Contacts of the helix formed by residues 184 - 193 (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 ARG 184 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B ALA 3.6 3.0 + - - -
128B ASN* 3.5 22.2 + - - +
130B LEU* 3.0 26.6 + - - +
132B GLY* 2.7 33.7 + - - +
171B GLU* 3.0 37.3 + - + +
176B TYR* 3.5 44.3 + - + +
182B ASN 3.0 11.4 + - - +
183B LYS* 1.3 72.7 - - - +
185B GLY* 1.3 62.8 + - - +
187B TYR* 3.2 7.7 + - + +
188B LEU* 3.0 35.2 + - + +
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Residues in contact with GLY 185 (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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128B ASN* 3.8 22.4 + - - -
183B LYS* 3.2 1.4 - - - +
184B ARG* 1.3 78.8 - - - +
186B ASP* 1.3 62.9 + - - +
188B LEU* 3.4 6.5 + - - +
189B ASN* 3.2 30.7 + - - -
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Residues in contact with ASP 186 (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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180B TYR* 3.7 19.8 - - + -
183B LYS* 3.1 46.3 + - + +
185B GLY* 1.3 74.4 - - - +
187B TYR* 1.3 65.9 + - - +
189B ASN* 3.3 11.9 + - - +
190B ALA* 3.1 21.7 + - - +
50F ASP* 4.9 5.7 - - - +
54F LYS* 3.6 32.8 + - - +
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Residues in contact with TYR 187 (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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24B TYR 5.4 0.2 - - - -
25B ILE* 4.1 22.7 - - + -
87B TYR* 2.8 25.2 + - - -
169B VAL* 4.1 16.8 - - + +
170B ASP 2.9 30.6 + - - -
171B GLU* 4.8 1.8 - - + -
175B ALA* 3.9 17.6 - - - +
176B TYR* 3.5 45.1 - + + -
180B TYR* 3.8 27.3 - + + -
183B LYS 3.3 3.6 + - - +
184B ARG* 3.2 11.5 + - + +
186B ASP* 1.3 80.3 - - - +
188B LEU* 1.3 66.4 + - + +
190B ALA* 3.1 2.1 + - + +
191B TRP* 2.8 33.8 + - + +
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Residues in contact with LEU 188 (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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124B SER* 4.7 4.7 - - - +
127B ALA* 4.0 27.1 - - + -
128B ASN* 3.5 37.2 - - - +
169B VAL* 4.0 26.7 - - + -
171B GLU* 4.1 13.5 - - + +
184B ARG* 3.0 30.0 + - - +
185B GLY* 3.6 7.0 - - - +
186B ASP 3.3 0.2 - - - -
187B TYR* 1.3 83.0 - - + +
189B ASN* 1.3 62.9 + - - +
191B TRP* 3.5 19.2 + - + +
192B TRP* 3.1 21.8 + - - +
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Residues in contact with ASN 189 (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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124B SER* 5.2 4.7 + - - -
185B GLY 3.2 19.8 + - - -
186B ASP* 3.6 13.7 + - - +
187B TYR 3.2 0.2 - - - -
188B LEU* 1.3 77.5 - - - +
190B ALA* 1.3 62.7 + - - +
192B TRP* 3.6 23.0 + - - +
193B ASN* 3.7 9.6 + - - -
54F LYS* 5.5 8.8 - - - +
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Residues in contact with ALA 190 (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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24B TYR* 4.1 24.3 - - + +
25B ILE* 6.1 0.4 - - + -
180B TYR* 3.2 28.0 - - + +
186B ASP 3.1 11.9 + - - +
187B TYR* 3.4 8.1 - - + +
189B ASN* 1.3 76.5 - - - +
191B TRP* 1.3 66.4 + - - +
193B ASN* 2.9 31.3 + - - +
194B VAL 4.1 1.0 + - - -
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Residues in contact with TRP 191 (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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24B TYR* 5.6 0.4 - - - -
25B ILE* 5.3 3.6 - - + +
87B TYR* 4.6 4.4 - + - -
90B ASN* 4.9 1.5 + - - -
91B MET* 4.1 31.6 - - - +
123B PHE* 3.8 11.4 - + - -
167B LEU* 3.9 25.4 - - + -
168B ILE 3.6 16.2 + - - -
169B VAL* 3.4 49.2 - - + +
187B TYR* 2.8 29.8 + + + +
188B LEU* 3.6 17.3 - - + +
189B ASN 3.4 0.2 - - - -
190B ALA* 1.3 76.7 - - - +
192B TRP* 1.3 102.9 + + - +
194B VAL* 2.9 26.4 + - + +
195B VAL* 3.4 27.6 - - + +
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Residues in contact with TRP 192 (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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98B GLY* 3.6 14.2 - - - -
99B GLY 4.5 3.6 + - - +
116B PHE* 4.5 3.4 - + - -
119B PHE* 4.2 7.0 - + - -
120B LYS* 3.5 56.8 - - + +
123B PHE* 3.7 33.7 - + + -
124B SER* 3.2 23.0 + - - -
167B LEU* 4.5 1.3 - - + -
188B LEU* 3.1 26.4 + - - +
189B ASN* 3.7 19.5 + - - +
190B ALA 3.1 0.6 + - - -
191B TRP* 1.3 102.7 - + - +
193B ASN* 1.3 62.5 + - - +
194B VAL 3.5 0.5 + - - -
195B VAL* 3.8 17.0 + - + +
197B TRP* 3.9 30.5 + + - -
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Residues in contact with ASN 193 (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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24B TYR* 3.7 39.0 + - + +
94B ALA* 3.9 8.3 - - - +
97B GLY 3.5 5.9 - - - +
98B GLY* 3.3 18.4 + - - -
99B GLY 5.4 0.2 - - - +
189B ASN 3.7 12.5 + - - -
190B ALA* 2.9 24.5 + - - +
192B TRP* 1.3 79.7 - - - +
194B VAL* 1.3 60.6 + - - +
195B VAL 3.6 0.4 - - - -
59F ASP* 5.3 6.1 + - - +
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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