Contacts of the helix formed by residues 148 - 153 (chain C) in PDB entry 3OLJ
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 ARG 148 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C ASN* 2.9 28.7 + - - +
146C VAL 3.5 0.6 - - - -
147C GLU* 1.3 91.7 - - + +
149C PHE* 1.3 67.0 + - - +
150C SER 3.5 1.3 - - - -
151C GLN* 3.0 5.0 + - - +
152C GLU* 2.9 32.6 + - - +
213C TRP 3.6 4.8 + - - -
214C ILE* 2.9 33.2 + - + -
216C ASP 2.9 28.3 + - - -
217C LYS* 4.9 6.8 + - - +
219C ALA 4.7 2.4 + - - -
224C ARG* 3.2 47.1 - - - +
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Residues in contact with PHE 149 (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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144C ASN* 3.1 35.1 + - - +
145C LEU* 3.9 22.0 - - + -
148C ARG* 1.3 75.0 - - - +
150C SER* 1.3 63.6 + - - +
151C GLN 3.2 1.0 + - - -
152C GLU* 3.4 12.8 - - - -
153C VAL* 3.2 29.8 + - - +
162C TYR* 3.6 30.4 - + + -
221C TYR* 3.6 17.3 - + - -
224C ARG* 3.6 47.3 - - + -
225C VAL* 3.6 24.5 - - + -
228C PHE* 4.2 12.6 - + + -
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Residues in contact with SER 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B VAL* 4.4 8.2 - - - +
145C LEU 2.7 28.5 + - - -
146C VAL* 3.5 13.7 + - - -
149C PHE* 1.3 72.6 - - - +
151C GLN* 1.3 65.2 + - - +
153C VAL* 4.1 2.6 - - - +
159C ARG* 3.4 34.5 + - - +
162C TYR* 4.2 25.0 - - - -
163C GLY* 5.2 1.3 - - - -
166C ILE* 4.2 10.5 - - - +
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Residues in contact with GLN 151 (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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146B VAL* 3.0 44.5 + - - +
147B GLU* 4.0 15.6 - - - +
151B GLN* 3.2 9.2 - - - +
146C VAL 3.0 21.1 + - - +
147C GLU* 3.4 24.0 - - - +
148C ARG 3.0 5.9 + - - +
150C SER* 1.3 84.7 + - - +
152C GLU* 1.3 60.9 + - + +
153C VAL 3.5 0.2 - - - -
154C GLN* 3.1 8.8 - - - +
159C ARG* 2.8 23.7 + - - +
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Residues in contact with GLU 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C LEU* 3.6 20.9 - - + +
148C ARG* 2.9 30.0 + - - +
149C PHE* 3.4 9.9 - - - +
151C GLN* 1.3 76.4 - - + +
153C VAL* 1.3 67.6 + - + +
154C GLN* 3.3 15.7 + - - +
221C TYR* 3.8 20.0 - - + +
224C ARG* 2.2 49.2 + - - -
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Residues in contact with VAL 153 (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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72C LEU* 3.6 14.6 - - + +
73C LEU* 4.0 8.7 - - + -
149C PHE 3.2 17.2 + - - +
150C SER 4.1 2.1 - - - +
152C GLU* 1.3 75.5 - - + +
154C GLN* 1.3 60.8 + - - +
155C ILE* 3.9 10.8 - - + +
158C ALA* 3.5 32.3 - - + -
159C ARG* 2.9 31.9 + - + +
162C TYR* 3.9 9.2 - - + -
221C TYR* 3.6 39.0 - - + +
276C MET* 5.0 2.5 - - - -
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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