Contacts of the strand formed by residues 147 - 152 (chain C) in PDB entry 3B94
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 THR 147 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C VAL* 4.8 3.6 - - + -
86C LYS* 4.2 30.1 + - - +
87C LEU 3.1 14.1 - - - +
88C GLU* 4.1 14.8 - - + -
118C TYR 3.7 0.3 - - - +
119C LYS* 3.1 5.0 - - - +
120C ASN* 2.7 49.8 + - - +
145C GLY 3.9 7.6 - - - +
146C ASP* 1.3 78.8 - - - +
148C ILE* 1.3 66.3 + - - +
149C ASP* 4.3 1.8 + - - +
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Residues in contact with ILE 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C LYS* 3.4 2.4 - - - -
87C LEU* 2.8 38.5 + - + -
89C ILE* 3.8 19.5 - - + -
97C ILE* 4.0 17.7 - - + -
117C LEU* 3.4 27.8 - - + -
118C TYR 3.0 9.4 - - - +
119C LYS* 4.4 7.2 - - + -
124C ILE* 5.3 1.1 - - + -
142C LEU* 3.5 34.3 - - + -
146C ASP* 5.2 0.7 - - + -
147C THR* 1.3 79.0 - - - +
149C ASP* 1.3 59.5 + - - +
165C TRP* 3.3 34.1 - - + -
167C ILE* 4.5 2.5 - - + -
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Residues in contact with ASP 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ASP 5.3 0.2 - - - +
85C TRP* 2.9 18.4 - - + +
86C LYS* 3.7 31.0 - - + +
116C ARG 3.4 2.9 - - - +
117C LEU* 3.5 7.4 - - - +
118C TYR* 2.9 41.8 + - - +
120C ASN 5.3 0.9 - - - +
147C THR* 5.3 2.1 + - - +
148C ILE* 1.3 74.4 - - - +
150C LEU* 1.3 66.7 - - - +
151C ILE* 4.0 17.6 - - - +
165C TRP* 4.3 0.9 - - - -
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Residues in contact with LEU 150 (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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85C TRP* 3.2 36.0 + - + +
101C VAL* 6.4 0.2 - - + -
115C VAL* 3.4 24.0 - - + -
116C ARG 3.2 20.0 - - - +
117C LEU* 3.9 13.7 - - + +
136C VAL* 4.7 16.2 - - + -
149C ASP* 1.3 79.8 - - - +
151C ILE* 1.3 63.8 + - - +
152C PHE* 3.2 39.6 - - + -
163C THR* 5.4 3.1 - - + -
164C TYR 5.9 1.1 - - - +
165C TRP* 3.6 30.5 - - + +
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Residues in contact with ILE 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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114C GLU 4.3 0.2 - - - +
115C VAL* 3.6 4.5 - - - +
116C ARG* 2.7 62.1 + - + +
118C TYR* 3.3 34.5 - - + +
149C ASP* 4.0 20.0 - - - +
150C LEU* 1.3 79.5 - - - +
152C PHE* 1.3 66.5 + - - +
153C ASN* 5.2 4.9 - - + -
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Residues in contact with PHE 152 (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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85C TRP* 3.7 44.9 - + - -
101C VAL 5.3 0.2 - - - -
114C GLU 3.9 4.7 - - - -
115C VAL* 3.6 25.4 - - + -
150C LEU* 3.2 34.1 - - + -
151C ILE* 1.3 79.5 - - - +
153C ASN* 1.3 68.2 + - - +
163C THR* 3.8 23.8 - - + -
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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