Contacts of the strand formed by residues 147 - 153 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B LEU* 4.2 16.6 - - + -
108B LEU* 3.7 36.1 - - + -
109B ILE* 3.9 27.8 - - + +
112B GLN* 2.8 17.6 + - - +
113B TYR* 2.9 28.3 + - + -
138B LEU* 3.9 25.4 - - + +
139B TYR 3.2 11.9 - - - +
140B TYR* 4.1 22.2 - - + -
146B ASN* 1.3 73.2 - - - +
148B GLN* 1.3 59.8 + - - +
166B ILE* 4.6 5.8 - - + -
204B LEU* 4.7 2.5 - - + -
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Residues in contact with GLN 148 (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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137B VAL 3.7 0.3 - - - +
138B LEU* 3.4 2.9 - - - -
139B TYR* 2.8 46.2 + - + +
141B ASP* 5.4 3.1 - - + -
146B ASN* 3.5 16.4 + - + +
147B LEU* 1.3 71.8 - - - +
149B ILE* 1.3 87.2 + - - +
150B MET* 4.5 7.8 - - + +
160B ILE* 3.8 28.9 - - + -
163B LEU* 5.3 4.5 - - + -
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Residues in contact with ILE 149 (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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113B TYR* 3.7 27.3 + - + +
119B PHE* 4.6 2.7 - - + -
122B VAL* 3.9 28.5 - - + -
123B PHE* 4.1 25.1 - - + +
126B SER* 3.7 27.1 - - - +
136B THR* 4.3 10.5 - - + -
137B VAL 3.4 8.5 - - - +
138B LEU* 3.8 14.8 - - + -
147B LEU 3.7 0.8 + - - -
148B GLN* 1.3 97.3 + - - +
150B MET* 1.3 71.4 + - - +
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Residues in contact with MET 150 (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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136B THR* 3.4 3.0 - - - +
137B VAL* 2.8 38.3 + - - +
139B TYR* 3.7 26.2 - - + -
148B GLN* 4.5 8.1 - - - +
149B ILE* 1.3 89.5 - - - +
151B THR* 1.3 82.9 + - - +
152B VAL* 3.8 3.0 + - + -
158B ASN* 3.4 32.3 - - - +
160B ILE* 4.4 17.3 - - + -
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Residues in contact with THR 151 (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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126B SER* 3.2 36.1 - - - +
129B SER* 4.2 6.5 + - - +
130B LEU* 4.0 25.5 - - + +
131B PRO* 5.3 2.9 - - - +
135B TRP 3.5 4.5 - - - -
136B THR* 3.8 12.8 - - + +
150B MET* 1.3 80.1 - - - +
152B VAL* 1.3 61.3 + - - +
153B GLU* 5.5 0.9 + - - -
158B ASN* 3.0 29.1 + - - +
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Residues in contact with VAL 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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83B LEU* 6.0 0.2 - - + -
130B LEU* 3.8 3.2 - - - +
134B GLY* 3.1 6.1 - - - -
135B TRP* 2.6 47.4 + - + +
137B VAL* 4.0 17.3 - - + -
139B TYR* 3.9 22.0 - - - +
150B MET* 4.5 4.7 - - + +
151B THR* 1.3 76.2 - - - +
153B GLU* 1.3 62.8 + - - +
154B ASN 3.7 14.6 - - - +
155B HIS 4.1 2.9 - - - +
157B MET 3.1 20.2 - - - +
158B ASN 4.6 6.7 - - - +
159B HIS* 4.0 25.6 - - + +
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Residues in contact with GLU 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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72A ARG* 2.7 47.9 + - - -
154A ASN* 5.1 4.0 + - - +
156A PHE* 4.6 4.6 - - - -
157A MET* 4.8 5.2 - - + +
130B LEU* 4.2 15.0 - - + -
131B PRO* 4.3 17.4 - - + +
133B SER 4.0 5.4 - - - +
151B THR* 4.0 1.7 + - - +
152B VAL* 1.3 70.9 - - - +
154B ASN* 1.3 74.8 + - - +
157B MET* 3.0 51.7 + - + +
158B ASN* 3.4 22.8 + - - +
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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