Contacts of the helix formed by residues 191 - 207 (chain B) in PDB entry 5TQB
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 ASP 191 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189B GLU* 3.8 17.7 - - - +
190B ASP* 1.3 77.6 + - + +
192B ALA* 1.3 62.1 + - - +
193B GLU 3.4 2.2 - - - -
194B GLN* 3.9 24.0 - - + +
195B ARG* 2.7 65.0 + - + +
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Residues in contact with ALA 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A PHE* 4.3 12.6 - - + -
92A GLY 5.9 0.2 - - - +
182B TYR* 4.0 32.3 - - + +
186B LEU 4.1 9.4 - - - +
187B SER 4.4 5.6 - - - +
189B GLU* 3.1 20.1 + - + +
190B ASP 3.1 3.2 - - - +
191B ASP* 1.3 79.5 + - - +
193B GLU* 1.3 62.4 + - - +
195B ARG* 3.9 1.9 - - - +
196B CYS* 3.1 28.4 + - - -
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Residues in contact with GLU 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A PHE* 3.6 47.6 - - + +
190B ASP 4.6 3.4 + - - +
191B ASP* 3.4 0.4 - - - +
192B ALA* 1.3 79.3 - - - +
194B GLN* 1.3 58.7 + - - +
196B CYS* 3.4 2.1 + - - +
197B GLU* 3.0 31.1 + - + +
220B VAL* 5.6 0.4 - - + -
224B GLN* 2.9 35.5 + - - +
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Residues in contact with GLN 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B ASP 5.5 0.2 + - - -
191B ASP* 3.6 24.2 + - + +
192B ALA 3.3 0.2 - - - -
193B GLU* 1.3 79.8 - - - +
195B ARG* 1.3 63.3 + - + +
197B GLU* 3.3 8.3 + - - +
198B ALA* 3.1 22.1 + - + +
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Residues in contact with ARG 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B HIS* 4.8 8.7 - - - -
182B TYR* 2.4 60.6 + - + -
189B GLU* 4.5 8.1 + - - -
191B ASP* 2.7 44.5 + - + +
192B ALA 3.9 2.7 - - - +
194B GLN* 1.3 80.6 - - + +
196B CYS* 1.3 61.9 + - - +
198B ALA* 3.2 8.5 + - - +
199B LEU* 3.1 31.7 + - + +
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Residues in contact with CYS 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A PHE* 4.2 9.4 - - + -
179B VAL* 3.7 34.1 - - + -
182B TYR* 3.8 14.4 - - - -
183B MSE 4.0 13.0 - - - -
192B ALA 3.1 23.5 + - - +
193B GLU* 3.7 6.5 - - - +
195B ARG* 1.3 75.1 - - - +
197B GLU* 1.3 64.0 + - - +
199B LEU* 3.1 10.6 + - - +
200B ILE* 3.0 28.9 + - - +
220B VAL* 4.3 16.6 - - + -
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Residues in contact with GLU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B GLU* 3.0 23.0 + - + +
194B GLN* 3.5 8.3 - - - +
196B CYS* 1.3 76.1 - - - +
198B ALA* 1.3 58.4 + - - +
200B ILE* 3.5 14.2 - - - +
201B THR* 3.1 39.9 + - - +
220B VAL* 4.9 2.2 - - + +
221B ARG* 3.1 24.1 + - - -
224B GLN* 3.1 28.6 + - - +
226B ARG* 3.6 8.4 + - - -
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Residues in contact with ALA 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B GLN* 3.1 12.2 + - + +
195B ARG* 3.6 10.5 - - - +
196B CYS 3.2 0.2 - - - -
197B GLU* 1.3 75.0 - - - +
199B LEU* 1.3 65.4 + - + +
201B THR* 2.8 19.3 + - - -
202B GLU* 3.3 14.0 + - - +
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Residues in contact with LEU 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B LEU* 3.7 41.9 - - + +
178B VAL* 3.6 30.7 - - + +
179B VAL* 3.5 33.9 - - + +
182B TYR* 4.7 5.2 - - + -
195B ARG* 3.1 26.5 + - + +
196B CYS* 3.1 2.7 + - - +
198B ALA* 1.3 78.1 - - + +
