 20.5 - - + -
101D PHE* 4.1 2.7 - - + -
165D LEU* 3.7 20.5 - - + +
167D ILE* 4.4 4.7 - - + -
186D ARG* 5.5 0.7 - - - +
187D SER 2.8 22.9 + - - -
188D VAL 3.2 5.4 + - - -
190D GLU* 1.3 78.4 - - - +
192D LEU* 1.3 60.1 + - - +
194D LEU* 3.4 9.4 + - - +
195D VAL* 3.0 22.7 + - - +
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Residues in contact with LEU 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D ARG* 3.5 15.9 - - - +
100D GLU* 3.2 59.2 - - + +
101D PHE* 3.5 33.4 - - + -
104D ILE* 4.3 9.4 - - + -
188D VAL* 2.9 22.5 + - + +
189D ASP* 3.7 5.8 - - - +
191D THR* 1.3 74.1 - - - +
193D ARG* 1.3 60.4 + - - +
195D VAL* 3.3 3.3 + - - +
196D GLN* 2.9 47.2 + - - +
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Residues in contact with ARG 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D ASP 3.0 14.3 + - - +
190D GLU* 2.8 45.9 + - - +
192D LEU* 1.3 76.7 - - - +
194D LEU* 1.3 70.0 + - - +
196D GLN* 3.4 12.6 + - - +
197D ALA* 2.9 34.9 + - - +
211D GLY* 3.6 8.2 - - - +
212D TRP* 2.9 56.7 + - + +
213D LYS* 4.1 28.0 - - + +
184F VAL* 5.2 0.4 - - - +
185F GLY 3.2 24.5 + - - -
186F ARG* 3.6 3.6 - - - +
187F SER* 3.6 19.4 - - - -
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Residues in contact with LEU 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D LEU* 6.2 0.7 - - + -
167D ILE* 3.6 18.8 - - + -
176D GLN* 3.8 31.6 - - + +
178D THR* 4.7 4.0 - - - +
190D GLU* 3.0 40.9 + - + +
191D THR* 3.7 2.5 - - - +
193D ARG* 1.3 89.8 - - - +
195D VAL* 1.3 65.1 + - - +
197D ALA* 3.2 3.7 + - - +
198D PHE* 2.9 34.8 + - + -
178F THR* 6.0 1.1 - - + -
180F ASN* 3.7 28.7 - - - +
184F VAL* 4.0 11.0 - - + -
186F ARG* 5.8 0.2 - - - -
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Residues in contact with VAL 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D TYR* 4.4 8.2 - - + -
75D VAL* 4.0 26.9 - - + -
101D PHE* 4.5 5.4 - - + -
104D ILE* 3.9 16.2 - - + -
106D THR* 3.5 29.8 - - + +
167D ILE* 4.2 20.0 - - + -
191D THR 3.0 19.5 + - - +
192D LEU* 3.7 8.1 - - - +
194D LEU* 1.3 75.4 - - - +
196D GLN* 1.3 58.2 + - - +
198D PHE* 3.8 4.3 - - - +
199D GLN* 2.9 38.6 + - + +
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Residues in contact with GLN 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D GLU 5.6 0.6 + - - -
104D ILE* 4.0 24.6 - - + +
192D LEU* 2.9 33.0 + - - +
193D ARG* 3.5 13.0 - - - +
195D VAL* 1.3 76.4 - - - +
197D ALA* 1.3 58.4 + - - +
199D GLN* 3.4 8.5 + - - +
200D TYR* 2.8 30.3 + - - +
212D TRP* 3.7 14.3 - - + -
214D PRO* 3.3 31.4 - - + +
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Residues in contact with ALA 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D ARG* 2.9 21.8 + - - +
194D LEU* 3.2 2.7 + - - +
196D GLN* 1.3 76.5 - - - +
198D PHE* 1.3 57.1 + - - +
200D TYR* 3.3 1.9 + - - +
201D THR* 2.9 34.1 + - - +
208D CYS* 4.1 7.6 - - + -
212D TRP* 3.4 24.9 - - + -
184F VAL* 3.6 31.0 - - + -
