Contacts of the helix formed by residues 184 - 194 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127D ALA 3.7 6.0 + - - -
128D ASN* 3.5 22.9 + - - +
130D LEU* 3.0 29.9 + - - +
132D GLY* 2.7 34.6 + - - +
171D GLU* 3.0 31.8 + - + +
176D TYR* 3.8 41.0 + - + +
182D ASN 3.0 8.9 + - - +
183D LYS* 1.3 74.6 - - - +
185D GLY* 1.3 57.3 + - - +
187D TYR* 3.1 8.7 + - + +
188D LEU* 3.0 38.6 + - + +
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Residues in contact with GLY 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D ASN* 3.8 22.6 + - - -
183D LYS* 3.2 1.4 - - - +
184D ARG* 1.3 79.0 - - - +
186D ASP* 1.3 63.2 + - - +
188D LEU* 3.4 6.3 + - - +
189D ASN* 3.2 30.2 + - - +
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Residues in contact with ASP 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D TYR* 3.7 18.6 - - + -
183D LYS* 3.1 42.0 + - + +
185D GLY* 1.3 74.4 - - - +
187D TYR* 1.3 65.2 + - - +
189D ASN* 3.4 12.8 + - - +
190D ALA* 3.1 22.9 + - - +
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Residues in contact with TYR 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D TYR 5.4 0.2 - - - -
25D ILE* 4.1 22.4 - - + -
87D TYR* 2.8 23.6 + - - -
169D VAL* 4.0 16.9 - - + +
170D ASP 2.8 30.0 + - - -
171D GLU* 4.7 2.7 - - + -
175D ALA* 3.9 18.8 - - + +
176D TYR* 3.5 43.5 - + + -
180D TYR* 3.8 27.7 - + + -
183D LYS 3.3 3.4 + - - +
184D ARG* 3.1 12.3 + - + +
186D ASP* 1.3 77.9 - - - +
188D LEU* 1.3 69.0 + - + +
190D ALA* 3.1 2.6 + - + +
191D TRP* 2.8 34.4 + - + +
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Residues in contact with LEU 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D PHE* 6.1 0.2 - - + -
124D SER* 4.8 7.4 - - - +
127D ALA* 3.9 24.2 - - + -
128D ASN* 3.6 37.5 - - - +
169D VAL* 4.1 26.2 - - + -
171D GLU* 3.9 26.7 - - + +
184D ARG* 3.0 20.9 + - + +
185D GLY* 3.7 7.2 - - - +
186D ASP 3.3 0.2 - - - -
187D TYR* 1.3 83.5 - - + +
189D ASN* 1.3 62.3 + - - +
191D TRP* 3.5 18.4 + - + +
192D TRP* 3.1 21.2 + - - +
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Residues in contact with ASN 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D SER* 5.0 6.2 + - - -
185D GLY 3.2 18.3 + - - +
186D ASP* 3.6 14.8 + - - +
188D LEU* 1.3 79.3 - - - +
190D ALA* 1.3 61.8 + - - +
192D TRP* 3.7 21.0 + - - +
193D ASN* 3.5 11.7 + - - -
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Residues in contact with ALA 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D TYR* 3.9 25.7 - - + +
25D ILE* 6.1 0.4 - - + -
180D TYR* 3.2 28.0 - - + +
186D ASP 3.1 11.5 + - - +
187D TYR* 3.5 8.3 - - + +
189D ASN* 1.3 76.3 - - - +
191D TRP* 1.3 65.1 + - - +
193D ASN* 3.0 30.1 + - - +
194D VAL 4.2 0.3 + - - -
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Residues in contact with TRP 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D TYR* 5.6 0.2 - - - -
25D ILE* 5.3 4.4 - - + +
87D TYR* 4.5 4.3 - + - -
90D ASN* 4.9 1.7 + - - -
91D MET* 4.1 30.5 - - - +
123D PHE* 3.8 15.7 - + - -
167D LEU* 3.9 24.9 - - + -
168D ILE 3.5 23.4 + - - -
169D VAL* 3.4 44.2 - - + +
187D TYR* 2.8 28.5 + + + +
188D LEU* 3.6 17.3 - - + +
190D ALA* 1.3 76.9 - - - +
192D TRP* 1.3 100.0 + + - +
194D VAL* 2.9 26.3 + - + +
195D VAL* 3.4 25.4 - - + +
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Residues in contact with TRP 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D GLY* 3.6 14.0 - - - -
99D GLY 4.5 3.5 + - - +
116D PHE* 4.5 2.2 - + - -
119D PHE* 4.1 11.9 - + - -
120D LYS* 3.6 57.6 - - + +
123D PHE* 3.6 39.0 - + + -
124D SER* 3.2 17.9 + - - -
167D LEU* 4.5 1.1 - - + -
188D LEU* 3.1 24.5 + - - +
189D ASN* 3.8 19.1 - - - +
190D ALA 3.2 1.0 + - - -
191D TRP* 1.3 100.2 - + - +
193D ASN* 1.3 63.4 + - - +
194D VAL 3.3 0.9 + - - -
195D VAL* 3.7 17.0 + - + +
197D TRP* 3.9 30.7 + + - -
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Residues in contact with ASN 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D TYR* 3.7 38.6 + - + +
94D ALA* 3.9 8.1 - - - +
97D GLY 3.5 5.7 - - - +
98D GLY* 3.4 18.5 + - - -
99D GLY 5.5 0.2 - - - +
189D ASN 3.5 13.1 + - - -
190D ALA* 3.2 23.1 + - - +
191D TRP 3.0 1.2 + - - -
192D TRP* 1.3 79.8 - - - +
194D VAL* 1.3 60.6 + - - +
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Residues in contact with VAL 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LEU* 4.2 23.3 - - + +
24D TYR* 3.6 30.7 - - + -
25D ILE* 4.7 9.9 - - + -
91D MET* 3.1 25.8 - - + -
92D ALA 2.7 47.0 + - - +
94D ALA 4.4 7.6 - - - +
98D GLY 3.8 2.2 - - - +
190D ALA 4.5 2.0 - - - +
191D TRP* 3.2 24.9 - - + +
193D ASN* 1.3 76.8 - - - +
195D VAL* 1.3 61.7 + - - +
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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