200B ILE* 1.3 57.1 + - - +
202B GLU* 3.4 8.0 + - - +
203B ALA* 3.0 28.7 + - - +
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Residues in contact with ILE 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B CYS* 5.8 0.9 - - - -
179B VAL* 4.0 17.3 - - + -
196B CYS 3.0 15.8 + - - +
197B GLU* 3.5 25.6 - - - +
199B LEU* 1.3 73.9 - - - +
201B THR* 1.3 64.3 + - + +
203B ALA* 3.8 6.5 - - + -
204B THR* 2.8 33.8 + - - +
213B THR 5.3 0.4 - - - +
216B THR* 4.0 19.7 - - + +
217B VAL* 4.0 20.8 - - + +
220B VAL* 4.0 26.7 - - + -
221B ARG* 4.0 22.9 - - - +
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Residues in contact with THR 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B GLU* 3.1 25.1 + - + +
198B ALA* 2.8 25.8 + - - -
200B ILE* 1.3 79.0 - - + +
202B GLU* 1.3 59.6 + - - +
204B THR* 3.0 18.4 + - - -
205B MSE 3.2 14.1 + - - +
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Residues in contact with GLU 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B ARG* 2.5 35.2 + - - -
171B LEU* 4.2 7.8 - - - +
175B LEU* 3.5 21.6 - - + +
198B ALA 3.3 13.7 + - - +
199B LEU* 3.8 6.3 - - - +
201B THR* 1.3 82.6 + - - +
203B ALA* 1.3 60.9 + - - +
205B MSE 3.2 24.7 + - + +
206B ILE* 3.1 28.7 + - + +
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Residues in contact with ALA 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B ALA* 4.3 16.6 - - + +
175B LEU* 4.3 7.6 - - + -
176B CYS* 4.6 6.7 - - - -
199B LEU 3.0 19.0 + - - +
200B ILE* 4.0 8.1 - - - +
201B THR 3.3 0.2 - - - -
202B GLU* 1.3 78.1 - - - +
204B THR* 1.3 56.8 + - + +
206B ILE* 3.5 12.3 - - - +
207B ALA 3.0 24.4 + - - -
213B THR* 3.7 27.8 - - + +
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Residues in contact with THR 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B ILE* 2.8 22.6 + - - +
201B THR* 3.0 15.2 + - - -
203B ALA* 1.3 75.3 - - + +
205B MSE 1.3 61.2 + - - +
207B ALA 4.2 0.4 - - - -
208B PRO* 3.3 30.5 - - - +
213B THR* 4.6 7.9 - - - -
214B TRP* 3.7 34.0 - - + -
217B VAL* 3.6 26.0 - - + -
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Residues in contact with MSE 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B THR 3.2 14.5 + - - +
202B GLU* 3.2 25.5 + - + +
203B ALA 3.2 0.6 - - - -
204B THR* 1.3 80.6 + - - +
206B ILE* 1.3 79.4 + - + +
208B PRO* 3.8 7.4 - - - +
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Residues in contact with ILE 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B ARG* 3.5 60.2 + - + +
171B LEU* 3.7 24.7 - - + -
172B ALA* 3.7 20.2 - - + +
175B LEU* 4.3 5.8 - - + -
202B GLU* 3.1 19.5 + - + +
203B ALA* 3.5 13.2 - - - +
205B MSE 1.3 94.3 - - + +
207B ALA* 1.3 62.5 + - - +
208B PRO* 3.7 3.8 - - - +
209B GLU* 4.4 3.1 - - - +
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Residues in contact with ALA 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B ARG* 4.4 4.9 - - + +
169B ARG* 4.6 6.5 - - + -
172B ALA* 3.9 21.5 - - + -
203B ALA 3.0 14.2 + - - +
206B ILE* 1.3 81.9 - - + +
208B PRO* 1.3 61.0 - - - +
209B GLU* 3.1 22.4 + - - +
210B TRP* 3.2 15.0 + - + -
213B THR* 3.1 21.2 + - + +
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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
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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