Contacts of the helix formed by residues 183 - 195 (chain A) in PDB entry 1A0P
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 GLU 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A GLY* 1.3 76.1 - - - -
184A GLU* 1.3 60.2 + - + +
186A VAL* 3.4 7.2 + - - +
187A TYR* 2.9 29.7 + - - +
260A ASP* 5.8 2.6 + - + +
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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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140A GLU* 4.3 14.4 - - - +
143A TYR* 6.0 2.4 - - - -
182A GLY 3.4 0.6 - - - -
183A GLU* 1.3 79.2 - - + +
185A ALA* 1.3 59.3 + - - +
187A TYR* 3.3 7.8 + - + +
188A TRP* 2.9 60.8 + - - -
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Residues in contact with ALA 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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137A ALA 5.7 0.2 - - - +
140A GLU* 3.6 35.4 + - - +
141A VAL* 4.2 12.0 - - + +
144A ALA* 4.2 4.0 - - + +
181A LEU* 3.7 28.6 + - + +
182A GLY 3.5 2.6 + - - -
183A GLU 3.3 0.6 - - - -
184A GLU* 1.3 79.5 - - - +
186A VAL* 1.3 58.9 + - - +
188A TRP* 3.2 2.1 + - - +
189A LEU* 2.8 35.2 + - - +
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Residues in contact with VAL 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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162A LEU* 4.2 23.4 - - + +
165A GLY* 3.9 28.0 - - - -
181A LEU* 4.0 13.0 - - + +
182A GLY 3.1 22.5 + - - +
183A GLU* 3.6 7.4 - - - +
184A GLU 3.3 0.2 - - - -
185A ALA* 1.3 76.4 - - - +
187A TYR* 1.3 54.1 - - - +
189A LEU* 3.2 8.1 + - - +
190A GLU* 2.8 55.6 + - - +
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Residues in contact with TYR 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 GLU 2.9 17.3 + - - +
184A GLU* 3.4 8.3 - - + +
186A VAL* 1.3 77.7 - - - +
188A TRP* 1.3 105.4 + + - +
190A GLU* 3.1 20.0 + - + +
191A THR* 3.0 44.6 + - - +
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Residues in contact with TRP 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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127A ILE* 3.7 34.5 - - + -
133A LEU* 4.3 16.7 - - + +
136A LYS* 3.5 39.0 - - + +
137A ALA* 4.0 13.0 - - + +
140A GLU* 3.5 37.3 + - + -
184A GLU* 2.9 53.4 + - - +
185A ALA 3.2 3.6 + - - +
187A TYR* 1.3 100.6 - + - +
189A LEU* 1.3 52.8 + - - +
191A THR* 3.5 8.0 + - + -
192A TYR* 2.7 34.1 + - - +
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Residues in contact with LEU 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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137A ALA* 3.9 10.5 - - + -
141A VAL* 3.5 25.8 - - + -
160A ILE* 4.2 11.7 - - + -
162A LEU* 3.8 25.1 - - + -
181A LEU* 4.0 18.8 - - + -
185A ALA 2.8 15.9 + - - +
186A VAL 3.4 4.7 - - - +
188A TRP* 1.3 75.2 - - - +
190A GLU* 1.3 51.2 + - - +
192A TYR* 3.2 11.0 + - + +
193A LEU* 2.6 45.2 + - + +
209A LEU* 4.8 7.4 - - + -
210A PHE* 3.8 34.1 - - + -
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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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162A LEU* 4.4 18.2 - - + +
186A VAL* 2.8 29.0 + - - +
187A TYR* 3.2 23.2 - - - +
189A LEU* 1.3 70.7 - - - +
191A THR* 1.4 57.4 + - - +
193A LEU* 2.7 28.9 + - - +
194A GLU* 3.0 17.8 + - - +
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Residues in contact with THR 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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127A ILE* 5.8 2.7 - - + +
133A LEU* 3.4 25.1 - - + -
187A TYR* 3.0 37.2 + - + +
188A TRP* 3.7 18.8 - - + -
190A GLU* 1.4 72.9 - - - +
192A TYR* 1.4 54.7 + - - +
194A GLU* 3.3 4.5 + - - +
195A HIS* 2.7 43.2 + - + +
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Residues in contact with TYR 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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133A LEU* 3.9 15.0 - - + -
134A ARG* 3.6 35.7 - - + +
137A ALA* 3.8 11.7 - - + -
188A TRP 2.7 22.7 + - - +
189A LEU* 3.5 13.2 - - + +
191A THR* 1.4 76.9 - - - +
193A LEU* 1.3 68.1 + - + +
196A GLY* 3.2 8.1 + - - -
197A ARG* 3.0 52.0 + - + +
200A LEU* 4.3 1.1 - - + -
209A LEU* 2.6 37.7 + - + -
210A PHE* 3.4 26.4 - + - -
211A PRO* 3.2 19.9 - - - +
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Residues in contact with LEU 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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157A MET* 3.9 31.6 - - + -
160A ILE* 5.4 3.6 - - + -
162A LEU* 3.3 34.8 - - + -
189A LEU* 2.6 29.3 + - + +
190A GLU* 2.7 9.8 + - - +
192A TYR* 1.3 78.5 - - + +
194A GLU* 1.3 58.6 + - - +
197A ARG* 3.9 20.1 - - - +
198A PRO* 3.1 26.0 - - - +
209A LEU* 4.3 11.0 - - + -
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Residues in contact with GLU 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 3.0 11.2 + - - +
191A THR* 3.7 8.7 - - - +
193A LEU* 1.3 81.7 - - + +
195A HIS* 1.3 76.6 + - + +
196A GLY 3.7 0.4 - - - -
198A PRO* 3.8 11.3 - - - +
199A TRP* 4.1 7.3 + - - -
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Residues in contact with HIS 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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127A ILE 5.6 5.2 - - - +
128A ASP* 6.1 3.8 - - - -
130A PRO* 4.2 9.0 - - - +
133A LEU* 3.3 15.7 - - + +
191A THR* 2.7 26.2 + - + +
194A GLU* 1.3 87.6 + - + +
196A GLY* 1.3 54.7 + - - +
199A TRP* 3.5 23.1 + - - +
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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