Contacts of the helix formed by residues 180 - 192 (chain B) in PDB entry 1ZQ1
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 THR 180 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314A PRO* 3.4 31.4 - - + +
337A THR* 4.9 4.0 + - - -
146B SER* 2.7 37.1 + - - +
147B GLU* 4.1 4.3 + - - -
149B MSE 4.2 9.4 - - + -
154B TRP* 4.6 1.6 - - - +
176B HIS* 3.9 3.6 - - + -
179B ASP* 1.3 77.4 - - - +
181B MSE 1.3 51.5 + - - +
182B GLY 2.6 3.4 + - - -
183B TYR* 2.5 47.7 + - + +
184B THR* 3.4 19.7 + - - +
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Residues in contact with MSE 181 (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 HIS* 3.4 32.1 - - + +
177B GLY 3.2 37.0 + - - +
178B THR* 3.5 10.7 + - - +
179B ASP 3.4 1.0 - - - -
180B THR* 1.3 74.4 - - - +
182B GLY* 1.3 55.9 + - - +
184B THR* 3.5 0.9 + - - -
185B ALA* 2.8 31.0 + - - +
201B LEU* 4.0 17.2 - - + +
202B VAL* 3.3 14.6 - - - -
203B GLY* 3.2 35.2 - - - +
235B VAL* 3.8 28.7 - - + -
237B MSE 4.6 4.9 - - - +
265B PHE* 4.2 13.7 - - + -
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Residues in contact with GLY 182 (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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179B ASP 4.7 1.6 + - - -
180B THR 2.6 5.9 + - - -
181B MSE 1.3 73.1 - - - +
183B TYR* 1.3 65.6 + - - +
185B ALA* 4.0 9.3 - - - +
186B ALA* 3.7 14.2 + - - +
235B VAL* 5.4 0.4 - - - -
251B GLY 4.6 1.4 - - - +
252B THR* 5.9 0.2 - - - -
254B VAL* 4.3 25.3 - - - +
255B ARG* 5.6 1.3 - - - -
256B LYS 6.0 0.7 - - - -
265B PHE* 4.4 12.4 - - - -
396B GLU* 5.4 7.4 - - - +
397B THR* 4.8 3.8 + - - -
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Residues in contact with TYR 183 (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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311A LYS* 4.4 3.1 - - - -
312A VAL 3.9 0.3 + - - -
313A TYR* 3.7 13.3 - - + +
314A PRO* 3.5 33.7 - - + -
337A THR* 5.2 3.6 - - - -
365A GLN* 2.9 33.4 + - - -
154B TRP* 4.1 14.6 - + + -
179B ASP 4.8 4.3 - - - -
180B THR* 2.5 39.1 + - + +
182B GLY* 1.3 71.2 - - - -
184B THR* 1.3 66.9 + - - +
186B ALA* 2.8 17.3 + - - +
187B ALA* 3.0 10.4 + - - +
309B LEU* 4.4 2.7 - - + +
396B GLU* 3.3 44.5 + - + +
399B TYR* 4.1 12.8 - + - -
400B VAL* 4.1 14.4 - - + +
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Residues in contact with THR 184 (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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149B MSE 5.6 0.4 - - - -
154B TRP* 3.5 28.8 + - + +
157B ILE* 5.3 7.4 - - + -
176B HIS* 2.4 49.2 + - + +
180B THR* 3.4 9.2 + - - +
181B MSE 3.7 5.4 - - - -
183B TYR* 1.3 77.9 - - - +
185B ALA* 1.3 64.1 + - - +
187B ALA* 2.8 13.5 + - - +
188B LEU* 2.9 32.4 + - + +
201B LEU* 4.3 8.1 - - + -
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Residues in contact with ALA 185 (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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181B MSE 2.8 24.3 + - - +
182B GLY* 4.0 8.1 - - - -
184B THR* 1.3 74.0 - - - +
186B ALA* 1.3 54.5 + - - +
189B SER* 2.7 31.0 + - - -
201B LEU* 3.6 17.9 - - + +
233B VAL* 3.6 7.3 - - - +
235B VAL* 3.8 25.4 - - + -
251B GLY* 3.1 17.2 - - - +
254B VAL* 5.4 0.7 - - + -
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Residues in contact with ALA 186 (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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182B GLY 3.7 6.9 + - - +
183B TYR* 2.8 10.5 + - - +
185B ALA* 1.3 75.3 - - - +
187B ALA* 1.3 65.0 + - - +
189B SER* 3.3 5.8 + - - -
