Contacts of the helix formed by residues 178 - 193 (chain A) in PDB entry 2A1I
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 PRO 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A LEU* 3.3 27.4 - - + -
173A VAL* 3.7 21.5 - - + -
175A VAL* 3.5 19.3 - - + +
176A LYS* 3.5 0.6 - - - -
177A ASP* 1.3 88.5 - - - +
179A GLN* 1.3 67.0 + - - +
180A GLN 3.2 1.9 + - - -
181A ALA* 3.3 7.5 + - + +
182A LEU* 2.8 38.8 + - + +
200A TRP* 5.4 5.2 - - + -
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Residues in contact with GLN 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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177A ASP* 2.7 45.8 + - - +
178A PRO* 1.3 93.8 - - - +
180A GLN* 1.3 61.5 + - + +
182A LEU* 3.4 8.4 + - - +
183A LYS* 3.0 29.6 + - - +
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Residues in contact with GLN 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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177A ASP 4.5 3.9 + - - +
178A PRO 3.3 0.4 - - - -
179A GLN* 1.3 80.8 - - + +
181A ALA* 1.3 67.6 + - - +
183A LYS* 3.3 22.0 + - + +
184A GLU* 3.2 31.7 + - - +
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Residues in contact with ALA 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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143A LEU* 4.3 15.7 - - + +
146A HIS* 4.3 21.1 - - + -
175A VAL* 5.7 2.9 - - + -
177A ASP 5.3 0.8 + - - +
178A PRO* 3.3 11.9 + - + +
180A GLN* 1.3 78.3 - - - +
182A LEU* 1.3 56.3 + - - +
184A GLU* 2.7 34.2 - - - +
185A LEU* 3.0 15.1 + - - +
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Residues in contact with LEU 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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143A LEU* 4.0 12.3 - - + -
171A VAL* 4.0 29.4 - - + -
173A VAL* 4.5 11.0 - - + -
178A PRO* 2.8 45.0 + - + +
179A GLN* 3.7 7.6 - - - +
181A ALA* 1.3 69.3 - - - +
183A LYS* 1.3 60.1 + - - +
185A LEU* 3.4 7.4 + - + +
186A ALA* 2.8 30.0 + - - +
196A LEU* 4.5 6.4 - - + +
198A LEU* 4.2 29.8 - - + -
200A TRP* 5.7 2.0 - - + -
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Residues in contact with LYS 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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179A GLN 3.0 17.2 + - - +
180A GLN* 3.8 21.5 - - + +
181A ALA 3.3 0.2 - - - -
182A LEU* 1.3 77.1 - - - +
184A GLU* 1.3 62.5 + - - +
186A ALA* 3.4 7.0 + - - +
187A LYS* 3.1 49.8 + - - +
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Residues in contact with GLU 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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146A HIS* 2.6 32.7 + - + +
180A GLN* 3.2 22.2 + - - +
181A ALA* 2.7 31.5 - - - +
183A LYS* 1.3 77.6 - - + +
185A LEU* 1.3 62.6 + - + +
187A LYS* 3.4 13.4 + - + +
188A MET* 3.1 31.9 + - + +
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Residues in contact with LEU 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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141A LEU* 3.9 17.7 - - + -
143A LEU* 3.5 31.4 - - + -
146A HIS* 3.9 16.4 - - + +
153A ILE* 3.8 29.6 - - + -
169A LEU* 4.2 11.9 - - + -
171A VAL* 4.3 11.9 - - + -
181A ALA 3.0 20.6 + - - +
182A LEU* 3.8 7.9 - - + +
183A LYS 3.3 0.2 - - - -
184A GLU* 1.3 74.8 - - + +
186A ALA* 1.3 60.1 + - - +
188A MET* 3.3 13.2 + - + +
189A CYS* 2.9 33.6 + - - -
196A LEU* 3.8 11.2 - - + -
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Residues in contact with ALA 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 LEU 2.8 17.6 + - - +
183A LYS* 3.5 8.3 - - - +
184A GLU 3.3 0.2 - - - -
185A LEU* 1.3 74.3 - - - +
187A LYS* 1.3 65.7 + - + +
189A CYS* 3.3 3.4 + - - +
190A ILE* 2.9 35.7 + - + +
196A LEU* 3.6 17.0 - - + +
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Residues in contact with LYS 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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183A LYS* 3.1 46.3 + - + +
184A GLU* 3.5 12.5 - - - +
186A ALA* 1.3 74.8 - - - +
188A MET* 1.3 62.5 + - - +
190A ILE* 3.3 10.5 + - + +
191A LEU* 3.1 35.6 + - + +
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Residues in contact with MET 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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146A HIS* 5.0 5.6 - - + -
153A ILE* 3.8 33.0 - - + -
154A HIS* 4.2 29.6 - - + +
157A LEU* 3.7 26.5 - - + -
169A LEU* 5.7 1.6 - - - -
184A GLU* 3.1 14.5 + - + +
185A LEU* 3.4 22.9 - - + +
186A ALA 3.2 0.2 - - - -
187A LYS* 1.3 79.5 - - - +
189A CYS* 1.3 56.8 + - - +
191A LEU* 3.4 7.7 + - - +
192A ALA* 2.9 29.6 + - + +
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Residues in contact with CYS 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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157A LEU* 4.9 2.7 - - - -
169A LEU* 3.7 33.2 - - - -
185A LEU 2.9 20.3 + - - +
186A ALA 3.7 4.0 - - - +
188A MET* 1.3 73.6 - - - +
190A ILE* 1.3 59.8 + - - +
193A ASP* 2.8 25.8 + - - -
194A CYS* 2.8 50.4 + - - +
196A LEU* 4.1 19.3 - - + -
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Residues in contact with ILE 190 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A ALA* 2.9 29.8 + - + +
187A LYS* 3.7 8.7 - - + +
189A CYS* 1.3 75.0 - - + +
191A LEU* 1.3 72.4 + - + +
193A ASP* 3.2 13.9 + - - +
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Residues in contact with LEU 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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162A LYS* 4.9 4.2 + - - -
187A LYS* 3.1 24.6 + - + +
188A MET* 3.9 5.4 - - - +
190A ILE* 1.3 85.6 - - + +
192A ALA* 1.3 60.0 + - - +
193A ASP* 3.6 1.4 + - - +
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Residues in contact with ALA 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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157A LEU* 4.0 26.0 - - + +
158A GLN* 4.7 12.6 - - - +
162A LYS* 3.6 9.6 + - - +
167A ARG* 2.9 17.7 + - - -
188A MET* 2.9 18.9 + - + +
189A CYS 4.3 1.3 - - - +
191A LEU* 1.3 75.8 - - + +
193A ASP* 1.3 68.3 + - - +
194A CYS* 3.4 5.1 - - - +
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Residues in contact with ASP 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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162A LYS* 4.1 11.9 - - - +
167A ARG* 2.7 44.4 + - - +
189A CYS 2.8 8.8 + - - -
190A ILE* 3.2 10.4 + - - +
191A LEU 3.3 1.3 - - - +
192A ALA* 1.3 79.6 - - - +
194A CYS* 1.3 57.2 + - - +
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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