Contacts of the helix formed by residues 151 - 156 (chain B) in PDB entry 2RIO
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 SER 151 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90B LEU 5.6 2.7 - - - -
92B ASN* 4.3 1.8 + - - +
149B SER* 3.0 16.3 + - - -
150B THR* 1.3 78.8 + - - +
152B SER* 1.3 57.2 + - - +
153B ARG* 3.1 30.1 + - - +
154B PHE* 2.8 35.1 + - - +
155B THR 3.1 9.4 + - - -
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Residues in contact with SER 152 (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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64A GLU* 5.1 6.7 + - - -
134A LEU* 3.4 9.2 - - - +
150B THR 3.3 3.6 + - - -
151B SER* 1.3 68.3 + - - +
153B ARG* 1.3 62.1 + - - +
154B PHE 2.8 5.7 + - - -
155B THR* 3.8 12.8 - - - +
156B ALA* 3.3 32.4 + - - +
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Residues in contact with ARG 153 (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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63A THR* 2.9 32.6 + - - +
64A GLU* 3.7 28.3 + - + +
66A ASP* 3.1 20.2 + - - +
67A ASP* 3.6 21.5 - - - +
130A HIS* 3.9 21.8 + - - -
134A LEU* 4.8 2.2 - - - -
40B ARG* 3.8 11.7 - - - +
73B ARG* 3.9 5.1 - - - +
75B TYR* 4.5 0.2 + - - -
89B GLU* 3.3 33.1 + - - -
151B SER* 3.1 15.7 - - - +
152B SER* 1.3 79.7 + - - +
154B PHE* 1.4 75.2 - - + +
166B ARG* 5.0 0.7 + - - -
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Residues in contact with PHE 154 (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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67A ASP* 3.3 33.4 - - + -
89B GLU* 3.7 38.1 - - + -
90B LEU 5.4 0.7 - - - -
149B SER* 3.6 35.0 - - - -
151B SER* 2.8 19.6 + - - +
152B SER 2.8 0.2 - - - -
153B ARG* 1.4 95.8 - - - +
155B THR* 1.3 62.9 + - + +
156B ALA 3.7 1.3 - - - -
157B ASP* 4.6 11.1 + - - +
166B ARG* 3.2 57.4 + - + +
168B LEU* 4.2 11.7 - - + -
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Residues in contact with THR 155 (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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149B SER 4.4 3.1 - - - +
150B THR 3.8 11.6 + - - +
151B SER 3.1 14.6 + - - +
152B SER* 3.7 6.4 + - - -
154B PHE* 1.3 82.5 - - + +
156B ALA* 1.3 66.7 + - - +
157B ASP 3.2 8.5 + - - +
158B GLN* 4.4 10.6 + - - +
163B GLU* 3.4 21.3 + - + +
164B ASN* 3.5 34.0 + - - +
165B LEU* 3.8 12.3 - - - +
166B ARG* 5.0 0.2 - - + -
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Residues in contact with ALA 156 (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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133A SER* 3.6 21.7 + - - +
134A LEU* 3.3 32.3 - - + -
152B SER* 3.3 17.6 + - - +
154B PHE 3.7 0.2 - - - -
155B THR* 1.3 80.5 + - - +
157B ASP* 1.3 59.9 + - - +
158B GLN* 3.4 12.0 + - - +
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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