Contacts of the helix formed by residues 178 - 194 (chain B) in PDB entry 1ATH
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 ASN 178 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174B ASP* 2.8 28.3 + - + +
177B GLU* 1.3 78.3 + - + +
179B ALA* 1.3 62.1 + - - +
180B GLU* 4.4 2.3 + - - +
181B GLN* 3.6 46.5 + - - +
182B SER* 3.2 21.7 + - - -
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Residues in contact with ALA 179 (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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174B ASP 3.3 2.6 + - - -
175B PHE* 3.5 22.7 - - - +
177B GLU 3.6 4.3 + - - +
178B ASN* 1.3 74.2 - - - +
180B GLU* 1.3 59.4 + - - +
182B SER* 2.9 20.1 + - - -
183B ARG 3.0 10.9 + - - -
207B ILE* 4.1 26.3 - - + +
208B ASN* 4.2 13.5 - - - -
209B GLU* 4.5 2.0 - - - +
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Residues in contact with GLU 180 (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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178B ASN* 3.5 3.1 + - - +
179B ALA* 1.3 76.5 - - - +
181B GLN* 1.3 65.0 + - + +
182B SER 3.2 0.2 + - - -
183B ARG* 3.2 48.2 + - - +
184B ALA* 2.9 26.9 + - - +
204B SER* 4.1 11.9 - - - +
207B ILE 6.0 0.4 - - - -
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Residues in contact with GLN 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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173B LEU* 5.5 0.2 - - - -
178B ASN* 3.6 36.5 + - - +
179B ALA 3.4 0.4 - - - -
180B GLU* 1.3 77.5 - - - +
182B SER* 1.3 57.1 + - - +
184B ALA* 3.6 8.2 - - + +
185B ALA* 2.9 28.2 + - - +
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Residues in contact with SER 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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173B LEU* 3.3 17.2 - - - +
174B ASP* 3.2 28.6 + - - +
175B PHE* 3.5 26.7 - - - -
178B ASN 3.2 12.1 + - - -
179B ALA* 2.9 13.2 + - - -
181B GLN* 1.3 73.9 - - - +
183B ARG* 1.3 62.8 + - - -
185B ALA* 2.9 12.8 + - - +
186B ILE* 3.0 18.9 + - - +
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Residues in contact with ARG 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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179B ALA 3.0 7.9 + - - +
180B GLU* 3.2 39.4 + - - +
182B SER* 1.3 73.3 - - - +
184B ALA* 1.3 77.3 + - - +
186B ILE* 2.9 24.3 + - - +
187B ASN* 3.1 32.8 + - - +
200B ASP* 4.4 4.1 + - - -
202B ILE* 3.0 37.7 + - + +
203B PRO 3.1 18.2 + - - -
204B SER* 3.4 26.9 - - - +
207B ILE* 3.7 28.4 - - + +
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Residues in contact with ALA 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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180B GLU* 2.9 25.7 + - - +
181B GLN* 3.6 9.4 - - + +
183B ARG* 1.3 89.4 - - - +
185B ALA* 1.3 60.7 + - - +
187B ASN* 4.1 4.4 - - - +
188B LYS* 3.3 27.0 + - - +
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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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147B PHE* 5.3 2.9 - - + -
171B GLN* 5.7 1.3 - - - +
173B LEU* 4.0 20.6 - - + -
181B GLN 2.9 14.1 + - - +
182B SER 2.9 9.8 + - - +
184B ALA* 1.3 77.7 - - - +
186B ILE* 1.3 64.7 + - - +
188B LYS* 3.2 17.7 + - - +
189B TRP* 3.2 11.6 + - - +
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Residues in contact with ILE 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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147B PHE* 3.9 44.9 - - + -
173B LEU* 4.9 2.5 - - + -
175B PHE* 4.0 13.5 - - + -
182B SER 3.2 14.4 - - - +
183B ARG* 2.9 6.0 + - - +
185B ALA* 1.3 72.4 - - - +
187B ASN* 1.3 60.1 + - - +
189B TRP* 2.8 22.7 + - - +
190B VAL* 3.1 14.7 + - + +
