Contacts of the helix formed by residues 136 - 146 (chain D) in PDB entry 4BPW
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 PRO 136 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134D ILE 3.9 4.5 - - - +
135D LEU* 1.3 89.2 - - + +
137D LYS* 1.3 64.6 + - - +
138D ASP* 4.4 11.4 - - + +
139D LYS* 3.3 29.2 + - + +
140D ILE* 3.3 18.6 + - - +
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Residues in contact with LYS 137 (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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135D LEU 5.4 1.1 - - - +
136D PRO* 1.3 71.2 - - - +
138D ASP* 1.3 72.5 + - - +
140D ILE* 3.2 34.2 + - + +
141D GLN* 3.8 7.4 + - - +
181D GLU* 5.3 13.9 - - - +
211D LEU* 4.2 22.0 - - + +
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Residues in contact with ASP 138 (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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136D PRO* 5.1 8.0 - - + +
137D LYS* 1.3 83.7 + - - +
139D LYS* 1.3 65.3 + - + +
141D GLN* 3.7 19.0 + - - +
142D ASP* 3.9 10.5 - - - +
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Residues in contact with LYS 139 (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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96D ARG* 6.1 1.0 - - - +
135D LEU* 5.4 4.0 - - + -
136D PRO* 3.3 33.7 + - + +
137D LYS 3.3 0.4 - - - -
138D ASP* 1.3 77.8 - - + +
140D ILE* 1.3 54.0 + - - +
142D ASP* 2.9 23.0 + - + +
143D PHE* 2.7 36.9 + - + +
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Residues in contact with ILE 140 (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 PHE* 3.5 39.5 - - + +
135D LEU* 4.6 8.5 - - + +
136D PRO 3.3 12.8 - - - +
137D LYS* 3.2 26.0 + - + +
139D LYS* 1.3 78.0 - - - +
141D GLN* 1.3 57.8 + - + +
143D PHE* 3.0 8.4 + - - +
144D LEU* 2.8 53.6 + - + +
184D TYR* 4.3 5.8 - - - +
211D LEU* 4.1 33.9 - - + -
214D ILE* 5.9 0.2 - - + -
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Residues in contact with GLN 141 (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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137D LYS 3.8 5.3 + - - +
138D ASP* 3.7 14.1 + - - +
139D LYS 3.2 0.8 - - - -
140D ILE* 1.3 78.1 - - - +
142D ASP* 1.3 66.5 - - - +
144D LEU* 3.5 11.3 + - + +
145D LYS* 3.5 18.4 + - - +
153D ALA* 4.2 20.8 - - - +
184D TYR* 4.7 18.4 - - + +
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Residues in contact with ASP 142 (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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138D ASP 3.9 13.0 - - - +
139D LYS* 2.9 25.9 + - + +
141D GLN* 1.3 79.6 - - - +
143D PHE* 1.3 63.4 + - - +
144D LEU 3.5 0.2 + - - -
145D LYS* 3.5 10.0 + - - +
146D ASP* 3.3 26.1 + - - +
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Residues in contact with PHE 143 (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 LEU* 5.1 20.4 - - + -
132D PHE* 3.3 46.7 - + + -
139D LYS* 2.7 20.4 + - + +
140D ILE* 3.0 7.4 + - - +
142D ASP* 1.3 70.7 - - - +
144D LEU* 1.3 64.8 + - + +
146D ASP* 3.5 19.6 + - + +
147D SER* 3.7 10.4 + - - -
218D ILE* 4.3 34.8 - - + -
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Residues in contact with LEU 144 (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 PHE* 6.0 1.6 - - + -
140D ILE* 2.8 41.3 + - + +
141D GLN* 3.7 13.7 - - + +
142D ASP 3.2 0.2 - - - -
143D PHE* 1.3 77.9 - - + +
145D LYS* 1.3 63.0 + - - +
146D ASP 3.2 0.2 - - - -
147D SER* 2.7 25.2 + - - -
148D GLN 4.1 1.4 + - - -
149D LEU 4.6 1.9 + - - +
151D PHE* 3.7 34.9 - - + -
184D TYR* 4.0 31.0 - - + -
214D ILE* 3.9 21.1 - - + -
218D ILE* 3.6 25.8 - - + -
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Residues in contact with LYS 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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141D GLN 3.5 9.4 + - - +
142D ASP* 3.5 10.2 + - - +
143D PHE 3.4 0.6 - - - -
144D LEU* 1.3 79.1 - - - +
146D ASP* 1.3 65.0 + - - +
148D GLN* 3.4 14.4 + - - +
149D LEU 5.5 6.7 - - - +
151D PHE* 5.7 0.2 - - - -
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Residues in contact with ASP 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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30D LEU* 4.4 11.6 - - - +
142D ASP* 3.3 19.9 + - - +
143D PHE* 3.8 16.3 - - + +
144D LEU 3.2 0.8 - - - -
145D LYS* 1.3 81.1 - - - +
147D SER* 1.3 59.3 + - - +
148D GLN* 3.1 15.6 + - - +
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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