Contacts of the helix formed by residues 131 - 139 (chain C) in PDB entry 2OOR
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 131 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C ALA* 1.3 77.3 - - - +
132C ASP* 1.3 68.6 + - - +
133C VAL 3.2 1.1 - - - +
134C THR* 2.7 24.9 + - - -
135C ASN* 3.3 9.1 + - - +
162C PHE* 4.6 1.1 - - - -
164C LYS* 4.1 4.3 - - + +
169C SER* 3.9 4.6 - - - +
170C GLY* 3.2 28.9 - - - +
174C VAL 4.7 4.4 + - - -
176C ASN* 2.9 25.8 + - - +
179C PHE* 3.3 27.1 - - + -
400C TXP 2.8 32.5 + - - +
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Residues in contact with ASP 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C ASN* 1.3 77.3 + - - +
133C VAL* 1.3 61.4 + - - +
134C THR 3.2 1.4 + - - -
135C ASN* 3.2 13.4 + - - -
146C ILE* 3.3 27.9 - - + +
149C MET* 3.5 8.4 - - + +
151C ILE* 3.9 0.9 - - - +
170C GLY* 3.8 12.0 + - - -
171C TYR 3.4 4.7 + - - -
172C ALA* 2.8 39.0 + - - +
173C GLY 5.0 0.2 + - - -
174C VAL* 4.7 8.1 - - - +
400C TXP 2.7 53.8 + - - +
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Residues in contact with VAL 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C VAL* 4.3 11.7 - - + -
53C PRO 5.3 1.6 - - - +
85C HIS* 3.4 47.9 - - + +
87C VAL* 4.4 3.4 - - + +
88C ALA* 4.0 11.4 - - + +
130C ALA* 4.3 7.2 - - + -
132C ASP* 1.3 77.4 - - - +
134C THR* 1.3 56.3 + - + +
149C MET* 4.6 2.2 - - + -
151C ILE* 3.3 8.4 - - - +
152C LEU* 3.1 40.3 + - + +
400C TXP 3.4 34.3 - - - +
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Residues in contact with THR 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C VAL* 4.2 10.3 - - + -
127C VAL* 4.1 20.4 - - + -
130C ALA* 4.9 1.8 - - + -
131C ASN 2.7 20.1 + - - -
133C VAL* 1.3 80.9 - - + +
135C ASN* 1.3 63.0 + - - +
136C PRO* 3.3 8.7 - - - +
151C ILE* 3.7 11.2 - - - +
152C LEU* 3.9 8.5 - - + +
154C VAL* 3.5 41.3 + - + +
155C GLU* 5.3 1.4 - - - +
162C PHE* 3.6 10.0 - - - -
176C ASN* 3.3 11.1 + - - -
178C LEU* 3.4 10.6 - - - +
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Residues in contact with ASN 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C ASN* 3.3 11.5 + - - +
132C ASP* 3.2 16.4 + - - +
133C VAL 3.6 0.4 - - - -
134C THR* 1.3 74.7 - - - +
136C PRO* 1.4 65.5 - - - +
137C ALA* 3.1 25.8 + - - +
138C ALA* 3.2 26.3 + - - +
146C ILE* 4.2 10.3 - - + +
151C ILE* 3.5 5.6 - - - +
174C VAL* 3.5 20.1 + - - +
175C GLU 3.1 25.9 + - - +
176C ASN* 3.5 21.0 - - - +
177C GLU* 4.6 2.4 + - - +
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Residues in contact with PRO 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C THR 3.3 8.2 - - - +
135C ASN* 1.4 86.3 - - - +
137C ALA* 1.3 53.7 + - - -
138C ALA 3.1 5.6 - - - -
139C LYS* 3.2 11.1 + - + +
140C THR* 2.9 34.5 + - - +
151C ILE* 3.8 10.8 - - + -
155C GLU* 3.6 24.5 - - - +
176C ASN* 3.5 12.3 - - - +
177C GLU* 3.6 28.3 - - + +
178C LEU* 3.7 17.7 - - + -
181C ARG* 4.8 1.8 - - - +
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Residues in contact with ALA 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C ASN* 3.1 19.5 + - - +
136C PRO* 1.3 76.6 - - - +
138C ALA* 1.3 61.4 + - - +
139C LYS 3.2 0.2 - - - -
140C THR* 3.7 3.6 - - - -
141C ASP* 3.1 48.8 + - + +
144C SER* 3.4 8.3 + - - +
146C ILE* 4.1 9.4 - - + -
174C VAL* 5.7 1.8 - - + -
175C GLU 5.3 3.6 - - - +
177C GLU* 3.8 8.5 + - - +
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Residues in contact with ALA 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C ASN 3.2 17.7 + - - +
137C ALA* 1.3 78.1 - - - +
139C LYS* 1.3 57.8 + - + +
146C ILE* 3.4 31.2 - - + +
147C TYR* 3.3 5.0 - - - +
148C GLY* 2.6 30.7 + - - -
149C MET 3.4 22.6 - - - +
151C ILE* 3.6 14.6 - - + -
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Residues in contact with LYS 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C PRO* 3.2 15.6 + - + +
138C ALA* 1.3 76.4 - - + +
140C THR* 1.3 66.9 + - - +
147C TYR* 3.9 14.2 + - - -
149C MET 5.9 0.4 - - - +
151C ILE* 3.5 32.7 - - + +
153C ASP* 3.7 24.0 + - - -
155C GLU* 4.6 8.4 + - - +
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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