Contacts of the helix formed by residues 184 - 194 (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 ARG 184 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E ALA 3.7 6.0 + - - -
128E ASN* 3.5 23.4 + - - +
130E LEU* 3.0 30.7 + - - +
132E GLY* 2.6 34.2 + - - +
171E GLU* 3.1 30.7 + - + +
176E TYR* 3.6 42.4 + - + +
182E ASN 3.0 9.2 + - - +
183E LYS* 1.3 75.2 - - - +
185E GLY* 1.3 56.4 + - - +
187E TYR* 3.2 8.4 + - + +
188E LEU* 3.0 38.0 + - + +
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Residues in contact with GLY 185 (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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128E ASN* 3.8 22.6 + - - -
183E LYS* 3.2 1.6 - - - +
184E ARG* 1.3 79.3 - - - +
186E ASP* 1.3 64.3 + - - +
188E LEU* 3.3 5.9 + - - +
189E ASN* 3.1 30.0 + - - -
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Residues in contact with ASP 186 (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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180E TYR* 3.8 19.5 - - + -
183E LYS* 3.1 41.9 + - + +
185E GLY* 1.3 77.0 - - - +
187E TYR* 1.3 63.9 + - - +
189E ASN* 3.4 12.7 + - - +
190E ALA* 3.1 21.8 + - - +
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Residues in contact with TYR 187 (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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24E TYR 5.4 0.4 - - - -
25E ILE* 4.2 23.3 - - + -
87E TYR* 3.1 19.8 + - - -
169E VAL* 4.0 10.0 - - + +
170E ASP 2.7 33.2 + - - -
171E GLU* 4.7 2.5 - - + -
175E ALA* 3.9 18.6 - - + +
176E TYR* 3.5 44.0 - + + -
180E TYR* 3.8 25.9 - + + -
183E LYS 3.3 3.9 + - - +
184E ARG* 3.2 12.9 + - + +
186E ASP* 1.3 80.0 - - - +
188E LEU* 1.3 74.8 - - + +
190E ALA* 3.1 2.4 + - - +
191E TRP* 2.9 32.0 + - + +
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Residues in contact with LEU 188 (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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123E PHE* 6.3 0.2 - - + -
124E SER* 4.8 7.4 - - - +
127E ALA* 4.0 27.8 - - + -
128E ASN* 3.5 37.5 - - - +
169E VAL* 4.1 26.0 - - + -
171E GLU* 4.1 22.0 - - + +
184E ARG* 3.0 22.0 + - + +
185E GLY* 3.7 6.3 - - - +
187E TYR* 1.3 82.3 - - + +
189E ASN* 1.3 64.4 + - - +
191E TRP* 3.5 16.2 + - + +
192E TRP* 3.2 21.1 + - - +
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Residues in contact with ASN 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASP* 5.9 1.4 + - - -
124E SER* 5.0 4.7 + - - -
185E GLY 3.1 19.0 + - - +
186E ASP* 3.6 14.7 + - - +
187E TYR 3.2 0.2 - - - -
188E LEU* 1.3 79.7 - - - +
190E ALA* 1.3 62.5 + - - +
192E TRP* 3.6 24.7 + - - +
193E ASN* 3.7 7.4 + - - -
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Residues in contact with ALA 190 (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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24E TYR* 3.7 25.0 - - + +
25E ILE* 6.0 0.2 - - + -
180E TYR* 3.2 29.2 - - + +
186E ASP 3.1 10.9 + - - +
187E TYR* 3.1 8.6 + - + +
189E ASN* 1.3 75.8 - - - +
191E TRP* 1.3 66.0 + - - +
193E ASN* 3.0 30.6 + - - +
194E VAL 4.2 0.5 + - - -
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Residues in contact with TRP 191 (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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25E ILE* 5.2 5.8 - - + +
87E TYR* 4.6 3.7 - + - -
90E ASN* 4.9 1.5 + - - -
91E MET* 4.0 32.3 - - - +
123E PHE* 3.8 16.4 - + - -
167E LEU* 4.0 22.2 - - + -
168E ILE 3.6 25.2 + - - -
169E VAL* 3.4 44.2 - - + +
187E TYR* 2.9 26.5 + - + +
188E LEU* 3.7 17.9 - - + +
190E ALA* 1.3 76.7 - - - +
192E TRP* 1.3 98.8 + + - +
194E VAL* 3.0 25.0 + - + +
195E VAL* 3.3 27.5 - - + +
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Residues in contact with TRP 192 (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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98E GLY* 3.6 14.6 - - - -
99E GLY 4.5 3.8 + - - +
116E PHE* 4.5 2.0 - + - -
119E PHE* 4.0 16.2 - + - -
120E LYS* 3.5 55.1 - - + +
123E PHE* 3.8 30.3 - + - -
124E SER* 3.2 26.0 + - - -
167E LEU* 4.6 0.4 - - + -
188E LEU* 3.2 23.8 + - - +
189E ASN* 3.6 20.5 + - - +
190E ALA 3.1 0.8 + - - -
191E TRP* 1.3 98.4 - + - +
193E ASN* 1.3 62.2 + - - +
194E VAL 3.4 0.7 + - - -
195E VAL* 3.7 16.7 + - + +
197E TRP* 4.0 29.6 + + - -
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Residues in contact with ASN 193 (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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59A ASP* 5.8 0.2 - - - +
24E TYR* 3.3 39.0 + - + +
94E ALA* 3.9 8.8 - - - +
97E GLY 3.5 5.9 - - - +
98E GLY* 3.4 17.2 + - - -
99E GLY 5.4 0.4 - - - +
189E ASN 3.7 12.7 + - - -
190E ALA* 3.0 22.9 + - - +
192E TRP* 1.3 80.9 - - - +
194E VAL* 1.3 61.0 + - - +
195E VAL 3.7 0.4 - - - -
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Residues in contact with VAL 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E LEU* 4.2 19.7 - - + +
24E TYR* 3.6 31.4 - - + -
25E ILE* 4.7 9.2 - - + -
91E MET* 3.1 26.2 - - - -
92E ALA 2.7 48.0 + - - +
94E ALA 4.5 5.8 - - - +
97E GLY* 4.2 0.2 - - - -
98E GLY 3.8 2.7 - - - +
190E ALA 4.5 0.9 - - - +
191E TRP* 3.2 23.8 - - + +
193E ASN* 1.3 81.0 - - - +
195E VAL* 1.3 60.5 + - - +
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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