Contacts of the helix formed by residues 188 - 197 (chain B) in PDB entry 1JUO
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 TYR 188 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A PHE* 4.7 7.3 - - - -
135A ARG* 3.5 28.9 + - + -
136A LEU* 3.5 21.1 - - + +
166A LEU* 5.1 0.7 - - - +
170A THR* 2.8 45.3 + - + +
173A PHE* 3.6 43.3 - + + -
182A GLY* 2.9 18.3 + - - +
186B PHE 3.5 1.0 + - - -
187B PRO* 1.3 70.8 - - - +
189B ASP* 1.3 68.2 + - + +
191B PHE* 3.1 2.4 + - - +
192B ILE* 2.9 44.1 + - + +
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Residues in contact with ASP 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ARG 5.0 0.9 - - - +
136A LEU* 3.9 5.8 - - - +
137A SER* 2.9 45.2 + - - -
139A GLN* 4.2 2.9 + - - -
140A ALA* 3.5 6.3 - - - +
187B PRO* 3.4 3.4 - - + +
188B TYR* 1.3 86.1 - - + +
190B ASP* 1.3 57.8 + - - +
192B ILE* 3.3 5.7 + - - +
193B GLN* 2.9 54.7 + - - +
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Residues in contact with ASP 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B ARG* 2.8 43.4 + - - -
185B ASN 5.2 0.3 - - - +
186B PHE* 3.5 10.8 - - - -
187B PRO* 3.1 27.3 + - + +
189B ASP* 1.3 77.7 + - - +
191B PHE* 1.3 64.3 + - - +
193B GLN* 3.5 10.3 + - - +
194B CYS* 3.0 26.3 + - - +
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Residues in contact with PHE 191 (chain B).
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* 3.7 40.6 - - + -
173A PHE* 3.7 27.4 - + + -
186A PHE* 3.6 37.9 - + - -
191A PHE* 4.1 14.6 - + - -
194A CYS* 4.9 4.7 - - - -
195A VAL* 4.2 12.3 - - + -
186B PHE* 3.6 22.1 - + + -
187B PRO 2.8 13.3 + - - +
188B TYR* 3.5 9.0 - + - +
190B ASP* 1.3 75.7 - - - +
192B ILE* 1.3 72.4 + - + +
194B CYS* 3.6 0.9 - - - +
195B VAL* 3.2 50.0 + - + +
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Residues in contact with ILE 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A LEU* 3.9 18.6 - - + -
140A ALA* 5.0 2.9 - - + -
144A ILE* 4.2 9.4 - - + -
166A LEU* 4.1 15.5 - - + -
169A LEU* 4.4 18.4 - - + -
170A THR* 4.2 8.5 - - - +
188B TYR* 2.9 53.2 + - + +
189B ASP 3.6 8.5 - - - +
191B PHE* 1.3 84.9 - - + +
193B GLN* 1.3 62.4 + - - +
195B VAL* 3.4 1.2 + - - -
196B MET* 2.9 48.9 + - + +
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Residues in contact with GLN 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A GLN* 3.1 38.9 - - - +
140A ALA* 3.5 32.8 - - + +
143A SER* 4.1 18.6 + - - +
144A ILE* 5.8 0.4 - - - -
176B ARG* 6.1 0.2 - - - +
189B ASP* 2.9 38.3 + - - +
190B ASP* 3.5 9.3 + - - +
192B ILE* 1.3 77.0 - - - +
194B CYS* 1.3 63.8 + - - +
196B MET* 4.1 3.0 - - - -
197B SER* 3.1 26.7 + - - -
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Residues in contact with CYS 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A PHE* 4.4 12.8 - - - -
169B LEU* 4.7 2.6 - - - +
172B SER* 3.5 36.0 + - - -
176B ARG* 3.6 24.4 - - - +
186B PHE* 4.1 15.5 - - + -
190B ASP 3.0 18.5 + - - +
191B PHE 3.6 5.4 - - - +
192B ILE 3.2 0.2 - - - -
193B GLN* 1.3 78.7 - - - +
195B VAL* 1.3 60.5 + - - +
197B SER* 3.0 18.0 + - - -
198B VAL* 4.0 10.4 - - - +
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Residues in contact with VAL 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LYS* 3.2 20.2 + - - +
169A LEU* 3.4 28.0 - - + -
191A PHE* 4.5 9.6 - - + -
195A VAL* 3.9 42.4 - - + +
198A VAL* 5.3 0.2 - - - +
169B LEU* 4.6 9.2 - - + -
191B PHE* 3.2 34.3 + - + +
192B ILE 4.3 0.4 - - - +
194B CYS* 1.3 75.8 - - + +
196B MET* 1.3 65.5 + - - +
197B SER 3.1 3.1 + - - -
198B VAL* 3.4 11.3 + - + +
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Residues in contact with MET 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A SER* 5.8 2.2 - - - +
144A ILE* 4.1 21.1 - - + -
147A ARG* 3.3 25.7 + - - +
148A TYR* 3.6 36.1 + - + +
162A CYS* 3.9 22.9 - - - +
165A LYS* 3.8 28.3 + - + +
166A LEU* 4.0 18.6 - - + -
169A LEU* 3.9 12.3 - - + -
192B ILE* 2.9 39.7 + - + +
193B GLN* 4.4 2.7 - - - +
195B VAL* 1.3 75.7 - - - +
197B SER* 1.3 60.4 + - - +
198B VAL* 3.3 2.8 + - - +
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Residues in contact with SER 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A SER* 4.7 10.3 + - - -
147A ARG* 3.8 14.2 - - - +
76B ARG* 5.3 0.2 + - - -
80B SER* 5.0 6.2 + - - -
193B GLN 3.1 14.4 + - - -
194B CYS* 3.0 20.1 + - - -
195B VAL 3.1 0.2 - - - -
196B MET* 1.3 77.1 - - - +
198B VAL* 1.3 66.3 + - - +
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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