Contacts of the helix formed by residues 181 - 197 (chain A) in PDB entry 3CNO
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 181 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A GLU* 5.5 1.0 - - - +
179A ILE* 3.4 17.4 - - - +
180A GLU* 1.3 78.8 - - + +
182A GLN* 1.3 67.5 + - - +
183A ARG* 3.2 50.6 + - - +
184A ILE* 3.3 30.0 + - + +
185A PHE* 3.9 1.8 + - - -
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Residues in contact with GLN 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A GLU 3.8 3.8 + - - +
181A ASP* 1.3 73.8 + - - +
183A ARG* 1.3 69.0 + - + +
184A ILE 3.2 0.2 - - - -
185A PHE* 3.3 19.4 + - + +
186A GLU* 3.1 40.3 + - + +
202A PHE* 5.0 9.7 - - + -
228A LEU* 6.1 2.0 - - + -
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Residues in contact with ARG 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A GLU* 3.8 27.2 + - - +
181A ASP* 3.2 29.7 + - - +
182A GLN* 1.3 79.6 - - + +
184A ILE* 1.3 60.0 + - + +
186A GLU* 3.2 17.8 + - - +
187A ARG* 2.9 29.3 + - - +
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Residues in contact with ILE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A GLU* 4.3 18.6 - - + +
165A ALA* 4.0 20.6 - - + +
166A ALA* 3.8 26.1 - - - +
169A LEU* 4.4 3.8 - - + -
174A LEU* 6.2 0.2 - - + -
179A ILE* 3.9 31.4 - - + -
180A GLU 5.9 0.2 - - - +
181A ASP* 3.3 32.6 + - + +
182A GLN 3.2 0.8 - - - -
183A ARG* 1.3 74.9 - - - +
185A PHE* 1.3 59.7 - - - +
187A ARG* 3.4 4.2 + - - -
188A ALA* 2.9 29.0 + - - +
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Residues in contact with PHE 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A LEU* 3.8 19.1 - - + -
176A VAL* 4.3 6.1 - - + -
179A ILE* 3.5 41.7 - - + -
180A GLU 5.8 0.7 - - - -
181A ASP 4.1 6.7 - - - -
182A GLN* 3.3 18.0 + - + +
184A ILE* 1.3 77.7 - - - +
186A GLU* 1.3 56.1 + - - +
188A ALA* 3.5 2.8 + - - -
189A PHE* 3.0 27.7 + - - +
202A PHE* 3.8 16.9 - - + -
225A GLU* 6.4 1.3 - - + -
228A LEU* 4.0 19.7 - - + -
229A MET* 3.4 32.1 - - + -
232A PHE* 3.5 35.6 - + + -
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Residues in contact with GLU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A GLN* 3.1 31.4 + - - +
183A ARG* 3.5 19.7 - - - +
184A ILE 3.2 0.6 - - - -
185A PHE* 1.3 73.7 - - - +
187A ARG* 1.3 61.3 + - - +
189A PHE* 3.4 4.2 + - - +
190A GLU* 2.9 31.2 + - - +
202A PHE* 3.9 39.6 - - + +
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Residues in contact with ARG 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A GLU* 3.3 31.9 - - + +
163A ASP* 2.3 49.7 + - - +
166A ALA* 3.7 11.9 - - + -
167A LYS* 4.8 2.4 - - - +
183A ARG 2.9 15.1 + - - +
184A ILE* 3.8 1.3 - - - +
186A GLU* 1.3 75.3 - - - +
188A ALA* 1.3 58.8 + - - +
190A GLU* 2.8 48.8 + - - +
191A ILE* 2.9 55.9 + - - +
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Residues in contact with ALA 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ALA* 3.5 19.5 - - + +
169A LEU* 3.9 14.1 - - + -
170A LEU* 3.6 13.8 - - + +
184A ILE 2.9 20.5 + - - +
185A PHE 3.6 3.1 - - - +
187A ARG* 1.3 77.8 - - - +
189A PHE* 1.3 56.8 + - - +
191A ILE* 3.5 1.6 + - - +
192A PHE* 2.9 27.4 + - - +
232A PHE* 3.5 24.0 - - + -
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Residues in contact with PHE 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A PHE 3.0 17.8 + - - +
186A GLU 3.7 4.7 - - - +
188A ALA* 1.3 73.7 - - - +
190A GLU* 1.3 59.0 - - + +
