Contacts of the helix formed by residues 139 - 150 (chain B) in PDB entry 3BDW
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 THR 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138B ARG* 1.3 73.8 - - - +
140B TRP* 1.3 60.2 + - - +
141B GLU* 3.3 11.9 - - + +
142B GLU* 3.0 48.1 + - + +
143B SER* 2.8 30.0 + - - -
174B TRP* 3.6 0.9 - - - -
221B CYS 3.3 13.8 + - - +
222B GLY* 3.4 19.9 + - - -
223B SER 3.6 7.6 - - - -
224B SER* 4.4 3.2 + - - +
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Residues in contact with TRP 140 (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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139B THR* 1.3 73.3 - - - +
141B GLU* 1.3 90.9 - - + +
143B SER* 3.1 4.9 + - - -
144B LEU* 3.0 44.9 + - + +
154B LEU* 3.7 7.6 - - + +
174B TRP* 3.5 45.6 - + + +
175B ILE 3.1 21.7 + - - -
176B GLY* 4.5 2.0 - - - -
177B VAL 3.9 13.6 + - - -
178B PHE* 4.0 31.2 - + + -
189B MET* 3.8 26.9 - - - -
208B CYS* 3.6 31.6 - - + -
209B ALA 4.4 0.2 - - - -
221B CYS* 3.1 15.8 + - + +
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Residues in contact with GLU 141 (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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139B THR* 3.3 9.4 - - + +
140B TRP* 1.3 103.4 - - + +
142B GLU* 1.3 57.9 + - + +
144B LEU* 3.4 9.2 + - + +
145B LEU* 3.0 43.7 + - + +
221B CYS* 6.4 1.1 - - + -
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Residues in contact with GLU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ARG* 3.3 30.4 + - - -
139B THR* 3.0 43.1 + - + +
141B GLU* 1.3 77.1 - - + +
143B SER* 1.3 58.1 + - - +
145B LEU* 3.9 1.7 - - - +
146B ALA* 2.9 28.4 + - - +
224B SER* 5.2 2.1 + - - -
138D ARG* 4.3 28.8 + - - +
142D GLU* 4.6 14.0 - - - +
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Residues in contact with SER 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ARG* 3.4 9.5 - - - +
139B THR 2.8 19.7 + - - -
140B TRP 3.1 8.3 + - - -
142B GLU* 1.3 75.4 - - - +
144B LEU* 1.3 55.4 + - - +
146B ALA* 3.1 5.0 + - - +
147B CYS* 2.8 38.3 + - - -
154B LEU* 3.7 11.7 - - - -
174B TRP* 3.0 20.0 - - - -
227B TYR* 3.3 32.8 - - - +
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Residues in contact with LEU 144 (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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140B TRP* 3.0 30.9 + - + +
141B GLU* 3.5 13.2 - - + +
143B SER* 1.3 76.4 - - - +
145B LEU* 1.3 70.6 + - + +
147B CYS* 3.4 2.4 + - - +
148B THR* 2.9 33.1 + - - +
154B LEU* 3.9 31.1 + - + +
189B MET* 3.4 49.4 - - + -
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Residues in contact with LEU 145 (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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141B GLU* 3.0 29.5 + - + +
142B GLU* 4.2 2.5 - - - +
144B LEU* 1.3 84.8 - - + +
146B ALA* 1.3 65.6 + - - +
148B THR* 3.9 8.5 - - - +
149B SER* 3.0 25.3 + - - -
136D GLU* 3.5 26.9 - - - +
138D ARG* 4.4 17.3 - - - +
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Residues in contact with ALA 146 (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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138B ARG* 4.7 8.3 - - - +
142B GLU 2.9 21.5 + - - +
143B SER 3.1 5.1 + - - +
145B LEU* 1.3 77.5 - - - +
147B CYS* 1.3 63.0 + - - +
149B SER* 3.4 6.8 - - - -
150B LYS* 3.3 27.5 + - - +
227B TYR* 3.5 32.1 - - + +
138D ARG* 5.9 0.2 - - - +
149D SER* 5.1 0.7 + - - -
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Residues in contact with CYS 147 (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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143B SER 2.8 21.5 + - - +
144B LEU 3.9 1.3 - - - +
146B ALA* 1.3 71.3 - - - +
148B THR* 1.3 60.6 + - - +
150B LYS* 2.8 21.2 + - - +
152B SER* 3.2 16.1 + - - +
153B SER 3.6 3.8 - - - -
154B LEU* 3.4 28.7 - - - +
227B TYR* 3.7 8.1 - - - -
228B HIS 3.5 14.8 - - - -
229B CYS* 2.0 50.5 - - + -
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Residues in contact with THR 148 (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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144B LEU* 2.9 24.3 + - - +
145B LEU* 4.0 10.0 - - - +
147B CYS* 1.3 75.5 - - - +
149B SER* 1.3 62.2 + - - +
151B ASN* 3.0 16.6 + - - +
152B SER 3.1 13.9 + - - +
153B SER* 5.2 2.4 - - - -
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Residues in contact with SER 149 (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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145B LEU 3.0 18.6 + - - -
146B ALA* 3.4 8.1 - - - -
148B THR* 1.3 77.0 - - - +
150B LYS* 1.3 57.7 + - - +
151B ASN* 3.1 16.6 + - - +
146D ALA 5.1 0.3 + - - -
149D SER* 3.9 10.9 + - - -
150D LYS* 3.7 40.0 - - - +
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Residues in contact with LYS 150 (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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123B TRP* 4.1 29.1 - - + -
132B TYR* 3.4 38.5 + - + -
136B GLU* 4.8 5.7 + - - -
146B ALA* 3.3 12.9 + - - +
147B CYS* 2.8 9.6 + - - +
149B SER* 1.3 74.0 - - - +
151B ASN* 1.3 73.7 + - - +
152B SER 3.3 1.9 + - - -
227B TYR* 3.1 32.1 + - - -
229B CYS* 4.4 13.0 - - - -
231B HIS* 4.8 1.4 - - - -
149D SER* 3.6 34.3 - - - +
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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