Contacts of the helix formed by residues 144 - 158 (chain D) in PDB entry 3H90
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 SER 144 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ARG* 3.3 26.1 - - - +
14D ILE* 3.7 22.1 - - - +
79D GLU* 2.9 14.0 + - - -
139D VAL* 4.5 1.2 - - - +
142D THR 2.7 9.6 + - - -
143D GLN* 1.3 71.6 - - - +
145D GLN* 1.3 60.7 + - - +
146D ALA* 3.4 2.4 + - - +
147D VAL* 3.1 32.6 + - - +
148D ARG* 3.2 18.7 + - - +
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Residues in contact with GLN 145 (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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79D GLU* 3.7 5.7 + - + +
80D SER* 2.9 39.9 + - - +
83D ALA* 3.9 13.2 - - + -
143D GLN 3.1 5.2 + - - +
144D SER* 1.3 70.3 - - - +
146D ALA* 1.3 60.5 + - - +
148D ARG* 3.5 33.5 - - - +
149D ALA* 2.8 33.1 + - - +
197D MET* 3.7 4.5 - - + +
200D GLU* 3.8 29.3 + - - +
201D ALA* 4.1 4.1 - - - +
204D SER* 4.0 10.7 + - - -
240D GLY* 6.5 0.9 - - - -
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Residues in contact with ALA 146 (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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56D ASN* 3.3 20.0 + - - +
60D VAL* 3.8 22.4 - - + -
79D GLU* 3.6 38.1 + - + +
82D ALA* 5.1 2.2 - - + -
83D ALA* 4.5 4.9 - - - +
86D GLN* 3.6 4.6 + - - +
144D SER* 3.2 8.7 - - - +
145D GLN* 1.3 80.0 - - - +
147D VAL* 1.3 60.0 + - + +
149D ALA* 3.7 0.7 + - - +
150D ASP 3.3 15.2 + - - -
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Residues in contact with VAL 147 (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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14D ILE* 3.7 20.9 - - + +
17D THR* 3.7 33.0 - - + +
18D ALA* 5.5 0.9 - - + +
56D ASN* 4.9 1.8 - - - +
60D VAL* 5.3 3.4 - - + -
135D GLN* 4.5 5.6 + - + +
138D VAL* 4.4 13.2 - - + -
139D VAL* 3.5 21.7 - - + +
144D SER* 3.1 29.6 + - - +
146D ALA* 1.3 77.3 - - + +
148D ARG* 1.3 63.5 + - - +
149D ALA 3.3 0.7 - - - -
150D ASP* 3.3 7.3 + - + +
151D MET* 2.8 30.7 + - - +
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Residues in contact with ARG 148 (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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139D VAL* 3.9 31.0 - - + -
143D GLN* 4.3 21.9 + - - +
144D SER 3.2 15.6 + - - +
145D GLN* 3.2 36.5 + - - +
147D VAL* 1.3 76.5 - - - +
149D ALA* 1.3 60.4 + - - +
151D MET* 3.6 15.8 + - + +
152D LEU* 3.1 25.8 + - - +
197D MET* 3.9 23.4 - - - +
200D GLU* 2.8 30.7 + - - +
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Residues in contact with ALA 149 (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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83D ALA* 3.8 25.8 - - - +
86D GLN* 3.6 17.7 - - + -
87D SER 5.3 0.2 - - - +
90D ILE* 3.4 13.9 - - + +
145D GLN 2.8 16.9 + - - +
146D ALA 3.8 5.2 - - - +
148D ARG* 1.3 74.0 - - - +
150D ASP* 1.3 65.9 + - - +
152D LEU* 3.1 17.6 + - - +
197D MET* 3.8 19.8 - - + +
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Residues in contact with ASP 150 (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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17D THR 4.7 3.1 - - - +
18D ALA* 5.3 2.3 - - - +
21D SER* 3.2 22.2 + - - -
52D ALA* 5.4 1.7 - - - +
53D SER* 3.4 25.0 + - - +
56D ASN* 3.2 30.3 + - - +
86D GLN* 3.3 15.3 + - - +
135D GLN* 3.9 5.1 + - - +
146D ALA 3.3 3.3 + - - +
147D VAL* 3.3 10.5 + - - +
149D ALA* 1.3 77.4 - - - +
151D MET* 1.3 62.4 + - - +
153D HIS* 3.2 17.0 + - - +
154D TYR* 3.2 24.8 - - - -
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Residues in contact with MET 151 (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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132D VAL* 3.9 10.5 - - + +
135D GLN* 3.3 31.1 - - + +
136D ARG* 3.6 43.5 - - + -