192A PHE* 3.1 13.5 + + - +
193A ALA* 2.6 52.5 + - + +
198A ILE* 4.4 3.6 - - + -
200A SER 3.6 20.9 - - - -
201A SER* 4.6 0.2 - - - -
202A PHE* 3.5 42.8 - + + -
205A PHE* 3.5 46.4 - + + -
206A PHE* 3.8 20.9 - + + -
231A PHE* 5.0 1.1 - + - -
232A PHE* 3.7 5.8 - - + -
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Residues in contact with GLU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A GLU 2.9 16.5 + - - +
187A ARG* 2.8 45.6 + - - +
189A PHE* 1.3 81.9 - - + +
191A ILE* 1.3 57.4 + - - +
193A ALA* 3.9 4.4 - - - +
194A ARG* 3.1 29.2 + - + +
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Residues in contact with ILE 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ASP* 3.5 20.9 - - - +
166A ALA* 3.9 12.8 - - + -
167A LYS* 3.8 22.2 - - + -
170A LEU* 3.8 6.7 - - + -
187A ARG* 2.9 44.3 + - - +
188A ALA 3.7 3.6 - - - +
190A GLU* 1.3 73.3 - - - +
192A PHE* 1.3 61.0 + - - +
194A ARG* 3.4 5.0 + - - +
195A SER* 2.6 32.9 + - - +
245A PHE* 3.4 43.3 - - + +
247A ARG* 4.4 2.1 + - - +
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Residues in contact with PHE 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A LEU* 4.3 8.0 - - + +
188A ALA 2.9 15.9 + - - +
189A PHE* 3.4 16.4 - + - +
191A ILE* 1.3 76.3 - - - +
193A ALA* 1.3 68.2 + - - +
195A SER* 3.1 8.4 + - - -
196A ILE* 3.0 58.7 + - + +
198A ILE* 3.9 14.6 - - + -
205A PHE* 4.3 3.1 - + - -
231A PHE* 3.6 39.5 - + + -
235A VAL* 4.0 25.1 - - + -
240A ALA* 4.1 15.0 - - + -
243A VAL* 4.3 17.5 - - + -
245A PHE* 4.5 6.1 - + - -
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Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A PHE* 2.6 41.0 + - + +
190A GLU* 3.9 5.4 - - - +
192A PHE* 1.3 77.0 - - - +
194A ARG* 1.3 57.9 + - - +
196A ILE* 4.3 0.4 - - - -
197A GLY* 2.8 26.7 + - - -
198A ILE* 2.8 41.8 + - + +
200A SER 5.3 0.7 - - - +
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Residues in contact with ARG 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A GLU* 3.1 19.3 + - + +
191A ILE* 3.9 4.9 - - - +
193A ALA* 1.3 76.3 - - - +
195A SER* 1.3 62.7 + - - +
196A ILE 3.4 0.3 + - - -
197A GLY* 3.7 7.4 + - - -
198A ILE 5.2 0.7 - - - -
247A ARG* 3.0 37.8 - - - +
250A ASP 3.7 21.2 + - - -
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Residues in contact with SER 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ILE 2.6 21.2 + - - -
192A PHE* 3.5 7.5 - - - -
194A ARG* 1.3 78.4 - - - +
196A ILE* 1.3 59.5 + - - +
243A VAL* 3.7 13.6 - - - +
244A SER 2.9 24.5 + - - -
245A PHE* 3.9 4.5 - - - -
247A ARG* 2.6 28.2 + - - +
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Residues in contact with ILE 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A PHE* 3.0 42.2 + - + +
193A ALA 4.0 0.2 - - - +
195A SER* 1.3 77.1 - - - +
197A GLY* 1.3 59.6 + - - +
198A ILE* 3.4 35.8 - - + +
240A ALA 4.0 10.5 - - - +
241A GLY* 5.6 0.7 - - - -
243A VAL* 3.8 25.4 - - + -
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Residues in contact with GLY 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A ALA 2.8 6.9 + - - -
194A ARG* 3.7 6.0 + - - -
195A SER 3.5 2.0 - - - -
196A ILE* 1.3 78.9 - - - +
198A ILE* 1.3 64.8 + - - +
199A GLU* 3.6 11.6 + - - +
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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
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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