Contacts of the helix formed by residues 192 - 201 (chain A) in PDB entry 2JFS
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 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A ARG* 4.5 4.9 - - - +
190A ALA 3.8 1.8 + - - -
191A ALA* 1.3 71.0 - - - +
193A GLU* 1.3 68.1 + - - +
194A ALA* 3.1 24.0 + - - +
195A LEU* 2.9 39.5 + - + +
196A ILE* 3.1 11.3 + - - +
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Residues in contact with GLU 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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115A TYR* 5.2 4.2 + - - -
122A MET* 4.4 14.0 - - - +
147A ARG* 5.2 2.0 - - - +
188A PHE* 3.7 28.3 - - + -
191A ALA 3.4 4.9 + - - -
192A ASP* 1.3 75.3 + - - +
194A ALA* 1.3 57.0 + - - +
196A ILE* 3.2 9.4 + - - +
197A VAL* 2.9 42.4 + - + +
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Residues in contact with ALA 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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192A ASP* 3.1 15.9 + - - +
193A GLU* 1.3 78.3 - - - +
195A LEU* 1.3 59.9 + - + +
197A VAL* 3.4 6.2 + - - +
198A ASP* 3.0 27.9 + - - +
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Residues in contact with LEU 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 ALA* 5.9 0.7 - - + -
192A ASP* 2.9 32.9 + - + +
194A ALA* 1.3 76.7 - - + +
196A ILE* 1.3 66.1 + - - +
198A ASP* 3.5 12.5 + - + +
199A ALA* 3.1 22.7 + - - +
215A VAL* 3.8 25.6 - - + +
218A ASP* 6.0 1.8 - - - +
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Residues in contact with ILE 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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122A MET* 4.0 11.0 - - + -
187A LEU* 3.6 31.2 - - + +
188A PHE* 3.6 50.5 - - + +
191A ALA* 3.9 19.3 - - + +
192A ASP 3.1 8.5 + - - +
193A GLU* 3.2 7.2 + - - +
195A LEU* 1.3 78.0 - - - +
197A VAL* 1.3 53.2 + - - +
199A ALA* 3.3 1.3 + - - -
200A ALA* 2.8 32.8 + - + +
212A LEU* 3.6 20.1 - - + +
215A VAL* 3.9 19.5 - - + -
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Residues in contact with VAL 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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120A GLY 3.6 24.2 - - - +
122A MET* 3.7 39.5 - - + +
193A GLU* 2.9 29.5 + - + +
194A ALA* 4.0 6.3 - - - +
196A ILE* 1.3 72.5 - - - +
198A ASP* 1.3 67.1 + - - +
200A ALA* 3.2 6.3 + - - -
201A THR* 3.0 33.8 + - + +
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Residues in contact with ASP 198 (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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194A ALA 3.0 17.9 + - - +
195A LEU* 3.8 13.0 - - + +
197A VAL* 1.3 75.9 - - - +
199A ALA* 1.3 63.2 + - - +
201A THR* 3.1 18.2 + - - -
202A SER 3.6 4.9 + - - -
211A ARG* 2.6 38.3 + - - -
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Residues in contact with ALA 199 (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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195A LEU 3.1 17.6 + - - +
196A ILE 3.7 3.4 - - - +
198A ASP* 1.3 75.2 - - - +
200A ALA* 1.3 63.7 + - - +
202A SER* 2.8 27.2 + - - -
208A ALA* 3.5 10.0 - - - -
211A ARG* 3.7 43.1 - - + +
212A LEU* 3.8 12.1 - - + +
215A VAL* 4.1 7.0 - - + -
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Residues in contact with ALA 200 (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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117A ILE* 3.8 21.9 - - + +
122A MET* 4.1 14.6 - - - -
179A ARG* 2.8 35.3 + - - -
181A LEU* 4.6 3.8 - - + -
196A ILE 2.8 21.7 + - - +
197A VAL* 3.2 4.9 + - - +
199A ALA* 1.3 72.6 - - - +
201A THR* 1.3 54.4 + - + +
202A SER 3.4 0.2 - - - -
208A ALA* 4.3 2.2 - - - +
212A LEU* 3.8 22.2 - - + +
229A VAL* 5.3 1.4 - - + +
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Residues in contact with THR 201 (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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117A ILE* 3.7 27.8 - - + -
120A GLY* 4.4 15.0 - - - +
179A ARG* 3.6 4.9 + - - +
197A VAL* 3.0 28.9 + - + +
198A ASP* 3.1 12.7 + - - -
199A ALA 3.1 0.2 - - - -
200A ALA* 1.3 77.3 - - + +
202A SER* 1.3 67.5 + - - +
203A PRO* 3.1 10.4 - - - +
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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