139D VAL* 4.3 9.2 - - + -
147D VAL 2.8 18.3 + - - +
148D ARG* 3.6 24.0 - - + +
150D ASP* 1.3 77.6 - - - +
152D LEU* 1.3 63.1 + - - +
154D TYR* 2.9 4.5 + - - +
155D GLN* 2.8 50.9 + - - +
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Residues in contact with LEU 152 (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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87D SER* 6.1 0.2 - - - -
90D ILE* 4.0 15.9 - - + +
148D ARG 3.1 13.1 + - - +
149D ALA* 3.1 13.1 + - - +
151D MET* 1.3 74.9 - - - +
153D HIS* 1.3 61.7 + - - +
155D GLN* 3.2 20.8 + - + +
156D SER* 3.3 18.0 + - - -
189D TYR* 5.9 1.6 - - + -
190D ILE* 4.3 15.2 - - + +
193D SER* 3.6 28.7 - - - +
194D ALA* 3.6 37.7 - - + +
197D MET* 4.3 14.4 - - + -
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Residues in contact with HIS 153 (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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45D ASP* 4.0 5.4 - - - -
49D ASP* 2.8 22.4 + - - -
52D ALA* 6.5 0.4 - - + -
86D GLN* 5.3 1.6 - - - +
90D ILE* 3.8 27.8 - - + +
93D SER* 6.4 0.2 - - - -
149D ALA 3.5 2.8 + - - -
150D ASP* 3.2 13.3 + - - +
151D MET 3.1 1.0 - - - -
152D LEU* 1.3 79.5 - - - +
154D TYR* 1.3 70.4 + + - +
156D SER* 3.0 27.8 + - - -
157D ASP* 3.0 20.1 + - - +
293D ZN 2.3 34.7 - - - -
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Residues in contact with TYR 154 (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 SER* 3.3 29.2 + - - -
24D LEU* 3.8 13.9 - - + -
49D ASP* 3.1 31.9 - - - +
53D SER* 2.4 30.3 + - - -
128D THR* 3.6 12.9 - - + +
131D LEU* 3.7 19.3 - - + -
132D VAL* 3.6 19.7 - - + -
135D GLN* 3.7 15.3 - - - +
150D ASP* 3.2 28.9 + - - -
151D MET 2.9 4.2 + - - +
153D HIS* 1.3 78.4 - + - +
155D GLN* 1.3 60.2 + - - +
156D SER 3.1 1.3 - - - -
157D ASP* 3.8 13.7 - - - -
158D VAL* 2.9 33.1 + - - +
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Residues in contact with GLN 155 (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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132D VAL* 3.8 22.4 - - + +
136D ARG* 5.5 7.4 + - - -
151D MET* 2.8 40.4 + - - +
152D LEU* 3.2 41.4 - - + +
153D HIS 3.3 0.2 - - - -
154D TYR* 1.3 76.7 - - - +
156D SER* 1.3 60.8 + - - +
158D VAL* 3.6 9.5 + - + +
159D MET* 3.5 29.8 + - + +
189D TYR* 5.4 5.0 + - + -
190D ILE* 4.7 4.3 - - + -
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Residues in contact with SER 156 (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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90D ILE* 5.8 0.9 - - - -
97D LEU* 5.8 2.4 - - - +
152D LEU 3.3 8.5 + - - -
153D HIS* 3.0 19.7 + - - -
155D GLN* 1.3 77.1 - - - +
157D ASP* 1.3 61.5 + - - +
159D MET* 2.9 30.1 + - - +
186D ILE* 5.0 5.9 - - - +
190D ILE* 4.2 32.3 - - - +
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Residues in contact with ASP 157 (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 LEU* 4.7 2.6 - - - +
27D LYS* 5.7 3.5 + - - +
45D ASP* 3.8 11.8 - - - +
49D ASP* 3.0 3.5 - - - +
125D LEU* 5.2 0.5 - - - +
128D THR* 4.1 16.1 - - + +
153D HIS* 3.0 24.7 + - - +
154D TYR* 3.6 12.4 - - - +
156D SER* 1.3 77.0 + - - +
158D VAL* 1.3 60.7 + - - +
159D MET 3.2 0.9 + - - -
160D MET* 3.4 32.3 + - + +
293D ZN 1.8 38.3 - - - -
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Residues in contact with VAL 158 (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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125D LEU* 3.3 20.7 - - - +
128D THR* 3.6 22.9 - - + +
129D ILE* 3.6 44.4 - - + +
132D VAL* 4.1 8.3 - - + -
154D TYR 2.9 19.2 + - - +
155D GLN* 3.6 12.3 - - + +
156D SER 3.1 0.2 - - - -
157D ASP* 1.3 69.8 - - - +
159D MET* 1.3 61.3 + - + +
160D MET 3.0 11.0 + - - +
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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