202B ILE* 3.8 24.5 - - + -
207B ILE* 3.6 31.4 - - + -
214B VAL* 4.1 11.4 - - + -
216B VAL* 4.1 13.0 - - + -
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Residues in contact with ASN 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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183B ARG* 3.1 35.4 + - - +
184B ALA* 4.1 5.4 - - - +
186B ILE* 1.3 76.7 - - - +
188B LYS* 1.3 63.7 + - + +
190B VAL* 3.2 9.8 + - - +
191B SER* 3.0 25.9 + - - -
199B THR 3.4 20.7 + - - +
200B ASP* 4.1 6.9 + - - +
201B VAL* 3.2 7.5 + - - +
202B ILE* 2.9 52.0 + - - +
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Residues in contact with LYS 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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184B ALA 3.3 14.0 + - - +
185B ALA* 3.2 14.7 + - - +
186B ILE 3.1 0.2 - - - -
187B ASN* 1.3 79.0 - - - +
189B TRP* 1.3 60.9 + - - +
191B SER* 3.5 12.8 + - - +
192B ASN* 3.2 20.1 + - - +
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Residues in contact with TRP 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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143B ALA* 3.9 17.5 - - + -
144B ASN 4.2 6.5 - - - -
145B ARG* 3.6 54.0 - - + +
147B PHE* 3.7 23.1 - + + -
185B ALA 3.2 6.6 + - - +
186B ILE 2.8 11.9 + - - +
188B LYS* 1.3 73.4 - - - +
190B VAL* 1.3 88.3 + - + +
192B ASN* 3.1 9.8 + - + +
193B LYS* 3.0 67.7 + - + +
216B VAL* 3.5 20.8 - - + +
218B THR* 4.9 3.0 + - - -
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Residues in contact with VAL 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 ILE* 3.1 10.3 + - + +
187B ASN* 3.2 8.3 + - - +
189B TRP* 1.3 92.2 - - + +
191B SER* 1.3 62.6 + - - +
193B LYS* 2.8 7.9 + - - +
194B THR* 2.8 24.7 + - - +
198B ILE* 3.5 21.8 - - + +
201B VAL* 3.5 25.4 - - + -
202B ILE* 6.5 0.4 - - + -
216B VAL* 4.0 21.8 - - + -
218B THR* 4.3 4.3 - - - +
385B SER* 3.3 26.5 - - - +
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Residues in contact with SER 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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187B ASN 3.0 13.9 + - - -
188B LYS* 3.6 18.9 - - - +
189B TRP 3.4 0.2 - - - -
190B VAL* 1.3 73.7 - - - +
192B ASN* 1.3 63.0 + - - +
194B THR* 3.1 2.0 + - - -
195B GLU 3.1 3.3 + - - -
196B GLY* 2.8 36.7 + - - +
198B ILE 3.4 18.0 + - - -
199B THR* 3.5 22.0 + - - +
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Residues in contact with ASN 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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188B LYS 3.2 7.6 + - - +
189B TRP* 3.1 12.2 + - + +
191B SER* 1.3 76.3 - - - +
193B LYS* 1.3 88.9 + - - +
195B GLU* 3.0 24.8 + - - +
196B GLY 5.1 0.4 - - - +
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Residues in contact with LYS 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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141B VAL* 5.4 3.1 - - - +
143B ALA* 3.9 11.2 - - + -
189B TRP* 3.0 60.3 + - + +
190B VAL* 2.8 8.9 + - - +
192B ASN* 1.3 107.5 - - - +
194B THR* 1.3 58.9 + - - +
195B GLU 3.5 0.8 + - - -
218B THR* 3.5 28.6 - - + +
220B TYR* 4.1 10.4 - - - +
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Residues in contact with THR 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 VAL 2.8 17.2 + - - +
191B SER 3.5 2.4 + - - -
193B LYS* 1.3 79.5 - - - +
195B GLU* 1.3 57.6 + - - +
196B GLY 2.7 16.3 + - - -
197B ARG* 3.0 15.4 + - - +
198B ILE* 3.2 39.5 + - + -
218B THR* 3.6 25.4 - - + +
219B ILE 4.3 6.5 - - - +
220B TYR* 4.0 11.9 - - - -
383B ALA* 4.0 20.0 - - + -
384B ALA 4.4 0.7 - - - +
385B SER* 4.2 4.7 - - - +
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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