Contacts of the strand formed by residues 147 - 153 (chain E) in PDB entry 1B06
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 LEU 147 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LEU* 5.4 2.1 - - - +
105E LEU* 4.2 13.7 - - + -
108E LEU* 3.8 37.2 - - + -
109E ILE* 3.9 27.4 - - + +
112E GLN* 2.9 19.4 + - - +
113E TYR* 2.9 29.5 + - + -
138E LEU* 3.8 24.4 - - + +
139E TYR 3.3 12.8 - - - +
140E TYR* 4.0 23.3 - - + -
146E ASN* 1.3 72.0 - - - +
148E GLN* 1.3 59.5 + - - +
166E ILE* 4.7 3.6 - - + -
204E LEU* 4.7 3.6 - - + -
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Residues in contact with GLN 148 (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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9C TYR* 5.2 2.3 + - - +
49C LEU* 4.0 21.1 - - - +
52C LEU* 4.0 12.4 - - - +
71C LEU* 4.7 1.0 - - - +
74C LEU* 3.6 25.7 - - - +
78C ILE* 4.0 13.4 - - + +
137E VAL 3.7 0.9 - - - +
138E LEU* 3.5 3.2 - - - -
139E TYR* 2.8 48.4 + - + +
141E ASP* 5.3 7.0 - - + -
146E ASN* 3.4 15.1 + - + +
147E LEU* 1.3 71.1 - - - +
149E ILE* 1.3 88.4 + - - +
150E MET* 4.8 1.9 - - + +
160E ILE* 3.9 25.8 - - + -
163E LEU* 5.4 1.1 - - + -
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Residues in contact with ILE 149 (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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71C LEU* 3.8 11.7 - - + +
113E TYR* 3.6 26.8 + - + +
119E PHE* 4.5 2.9 - - + -
122E VAL* 3.9 28.0 - - + -
123E PHE* 4.0 24.2 - - + +
126E SER* 3.7 28.3 - - - +
136E THR* 4.4 9.4 - - + -
137E VAL 3.4 8.7 - - - +
138E LEU* 3.7 14.4 - - + -
147E LEU 3.7 1.2 + - - -
148E GLN* 1.3 94.5 + - - +
150E MET* 1.3 74.1 + - - +
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Residues in contact with MET 150 (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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71C LEU* 3.3 38.4 - - - +
72C ARG* 5.3 0.7 - - - -
74C LEU* 4.2 8.1 - - + -
75C THR* 3.8 30.7 - - + +
136E THR* 3.4 1.7 - - - +
137E VAL* 2.8 37.2 + - - +
139E TYR* 3.7 26.7 - - + -
148E GLN* 4.8 2.5 - - - +
149E ILE* 1.3 90.1 - - - +
151E THR* 1.3 82.5 + - - +
152E VAL* 3.8 3.6 + - + +
158E ASN* 3.4 21.5 - - - +
160E ILE* 4.3 12.3 - - + -
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Residues in contact with THR 151 (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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68C GLN* 3.1 29.0 + - - +
71C LEU* 3.9 15.8 - - + +
126E SER* 3.3 30.5 - - - +
130E LEU* 4.1 19.5 - - + +
135E TRP 3.5 3.8 - - - -
136E THR* 3.8 15.7 - - + +
150E MET* 1.3 80.4 - - - +
152E VAL* 1.3 60.8 + - - +
153E GLU* 5.4 0.7 + - - -
158E ASN* 2.9 30.9 + - - +
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Residues in contact with VAL 152 (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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130E LEU* 3.8 4.2 - - - +
134E GLY* 3.0 6.2 - - - -
135E TRP* 2.6 50.9 + - + +
137E VAL* 4.4 11.9 - - + -
139E TYR* 3.9 10.5 - - - +
150E MET* 3.8 4.7 + - + +
151E THR* 1.3 74.8 - - - +
153E GLU* 1.3 62.1 + - - +
154E ASN 3.5 14.8 - - - +
155E HIS 4.0 5.4 - - - +
157E MET 3.2 18.2 - - - +
158E ASN 4.4 2.7 - - - +
159E HIS* 3.8 46.4 - - + +
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Residues in contact with GLU 153 (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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68C GLN* 4.5 4.9 - - - +
72C ARG* 3.9 5.6 + - - -
130E LEU* 4.1 15.7 - - + -
131E PRO* 4.5 16.6 - - + +
133E SER 3.9 4.7 - - - +
151E THR* 5.4 0.2 + - - -
152E VAL* 1.3 70.5 - - - +
154E ASN* 1.3 73.5 + - - +
157E MET* 3.0 49.4 + - + +
158E ASN* 3.1 23.3 + - - +
72F ARG* 2.8 44.2 + - - -
154F ASN* 5.1 4.0 + - - +
156F PHE* 4.6 4.3 - - - -
157F MET* 4.8 4.6 - - + +
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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