190B PHE* 2.8 30.6 - - + -
251B GLY 3.0 15.1 + - - +
252B THR* 3.7 17.0 - - + -
397B THR* 3.9 26.5 - - + +
400B VAL* 4.1 5.8 - - + -
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Residues in contact with ALA 187 (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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154B TRP* 3.5 51.6 - - + -
183B TYR 3.0 7.3 + - - +
184B THR 2.8 9.6 + - - +
186B ALA* 1.3 72.7 - - - +
188B LEU* 1.3 57.3 + - + +
189B SER 2.7 14.5 + - - -
190B PHE* 2.9 15.2 + - - +
191B MSE 3.0 21.9 + - + +
400B VAL* 3.7 10.5 - - + +
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Residues in contact with LEU 188 (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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154B TRP* 3.7 25.8 - - - +
157B ILE* 3.7 32.8 - - + -
158B ALA* 4.1 9.2 - - + +
161B VAL* 4.6 12.1 - - + -
174B VAL* 4.6 7.6 - - + -
184B THR* 2.9 29.1 + - + +
185B ALA 4.1 2.7 - - - +
187B ALA* 1.3 75.8 - - - +
189B SER* 1.3 60.8 + - - +
190B PHE 3.4 0.2 - - - -
191B MSE 4.6 3.6 - - - -
192B LEU* 3.2 33.8 + - + +
199B VAL* 4.6 7.9 - - + -
201B LEU* 4.2 18.2 - - + -
233B VAL* 3.5 17.0 - - + +
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Residues in contact with SER 189 (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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185B ALA 2.7 19.0 + - - -
186B ALA 3.3 10.7 + - - -
187B ALA 2.7 6.9 + - - -
188B LEU* 1.3 77.3 - - - +
190B PHE* 1.3 59.5 + - - -
192B LEU 3.8 5.9 - - - +
193B ARG* 3.3 19.1 + - - -
233B VAL* 3.7 17.9 + - - +
251B GLY* 3.6 13.3 + - - -
252B THR* 3.9 16.8 + - - -
290B ARG* 5.7 0.5 + - - -
424B ALA* 4.1 15.7 - - - +
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Residues in contact with PHE 190 (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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186B ALA* 2.8 32.1 - - + -
187B ALA* 2.9 4.2 + - - +
189B SER* 1.3 78.4 - - - +
191B MSE 1.3 61.7 + - - +
193B ARG* 2.9 32.4 + - - +
252B THR* 4.0 17.0 - - + -
397B THR* 4.2 7.0 - - + -
400B VAL* 4.5 6.3 - - + -
401B LYS* 3.1 52.7 - - + -
404B TRP* 3.6 45.0 - + + +
423B TYR* 4.1 9.4 - - + -
424B ALA* 4.8 1.8 - - + -
426B GLU* 3.0 35.7 - - - -
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Residues in contact with MSE 191 (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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154B TRP* 2.9 51.8 - - + +
155B VAL* 3.9 24.9 - - + -
158B ALA* 4.0 15.5 - - + -
187B ALA* 3.0 20.5 + - + +
188B LEU* 4.6 0.7 - - - -
190B PHE* 1.3 77.9 - - + +
192B LEU* 1.3 59.4 + - - +
193B ARG 2.8 9.0 + - - -
298B GLU 3.2 2.9 - - - +
299B VAL* 3.3 1.8 - - - -
300B ASP* 3.1 48.3 + - - +
301B ASP* 4.7 3.8 - - - +
303B ILE* 3.8 31.4 - - + -
400B VAL* 6.2 0.7 - - + -
404B TRP* 4.3 7.2 - - + +
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Residues in contact with LEU 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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158B ALA* 3.5 34.3 - - + +
161B VAL* 3.8 26.5 - - + -
162B ALA 4.7 1.6 - - - +
188B LEU* 3.2 33.2 + - + +
189B SER 3.8 10.0 - - - +
190B PHE 4.1 2.2 - - - -
191B MSE 1.3 72.2 - - - +
193B ARG* 1.3 67.0 + - - +
194B ASN 3.9 0.7 + - - -
195B LEU* 4.2 18.7 + - + +
199B VAL* 4.0 22.9 - - + -
233B VAL* 4.0 7.6 - - + -
290B ARG* 5.0 1.7 + - - -
297B VAL* 4.1 22.0 - - + -
298B GLU 4.3 0.2 - - - -
299B VAL* 4.4 6.5 - - + -
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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