Contacts of the helix formed by residues 176 - 190 (chain A) in PDB entry 2DOU
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A ALA* 1.3 76.5 - - - +
177A TRP* 1.3 65.1 + - + +
178A GLY* 3.2 6.1 + - - -
179A TYR* 2.9 26.5 + - - +
180A PHE* 3.4 21.0 + - - -
210A PRO* 3.7 9.9 - - - -
310A ARG* 6.3 0.7 - - - +
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Residues in contact with TRP 177 (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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80A TYR* 3.7 15.3 - + + -
176A ASP* 1.3 76.9 - - + +
178A GLY* 1.3 58.0 + - - +
180A PHE* 3.3 3.5 + - + +
181A GLU* 2.8 31.2 + - - +
208A GLU* 5.3 4.4 + - + -
209A ALA 5.4 0.4 - - - -
210A PRO* 3.8 27.5 - - + +
211A SER 3.5 30.7 - - - -
214A ALA* 3.6 24.5 - - + -
215A LEU* 3.7 30.1 - - + +
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Residues in contact with GLY 178 (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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176A ASP* 3.2 8.3 + - - -
177A TRP* 1.3 79.2 - - - +
179A TYR* 1.3 56.2 + - - +
181A GLU* 3.2 6.2 + - - +
182A GLU* 2.8 40.8 + - - +
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Residues in contact with TYR 179 (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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141A ARG* 4.0 26.5 - - - +
145A LEU* 4.0 15.9 - - + -
146A ALA* 2.7 42.1 + - - +
148A LEU* 3.2 30.0 - - + +
164A LEU* 4.2 13.6 - - + +
166A TYR* 3.8 22.4 + + - -
175A ALA* 3.7 19.1 - - + -
176A ASP* 2.9 25.3 + - - +
178A GLY* 1.3 75.4 - - - +
180A PHE* 1.3 63.6 + + - +
182A GLU* 3.1 17.1 + - - +
183A ALA* 2.8 26.9 + - + +
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Residues in contact with PHE 180 (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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164A LEU* 5.1 5.8 - - + -
166A TYR* 4.1 22.2 - + + -
175A ALA* 3.8 15.9 - - + -
176A ASP 3.4 16.5 + - - +
177A TRP* 3.3 6.6 + - + +
178A GLY 3.3 0.4 - - - -
179A TYR* 1.3 81.7 - + - +
181A GLU* 1.3 60.3 + - - +
183A ALA* 3.5 9.1 - - + +
184A LEU* 2.8 33.1 + - - +
194A LEU* 5.8 1.8 - - + -
196A HIS* 3.3 44.4 - + - -
210A PRO* 3.6 31.9 - - + -
211A SER 5.1 0.2 - - - -
212A PRO* 3.6 33.7 - - + +
215A LEU* 3.7 17.2 - - + +
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Residues in contact with GLU 181 (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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177A TRP 2.8 19.1 + - - +
178A GLY* 3.6 7.9 - - - +
180A PHE* 1.3 75.8 - - - +
182A GLU* 1.3 62.8 + - + +
184A LEU* 4.0 7.1 - - - +
185A GLY* 3.1 24.3 + - - -
215A LEU* 3.5 32.2 - - + +
216A PRO* 4.5 7.6 - - - +
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Residues in contact with GLU 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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141A ARG* 4.7 6.9 + - - -
148A LEU* 4.4 10.9 - - + +
178A GLY* 2.8 25.0 + - - +
179A TYR* 3.2 25.8 - - - +
181A GLU* 1.3 79.3 - - + +
183A ALA* 1.3 62.5 + - - +
185A GLY* 3.2 2.6 + - - -
186A LEU* 3.1 28.2 + - + +
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Residues in contact with ALA 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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148A LEU* 3.6 22.1 - - + +
162A LEU* 4.4 7.5 - - + +
164A LEU* 4.0 22.7 - - + -
179A TYR* 2.8 17.9 + - + +
180A PHE* 3.5 13.7 - - + +
182A GLU* 1.3 74.4 - - - +
184A LEU* 1.3 61.6 + - - +
186A LEU* 3.3 5.4 + - - +
187A ALA* 3.0 22.9 + - - +
194A LEU* 4.4 10.3 - - + -
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Residues in contact with LEU 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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180A PHE 2.8 19.9 + - - +
181A GLU* 4.0 7.9 - - - +
183A ALA* 1.3 73.1 - - - +
185A GLY* 1.3 57.7 + - - +
187A ALA* 3.4 1.0 + - + +
188A ARG* 2.9 33.8 + - + +
194A LEU* 4.0 12.0 - - + +
212A PRO* 4.1 4.5 - - + +
215A LEU* 3.8 24.5 - - + -
216A PRO 3.6 24.5 - - - +
217A GLY 4.6 1.8 - - - +
218A ALA* 3.9 15.9 - - + +
221A ARG* 4.0 19.5 - - + -
222A VAL* 3.6 27.6 - - + -
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Residues in contact with GLY 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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181A GLU* 3.1 19.0 + - - -
182A GLU 3.2 4.2 + - - -
184A LEU* 1.3 78.9 - - - +
186A LEU* 1.3 50.9 + - - +
188A ARG* 3.3 13.9 + - - +
189A LYS* 2.7 37.5 + - - +
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Residues in contact with LEU 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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148A LEU* 3.9 28.9 - - + +
156A TRP* 3.6 41.3 - - + +
182A GLU* 3.1 17.6 + - + +
183A ALA* 3.7 5.8 - - - +
185A GLY* 1.3 72.8 - - - +
187A ALA* 1.3 66.2 + - - +
189A LYS* 3.1 12.3 + - + +
190A HIS* 2.8 49.5 + - + +
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Residues in contact with ALA 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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156A TRP* 5.0 0.8 - - - -
162A LEU* 5.0 5.8 - - + +
183A ALA 3.0 16.6 + - - +
184A LEU* 3.6 6.3 - - - +
186A LEU* 1.3 76.5 - - - +
188A ARG* 1.3 57.4 + - - +
190A HIS 3.5 0.2 - - - -
191A GLY 2.9 8.8 + - - -
192A LEU* 2.7 56.7 + - + +
193A TRP 4.9 0.4 - - - +
194A LEU* 4.3 20.6 - - + -
221A ARG* 4.0 8.3 - - - -
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Residues in contact with ARG 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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184A LEU* 2.9 21.7 + - + +
185A GLY* 3.6 12.1 + - - +
187A ALA* 1.3 74.9 - - - +
189A LYS* 1.3 79.5 + - - +
191A GLY* 3.1 12.1 + - - -
217A GLY* 6.2 4.5 - - - -
220A GLU* 5.8 4.0 - - - -
221A ARG* 3.4 33.5 + - - +
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Residues in contact with LYS 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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153A GLU* 4.9 9.1 + - - -
185A GLY 2.7 21.9 + - - +
186A LEU* 3.6 13.2 - - + +
188A ARG* 1.3 85.4 - - - +
190A HIS* 1.3 86.8 + - + +
191A GLY 3.3 0.6 + - - -
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Residues in contact with HIS 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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153A GLU* 3.5 27.0 + - - -
156A TRP* 3.5 63.4 - + + +
157A ARG* 4.5 6.4 - - - +
159A ALA 4.8 0.5 - - - +
186A LEU* 2.8 37.1 + - + +
189A LYS* 1.3 103.4 - - + +
191A GLY* 1.3 66.8 + - - +
192A LEU* 3.1 20.1 - - + +
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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