Contacts of the helix formed by residues 176 - 187 (chain N) in PDB entry 2A69
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 176 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174N GLY* 3.7 0.4 - - - -
175N VAL* 1.3 86.1 - - - +
177N ALA* 1.3 66.4 + - - +
178N LEU 3.8 0.2 - - - -
179N VAL* 4.3 2.5 - - - -
180N LYS* 3.4 25.2 - - - +
218N LYS 3.5 14.7 - - - +
219N GLU* 3.3 25.8 - - - +
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Residues in contact with ALA 177 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174N GLY* 5.1 4.7 - - - +
175N VAL 4.9 0.8 - - - +
176N ASP* 1.3 80.6 - - - +
178N LEU* 1.3 62.4 + - - +
180N LYS* 4.0 1.0 - - - +
181N ASP* 2.9 22.7 + - - +
199N LEU* 3.1 43.8 - - + +
200N ASP* 5.3 1.1 - - + +
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Residues in contact with LEU 178 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171N LEU 5.6 0.2 - - - -
172N PRO* 3.4 41.7 - - + +
173N PRO* 4.2 10.5 - - + +
174N GLY 5.5 2.8 + - - +
177N ALA* 1.3 75.6 - - - +
179N VAL* 1.3 65.3 + - - +
180N LYS 3.1 3.1 - - - -
181N ASP* 3.5 2.9 - - - +
182N GLY* 3.1 23.6 + - - -
197N SER* 2.9 29.4 - - - +
199N LEU 3.4 16.4 - - - +
200N ASP* 3.4 28.5 - - + +
203N ALA* 3.6 24.7 - - + -
205N TYR* 4.8 1.1 - - - +
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Residues in contact with VAL 179 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172N PRO* 4.1 5.8 - - + -
174N GLY 3.5 11.7 - - - +
175N VAL* 3.2 23.8 - - + +
176N ASP* 4.7 0.2 - - - -
177N ALA 3.4 0.8 - - - -
178N LEU* 1.3 77.1 - - - +
180N LYS* 1.3 58.0 + - - +
183N GLU* 3.1 37.9 + - - +
215N TYR 4.4 0.9 - - - +
216N VAL* 4.3 15.9 - - + -
217N LYS 5.4 0.2 - - - +
219N GLU* 5.3 5.2 - - + -
389N GLU* 3.1 46.0 - - + +
9316N MG 3.8 16.5 - - - -
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Residues in contact with LYS 180 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176N ASP* 3.4 20.6 + - + +
177N ALA 4.0 2.5 - - - +
178N LEU 3.1 0.2 - - - -
179N VAL* 1.3 79.4 - - - +
181N ASP* 1.3 67.6 + - - +
182N GLY 3.3 0.2 - - - -
183N GLU* 4.6 2.0 - - - -
184N GLU* 2.9 52.5 + - + +
219N GLU* 6.3 2.7 - - + -
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Residues in contact with ASP 181 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177N ALA 2.9 9.9 - - - +
178N LEU* 3.4 4.1 + - - +
180N LYS* 1.3 76.4 - - - +
182N GLY* 1.3 59.4 + - - +
184N GLU* 3.8 12.1 + - - +
185N VAL* 3.1 30.0 + - - +
197N SER* 3.4 18.1 - - - +
198N ARG* 3.6 27.3 - - + +
199N LEU* 2.8 51.0 + - - +
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Residues in contact with GLY 182 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178N LEU 3.1 12.9 + - - -
179N VAL* 5.6 0.2 - - - -
181N ASP* 1.3 77.9 - - - +
183N GLU* 1.3 53.5 + - - +
185N VAL* 3.2 5.2 + - - +
186N VAL* 2.8 40.1 + - - +
191N LEU* 5.5 1.0 - - - +
197N SER* 3.8 0.8 + - - -
205N TYR* 3.6 23.1 - - - -
213N VAL* 5.4 2.0 - - - -
391N ALA* 5.4 8.1 - - - -
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Residues in contact with GLU 183 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179N VAL* 3.1 25.4 + - - +
180N LYS* 3.4 3.8 + - - +
182N GLY* 1.3 72.2 - - - +
184N GLU* 1.3 65.1 + - + +
186N VAL* 3.1 23.3 + - + +
187N LYS* 5.7 1.7 - - + +
213N VAL* 5.0 13.3 - - + +
216N VAL* 3.0 40.0 - - - +
220N ARG 4.7 4.6 - - - +
222N GLY 3.5 25.9 + - - +
224N ARG* 5.4 4.0 - - - +
9229N MG 2.9 28.9 - - - -
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Residues in contact with GLU 184 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180N LYS* 2.9 48.3 - - + +
181N ASP* 3.8 15.8 - - - +
183N GLU* 1.3 78.3 - - + +
185N VAL* 1.3 63.4 + - + +
187N LYS 5.3 0.7 + - - -
189N GLN* 4.6 7.3 - - - +
198N ARG* 6.1 1.2 - - - -
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Residues in contact with VAL 185 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181N ASP 3.1 21.1 - - - +
182N GLY* 3.2 2.6 + - - +
183N GLU 3.2 0.6 - - - -
184N GLU* 1.3 82.2 - - + +
186N VAL* 1.3 58.7 + - - +
187N LYS 4.0 0.4 - - - -
189N GLN* 3.0 49.9 - - - +
191N LEU* 3.2 44.4 - - + +
195N VAL* 5.2 5.2 - - + -
197N SER* 6.5 1.1 - - - -
205N TYR* 6.0 1.1 - - + -
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Residues in contact with VAL 186 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182N GLY* 2.8 16.1 + - - +
183N GLU* 3.1 32.7 + - + +
184N GLU 3.5 0.2 - - - -
185N VAL* 1.3 76.1 - - - +
187N LYS* 1.3 76.2 + - + +
188N GLY 3.7 0.6 + - - -
189N GLN 4.0 4.5 - - - +
191N LEU* 4.8 2.0 - - + -
210N ARG* 5.1 0.2 - - - -
211N VAL* 2.8 52.5 + - + +
212N ARG 3.8 0.4 - - - -
213N VAL* 3.2 54.1 - - + +
391N ALA* 5.6 3.1 - - + -
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Residues in contact with LYS 187 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183N GLU* 5.7 2.2 - - + -
184N GLU 5.3 0.4 + - - -
185N VAL 4.0 0.4 - - - -
186N VAL* 1.3 85.4 - - + +
188N GLY* 1.3 58.6 + - - +
210N ARG* 3.8 10.2 + - - -
211N VAL 4.0 6.0 - - - +
212N ARG* 4.0 18.8 - - - +
213N VAL* 3.5 39.3 + - + +
223N LEU 4.8 10.3 - - - +
224N ARG* 5.7 5.6 - - - +
445N ARG* 4.8 10.2 + - - +
9229N MG 3.2 19.2 - - - -
9259N MG 3.4 17.2 - - - -
9327N MG 3.2 20.2 - - - -
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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