Contacts of the helix formed by residues 186 - 197 (chain A) in PDB entry 5E1O
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 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-2A PRO* 5.8 0.3 - - - +
170A ALA* 3.2 21.7 - - - +
171A GLN 4.0 3.6 - - - +
172A GLU* 3.6 12.0 - - - +
173A GLY* 2.8 40.6 + - - +
185A ARG* 1.3 77.0 - - - +
187A LEU* 1.3 64.1 + - - +
188A ASP* 3.0 15.4 + - - +
189A VAL* 2.9 30.2 + - - +
190A VAL* 3.1 20.5 + - - +
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Residues in contact with LEU 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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169A MET* 3.8 16.2 - - + +
170A ALA 4.2 2.0 + - - -
185A ARG 4.0 0.4 + - - -
186A ASP* 1.3 74.5 - - - +
188A ASP* 1.3 58.7 + - - +
190A VAL* 3.4 2.2 + - - +
191A ARG* 2.9 63.7 + - - +
204A GLU* 4.5 0.9 - - - +
218A TYR* 3.8 38.4 - - + +
220A PHE* 3.5 30.1 - - + -
321A UNX 3.6 24.0 - - - -
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Residues in contact with ASP 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ASP* 3.0 13.3 + - - +
187A LEU* 1.3 76.0 - - - +
189A VAL* 1.3 59.2 + - + +
191A ARG* 3.0 27.3 + - - +
192A ARG* 2.9 29.5 + - - +
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Residues in contact with VAL 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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-1A ARG 4.9 1.1 - - - +
0A GLY* 3.7 32.5 - - - +
143A ASP* 4.9 1.1 - - - +
173A GLY* 4.5 1.1 - - - +
174A VAL* 4.2 13.5 - - + -
185A ARG* 3.8 30.5 - - + +
186A ASP* 2.9 29.6 + - - +
188A ASP* 1.3 75.2 - - + +
190A VAL* 1.3 65.1 + - - +
192A ARG* 3.2 23.6 + - - +
193A ILE* 3.1 25.6 + - + +
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Residues in contact with VAL 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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138A ILE* 4.3 17.3 - - + -
146A LEU* 6.1 2.0 - - + -
165A ILE* 5.2 4.0 - - + -
169A MET* 3.7 27.1 - - + -
185A ARG* 3.8 22.9 - - + -
186A ASP 3.1 18.2 + - - +
187A LEU* 3.8 3.6 - - - +
189A VAL* 1.3 77.0 - - - +
191A ARG* 1.3 64.5 + - - +
193A ILE* 3.2 10.1 + - + +
194A ILE* 3.0 39.3 + - + +
220A PHE* 4.0 19.3 - - + -
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Residues in contact with ARG 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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187A LEU* 2.9 46.5 + - - +
188A ASP* 3.0 30.6 + - - +
190A VAL* 1.3 78.8 - - - +
192A ARG* 1.3 60.1 + - - +
194A ILE* 3.5 9.9 + - - +
195A CYS* 3.1 24.1 + - - +
201A LEU* 4.7 15.6 - - + +
204A GLU* 2.7 43.1 + - - +
220A PHE* 4.4 11.4 - - + -
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Residues in contact with ARG 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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0A GLY* 2.8 34.1 + - - -
1A SER* 4.3 4.5 - - - -
143A ASP* 3.4 21.2 + - - +
188A ASP 2.9 17.8 + - - +
189A VAL* 3.2 24.0 + - - +
191A ARG* 1.3 74.3 - - - +
193A ILE* 1.3 74.3 + - - +
195A CYS* 3.3 7.3 + - - +
196A SER* 2.9 30.6 + - - -
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Residues in contact with ILE 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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143A ASP* 3.5 35.0 - - + +
146A LEU* 3.9 31.6 - - + -
147A ALA* 4.1 19.5 - - + +
150A LEU* 4.4 5.6 - - + -
185A ARG* 3.6 20.4 - - - +
189A VAL* 3.1 18.0 + - + +
190A VAL* 3.2 7.8 + - + +
192A ARG* 1.3 89.3 - - - +
194A ILE* 1.3 65.3 + - + +
196A SER* 2.7 22.8 + - - +
197A ALA* 3.0 10.4 + - - +
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Residues in contact with ILE 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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150A LEU* 4.6 11.0 - - + -
165A ILE* 4.3 11.0 - - + -
190A VAL* 3.0 39.4 + - + +
191A ARG* 3.7 6.7 - - - +
193A ILE* 1.3 77.6 - - + +
195A CYS* 1.3 62.9 + - - +
197A ALA* 3.2 10.4 + - - +
199A LEU* 3.2 45.9 + - + +
201A LEU* 4.1 19.5 - - + -
220A PHE* 4.3 12.8 - - + -
222A LEU* 3.8 39.7 - - + -
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Residues in contact with CYS 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 ARG 3.1 18.1 + - - +
192A ARG* 3.7 5.8 - - - +
194A ILE* 1.3 78.3 - - - +
196A SER* 1.3 57.3 + - - +
198A GLY* 2.9 21.1 + - - -
199A LEU 3.9 10.9 - - - +
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Residues in contact with SER 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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147A ALA* 3.8 14.6 - - - +
151A ARG* 2.8 24.2 + - - -
192A ARG* 2.9 19.2 + - - -
193A ILE* 2.7 24.4 + - - +
195A CYS* 1.3 72.8 - - - +
197A ALA* 1.3 58.5 + - - +
198A GLY 3.3 1.2 + - - -
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Residues in contact with ALA 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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147A ALA 3.7 22.2 - - - +
150A LEU* 3.7 21.3 - - + -
151A ARG* 3.7 25.5 - - + +
154A LYS* 4.3 9.0 + - - +
193A ILE 3.0 12.6 + - - +
194A ILE 3.5 9.6 - - - +
195A CYS 3.1 0.8 - - - -
196A SER* 1.3 76.9 + - - +
198A GLY* 1.3 61.2 + - - +
199A LEU* 3.3 9.8 + - + +
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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