Contacts of the helix formed by residues 146 - 153 (chain A) in PDB entry 1B0K
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 ILE 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A ALA* 4.2 17.5 - - + +
71A MET* 4.0 27.8 - - - +
72A GLN* 4.0 17.0 - - + +
98A HIS* 3.9 28.2 - - + -
100A ASP* 3.0 19.3 + - - +
144A GLY 3.7 1.8 + - - -
145A ILE* 1.3 70.6 - - + +
147A HIS* 1.3 84.9 + - + +
149A ILE* 3.7 3.0 + - - +
150A ILE* 3.0 41.1 + - + +
163A GLY* 5.7 0.7 - - - -
164A THR 5.4 1.1 - - - +
165A ASP* 4.8 7.0 - - + +
168A THR* 5.5 2.0 - - - +
755A SF4 4.9 2.7 - - - -
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Residues in contact with HIS 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ILE 2.9 1.2 + - - -
146A ILE* 1.3 100.9 + - + +
148A GLN* 1.3 60.5 + - - +
150A ILE* 3.9 10.7 - - + +
151A LEU* 3.0 23.0 + - - +
165A ASP* 3.1 27.2 + - + -
167A HIS* 3.4 29.8 + - + +
168A THR* 3.6 20.3 + - - +
170A ASN* 3.4 31.9 + - + +
258A ASN* 4.7 0.4 - - - -
358A CYS* 3.4 41.7 - - + +
755A SF4 4.3 1.3 - - - -
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Residues in contact with GLN 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ILE* 3.1 7.3 + - + +
147A HIS* 1.3 76.8 - - - +
149A ILE* 1.3 56.2 + - - +
151A LEU* 3.3 21.4 + - - +
152A GLU* 2.9 44.9 + - - +
170A ASN* 5.3 3.6 - - - +
251A THR* 5.0 3.6 - - - +
279A TYR* 4.8 3.8 + - - -
358A CYS* 4.4 10.3 + - - +
361A SER* 3.1 33.0 + - - +
362A SER* 4.2 10.6 + - - -
392A GLY* 3.5 25.8 - - - +
393A SER* 4.5 0.9 - - - -
396A ILE* 3.6 28.7 - - + +
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Residues in contact with ILE 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A HIS* 3.4 29.8 - - + +
139A TRP* 3.8 40.8 - - + -
143A SER* 3.6 17.7 - - - +
144A GLY* 4.3 10.3 - - - +
145A ILE 3.4 10.1 + - - +
146A ILE 3.9 7.2 - - - +
148A GLN* 1.3 73.0 - - - +
150A ILE* 1.3 63.7 + - - +
152A GLU* 4.1 6.3 - - - +
153A ASN* 2.9 33.0 + - - +
154A TYR* 3.6 2.9 - - + -
393A SER* 3.5 28.0 - - - -
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Residues in contact with ILE 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ALA* 3.5 30.7 - - + -
96A THR* 5.4 0.2 - - - +
98A HIS* 4.5 5.6 - - - +
146A ILE* 3.0 32.1 + - + +
147A HIS* 3.9 11.7 - - + +
148A GLN 3.3 0.4 - - - -
149A ILE* 1.3 75.3 - - - +
151A LEU* 1.4 64.3 + - - +
153A ASN 3.0 0.3 + - - -
154A TYR* 2.8 43.6 + - + -
155A ALA* 3.2 21.5 + - + +
161A LEU* 4.2 26.5 - - + -
168A THR* 5.8 3.8 - - + -
171A GLY* 5.5 7.2 - - - -
178A CYS* 5.9 0.4 - - - -
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Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A HIS 3.0 17.9 + - - +
148A GLN* 3.3 12.3 + - - +
150A ILE* 1.4 74.8 - - - +
152A GLU* 1.3 59.1 + - - +
155A ALA* 4.0 7.4 - - + +
170A ASN* 3.9 26.9 - - - +
171A GLY* 4.4 7.0 - - - -
173A GLY 4.5 1.8 - - - -
174A LEU* 3.7 31.6 - - + +
250A CYS* 4.7 3.6 - - - +
251A THR* 4.0 19.7 - - + -
254A ALA* 4.0 20.0 - - + -
279A TYR* 3.6 35.7 - - + +
285A ARG* 2.9 23.2 + - - -
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Residues in contact with GLU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A GLN* 2.9 24.2 + - + +
149A ILE* 4.1 6.2 - - - +
151A LEU* 1.3 76.4 - - - +
153A ASN* 1.3 71.5 + - - +
279A TYR* 3.5 19.3 - - + +
283A THR* 3.7 18.5 - - + +
285A ARG* 3.4 14.2 + - - +
393A SER* 2.9 33.5 + - - -
395A GLN* 3.7 29.5 - - - +
396A ILE* 3.4 23.0 - - - +
510A PHE* 5.3 4.3 - - + -
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Residues in contact with ASN 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A MET 4.3 2.8 - - - +
8A SER* 3.7 21.3 - - - -
9A HIS* 6.0 1.7 - - - -
10A PHE* 3.6 27.3 - - + -
139A TRP* 3.6 14.4 - - - -
149A ILE* 2.9 31.6 + - - +
150A ILE 3.0 3.0 + - - -
151A LEU 3.3 0.4 - - - -
152A GLU* 1.3 97.0 + - - +
154A TYR* 1.3 72.1 + - + +
285A ARG* 3.9 18.5 + - - +
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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