Contacts of the helix formed by residues 190 - 198 (chain A) in PDB entry 7EHI
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 HIS 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A PHE* 3.8 19.7 - - + -
154A ALA* 3.5 22.0 - - + +
186A GLY 3.1 21.2 + - - -
187A ILE 2.9 6.2 + - - -
189A ASP* 1.3 86.6 - - + +
191A LEU* 1.3 67.6 + - - +
192A ASP 3.1 2.5 - - - -
193A HIS* 3.0 13.0 + - + +
194A LEU* 3.3 13.2 + - - +
493A TRP* 3.3 39.4 + + + -
608A SO4 2.8 33.4 + - - +
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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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187A ILE* 3.2 22.6 + - + +
188A LEU* 3.4 21.1 + - + +
189A ASP 3.6 0.4 - - - -
190A HIS* 1.3 77.8 - - - +
192A ASP* 1.3 62.5 + - - +
194A LEU* 3.1 12.6 + - + +
195A GLN* 2.9 23.6 + - - +
202A ILE* 3.9 28.5 - - + -
237A LEU* 4.3 7.4 - - + -
240A ALA* 3.7 32.5 - - + -
241A ALA* 4.0 12.8 - - + +
244A ARG* 3.6 26.5 + - - +
246A ILE* 4.9 7.4 - - + +
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Residues in contact with ASP 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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189A ASP 5.0 2.2 + - - +
190A HIS 3.1 1.0 - - - -
191A LEU* 1.3 77.0 - - - +
193A HIS* 1.3 62.6 + - - +
195A GLN* 3.3 2.1 + - - +
196A GLU* 2.9 26.6 + - - +
244A ARG* 2.6 45.3 + - - +
608A SO4 3.3 19.6 + - - +
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Residues in contact with HIS 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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146A TYR* 4.3 2.5 - + - -
153A PHE* 4.8 0.7 - + - -
190A HIS* 3.0 12.9 + - + +
192A ASP* 1.3 75.8 - - - +
194A LEU* 1.3 80.9 + - + +
196A GLU* 3.4 8.0 + - - +
197A LEU* 3.0 25.3 + - + +
476A GLU* 2.7 27.1 + - - +
477A TYR* 3.0 37.4 + + - -
491A MET* 4.2 0.8 - - - +
493A TRP* 4.2 19.6 - + + -
503A TYR* 3.4 26.7 + + - -
608A SO4 2.8 30.2 + - - +
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Residues in contact with LEU 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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146A TYR* 3.5 44.2 - - + -
148A ILE* 4.2 15.0 - - + -
153A PHE* 4.4 6.7 - - + -
187A ILE* 5.1 1.1 - - + -
190A HIS 3.8 9.2 - - - +
191A LEU* 3.1 18.0 + - + +
193A HIS* 1.3 88.0 - - + +
195A GLN* 1.3 62.0 + - - +
197A LEU* 3.3 4.0 + - + +
198A GLY 3.1 16.8 + - - -
199A ILE* 3.2 28.7 + - + +
202A ILE* 3.6 35.7 - - + -
246A ILE* 4.5 6.1 - - + -
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Residues in contact with GLN 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 LEU 2.9 15.1 + - - +
192A ASP* 3.9 3.6 - - - +
194A LEU* 1.3 77.6 - - - +
196A GLU* 1.3 62.6 + - - +
198A GLY* 3.1 14.3 + - - +
199A ILE 4.9 6.3 - - - +
244A ARG* 2.7 70.0 + - - +
246A ILE* 4.7 5.3 - - + +
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Residues in contact with GLU 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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192A ASP 2.9 18.6 + - - +
193A HIS* 3.7 6.8 + - - +
195A GLN* 1.3 78.9 - - - +
197A LEU* 1.3 60.0 + - - +
198A GLY* 3.4 0.9 + - - -
477A TYR* 5.4 0.3 + - - -
503A TYR* 2.5 31.6 + - - +
507A GLN* 3.0 32.3 + - - +
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Residues in contact with LEU 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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146A TYR* 3.7 35.7 - - + -
193A HIS* 3.0 18.8 + - - +
194A LEU* 3.6 7.2 - - + +
196A GLU* 1.3 76.4 - - - +
198A GLY* 1.3 58.7 + - - +
199A ILE* 4.0 14.1 - - + +
471A ILE* 4.3 8.3 - - + -
476A GLU* 4.2 18.6 - - + +
503A TYR* 3.6 24.8 + - + +
506A MET* 4.1 27.1 - - + +
507A GLN* 4.0 18.0 - - + +
510A VAL* 3.7 17.9 - - + +
511A GLN* 4.9 0.9 + - - -
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Residues in contact with GLY 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 LEU 3.1 3.4 + - - -
195A GLN 3.1 14.6 + - - -
196A GLU 4.4 0.7 - - - -
197A LEU* 1.3 78.6 - - - +
199A ILE* 1.3 62.8 + - - +
510A VAL* 3.4 20.2 - - - +
511A GLN* 4.3 12.3 - - - -
514A ARG* 3.0 27.6 + - - -
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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