Contacts of the helix formed by residues 138 - 143 (chain E) in PDB entry 1R8Y
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 ASN 138 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E GLY* 1.3 77.0 - - - +
139E SER* 1.3 62.3 + - - +
140E PHE 3.3 3.6 + - - -
141E ALA* 3.4 22.7 + - - +
142E HIS* 4.1 8.0 + - - -
173E ASP* 3.0 19.3 + - - -
174E HIS* 3.2 9.4 - - - +
175E ARG* 3.0 39.7 + - + +
177E TYR* 3.0 27.8 + - - -
242E TYR* 4.1 10.1 - - - -
283E TYR* 4.1 13.7 - - + +
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Residues in contact with SER 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E ALA* 3.6 28.6 + - - +
117E TRP* 3.2 13.5 - - - -
135E CYS* 4.8 3.1 - - - -
136E LEU 3.5 14.7 + - - -
137E GLY 3.1 5.8 + - - -
138E ASN* 1.3 73.4 - - - +
140E PHE* 1.3 65.0 + - - +
141E ALA 3.2 2.2 - - - -
142E HIS* 3.2 27.2 + - - +
173E ASP* 4.5 1.2 + - - -
15F GLU* 3.7 30.9 + - - +
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Residues in contact with PHE 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E TRP* 3.7 14.3 - + - -
135E CYS* 4.4 6.8 - - - -
138E ASN 3.3 1.0 - - - -
139E SER* 1.3 79.6 - - - +
141E ALA* 1.3 56.6 + - - +
142E HIS 3.0 0.4 - - - -
143E LEU* 3.0 30.2 + - + +
153E HIS* 3.9 20.2 - + + -
156E ALA* 3.6 24.2 - - + -
157E LEU* 3.4 41.5 - - + -
160E ILE* 4.2 12.1 - - + -
172E ILE* 4.2 22.9 - - + -
173E ASP 4.9 7.1 + - - +
174E HIS* 6.2 1.1 - - + -
245E HIS* 3.7 29.4 - + - -
250E PHE* 3.8 16.8 - + + -
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Residues in contact with ALA 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E ASN* 3.4 36.4 + - - +
139E SER 3.2 0.4 - - - -
140E PHE* 1.3 77.0 - - - +
142E HIS* 1.3 63.6 + - - +
143E LEU 3.1 0.8 + - - -
173E ASP 5.8 0.2 + - - -
174E HIS* 5.5 2.1 - - + +
177E TYR* 4.0 9.4 - - + +
242E TYR* 3.2 7.2 - - + -
243E TYR* 2.7 48.2 + - - +
245E HIS* 4.2 10.9 + - - +
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Residues in contact with HIS 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E GLY 5.3 2.3 + - - -
138E ASN 4.1 7.2 + - - -
139E SER* 3.3 30.3 + - - +
140E PHE 3.0 0.2 - - - -
141E ALA* 1.3 77.8 - - - +
143E LEU* 1.3 59.2 + - - +
144E PRO* 3.1 15.6 - - - +
240E LEU* 6.0 2.0 - - - +
241E SER 4.3 12.4 - - - +
242E TYR* 3.6 34.2 + + - -
14F ALA* 3.7 21.1 - - + +
15F GLU* 3.1 42.9 + - - -
16F GLY* 4.0 4.9 + - - +
17F LEU* 3.7 17.8 - - + +
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Residues in contact with LEU 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E ASN* 6.1 0.4 - - - +
117E TRP* 3.9 23.6 - - + -
118E LEU* 4.6 20.9 - - + -
139E SER 4.4 0.2 + - - -
140E PHE* 3.0 19.4 + - + +
141E ALA 3.1 1.3 - - - -
142E HIS* 1.3 76.5 - - - +
144E PRO* 1.3 74.3 - - + +
152E GLU* 4.0 17.5 - - + +
153E HIS* 2.7 40.4 + - + -
156E ALA* 3.5 31.9 - - + -
243E TYR* 3.9 6.6 - - - +
245E HIS* 5.0 0.2 - - - -
17F LEU* 4.0 14.4 - - + -
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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