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Residues in contact with PHE 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D TYR* 3.4 21.1 - - + +
167D ILE* 4.9 5.6 - - + -
175D ARG* 3.3 57.0 - - + -
176D GLN* 3.9 21.8 - - + -
194D LEU* 2.9 32.4 + - + +
195D VAL 3.9 3.1 - - - +
197D ALA* 1.3 72.5 - - - +
199D GLN* 1.3 61.6 + - - +
201D THR* 3.2 4.7 + - - -
202D ASP* 2.9 34.5 + - - -
180F ASN* 4.8 1.6 - - + -
181F ASP* 3.6 28.9 - - + -
183F PRO* 4.3 3.6 - - + -
184F VAL* 3.6 34.3 - - + -
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Residues in contact with GLN 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D TYR* 3.7 30.3 - - + +
104D ILE* 2.8 47.0 + - - +
105D ASN* 4.5 6.3 + - - +
106D THR* 3.4 11.5 + - - -
195D VAL* 2.9 24.8 + - + +
196D GLN* 3.8 6.1 - - - +
198D PHE* 1.3 75.6 - - - +
200D TYR* 1.3 64.1 + - - +
202D ASP* 3.3 9.2 + - - +
203D LYS* 3.1 24.3 + - - +
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Residues in contact with TYR 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D GLN 2.8 18.0 + - - +
197D ALA 3.6 4.5 - - - +
199D GLN* 1.3 76.8 - - - +
201D THR* 1.3 61.7 + - + +
203D LYS* 3.1 3.4 + - - -
204D HIS* 2.9 76.8 + + + -
206D GLU* 4.8 7.1 + - + -
208D CYS* 4.3 6.7 - - - -
212D TRP* 3.9 24.0 - + + -
216D SER 5.6 1.6 + - - -
218D THR* 3.6 39.8 + - + +
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Residues in contact with THR 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D ARG* 4.7 0.2 + - - -
197D ALA 2.9 18.8 + - - +
198D PHE* 3.2 17.5 + - - -
200D TYR* 1.3 71.8 - - + +
202D ASP* 1.3 68.1 + - - +
205D GLY* 3.2 19.7 + - - +
206D GLU 3.2 25.4 - - - +
207D VAL* 3.9 0.9 - - - -
208D CYS* 3.4 22.9 - - - -
183F PRO* 3.7 39.0 - - + +
184F VAL* 4.0 2.8 - - + +
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Residues in contact with ASP 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D TYR* 2.6 32.1 + - - -
169D ASP* 4.5 2.0 - - - +
170D ASP* 4.2 7.1 - - - +
175D ARG* 3.0 27.6 + - - -
198D PHE 2.9 20.3 + - - +
199D GLN* 3.4 7.4 - - - +
200D TYR 3.2 0.2 - - - -
201D THR* 1.3 77.8 + - - +
203D LYS* 1.3 60.8 + - - +
204D HIS 3.7 0.2 + - - -
205D GLY 4.6 1.0 + - - -
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Residues in contact with LYS 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D GLN 3.1 14.1 + - - +
200D TYR* 3.1 5.6 + - - +
202D ASP* 1.3 80.4 - - + +
204D HIS* 1.3 88.1 + - + +
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Residues in contact with HIS 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D TYR* 2.9 72.8 + + + +
203D LYS* 1.3 113.6 + - + +
205D GLY* 1.3 66.2 + - - +
206D GLU* 3.2 15.3 + - + +
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Residues in contact with GLY 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D THR 3.2 16.4 + - - -
202D ASP 4.6 1.6 + - - -
203D LYS 3.8 0.8 - - - -
204D HIS* 1.3 78.4 - - - +
206D GLU* 1.3 62.9 + - - +
207D VAL* 5.4 0.7 - - - -
221D 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