Contacts of the helix formed by residues 128 - 139 (chain B) in PDB entry 3BWB
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 ASP 128 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B THR* 2.9 43.1 + - - +
46B LYS* 4.9 1.8 + - - +
47B PHE* 4.3 10.5 - - + +
48B GLN* 3.4 22.1 - - - +
105B GLY* 5.5 0.3 - - - -
126B ASP* 2.8 24.7 + - - +
127B ILE* 1.3 76.4 - - + +
129B GLY* 1.3 61.9 + - - +
130B GLU 3.2 10.6 + - - -
131B VAL* 3.1 33.2 + - + +
132B MSE 3.9 11.8 + - - +
155B VAL* 4.6 1.3 - - - -
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Residues in contact with GLY 129 (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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127B ILE 3.5 5.5 + - - -
128B ASP* 1.3 72.4 + - - +
130B GLU* 1.3 63.1 + - - +
131B VAL 3.4 0.2 - - - -
132B MSE 3.2 14.5 - - - +
133B GLU* 3.2 26.6 + - - +
155B VAL* 3.9 21.0 - - - +
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Residues in contact with GLU 130 (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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41B TYR* 3.8 21.8 - - + +
45B THR* 3.2 28.7 - - - +
50B LEU* 4.3 2.0 - - + -
128B ASP* 3.2 1.8 + - - -
129B GLY* 1.3 75.8 - - - +
131B VAL* 1.3 59.3 + - - +
133B GLU* 3.3 19.5 + - - +
134B GLN* 2.7 66.5 + - + +
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Residues in contact with VAL 131 (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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45B THR* 4.9 0.7 - - + -
48B GLN* 4.5 2.7 - - - +
50B LEU* 3.8 17.7 - - + -
65B MSE 4.3 21.9 - - - +
67B LEU* 3.8 31.0 - - + -
105B GLY* 5.3 3.4 - - - -
106B ASP* 5.1 9.9 - - + +
126B ASP* 5.7 3.1 - - - +
128B ASP* 3.1 37.4 + - + +
129B GLY 3.4 0.4 - - - -
130B GLU* 1.3 78.2 - - - +
132B MSE 1.3 56.2 + - - +
134B GLN* 3.4 2.4 + - - +
135B SER* 2.9 30.7 + - - +
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Residues in contact with MSE 132 (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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105B GLY* 3.3 32.5 - - - +
124B LEU* 6.1 0.2 - - - -
126B ASP* 5.9 4.0 - - - -
128B ASP 3.9 5.1 + - - +
129B GLY* 3.2 21.7 + - - +
131B VAL* 1.3 75.8 - - - +
133B GLU* 1.3 62.1 - - + +
135B SER* 3.7 3.9 - - - -
136B LYS* 2.9 52.3 + - - +
146B LEU* 3.4 29.5 - - + +
153B VAL* 3.8 30.5 - - + -
154B ARG 5.8 0.2 - - - +
155B VAL* 4.0 22.0 - - + -
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Residues in contact with GLU 133 (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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129B GLY 3.2 18.5 + - - +
130B GLU* 3.7 26.5 - - - +
132B MSE 1.3 79.4 - - + +
134B GLN* 1.3 63.2 + - - +
136B LYS* 3.4 17.8 - - + +
137B GLN* 3.2 26.2 + - - +
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Residues in contact with GLN 134 (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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40B LEU 5.4 0.2 - - - +
41B TYR* 3.2 32.0 - - + -
50B LEU* 3.6 18.8 - - + -
52B ILE* 3.4 21.6 - - + +
130B GLU* 2.7 42.3 + - - +
131B VAL 3.9 3.6 - - - +
133B GLU* 1.3 76.0 - - - +
135B SER* 1.3 59.9 + - - +
137B GLN* 4.4 5.4 - - - +
138B HIS* 3.0 54.2 + - - +
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Residues in contact with SER 135 (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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65B MSE 3.3 21.7 - - - +
105B GLY 4.9 0.4 - - - -
106B ASP* 3.3 35.7 - - - +
131B VAL* 2.9 19.3 + - - +
132B MSE 3.7 5.4 - - - -
133B GLU 3.3 0.2 - - - -
134B GLN* 1.3 74.8 - - - +
136B LYS* 1.3 61.0 + - - +
137B GLN 3.1 0.2 - - - -
139B PHE* 2.8 33.6 + - - +
143B SER* 2.9 18.0 + - - -
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Residues in contact with LYS 136 (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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132B MSE 2.9 49.7 + - - +
133B GLU* 3.4 22.7 - - + +
135B SER* 1.3 75.1 - - - +
137B GLN* 1.3 63.1 + - - +
140B PRO* 4.3 12.0 - - - +
143B SER* 3.3 15.3 + - - +
146B LEU* 4.4 16.9 - - + +
147B ALA* 6.0 4.0 - - - +
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Residues in contact with GLN 137 (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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133B GLU 3.2 14.6 + - - +
134B GLN* 3.7 11.2 - - - +
135B SER 3.1 0.6 - - - -
136B LYS* 1.3 83.3 - - - +
138B HIS* 1.3 82.7 + - + +
139B PHE 3.6 0.2 - - - -
140B PRO* 3.9 10.4 - - - +
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Residues in contact with HIS 138 (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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40B LEU* 3.2 52.3 + - + +
41B TYR* 5.2 0.2 - - + -
52B ILE* 3.8 29.6 - - + -
63B THR* 4.3 11.9 + - + +
75B ASP* 4.9 1.4 - - - +
134B GLN* 3.0 39.7 + - - +
137B GLN* 1.3 90.3 + - + +
139B PHE* 1.3 70.5 + - + +
140B PRO* 3.4 10.4 - - - +
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Residues in contact with PHE 139 (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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52B ILE* 4.1 13.2 - - + -
63B THR* 3.4 38.4 - - + -
65B MSE 3.2 55.0 - - + -
73B VAL* 3.8 14.4 - - + -
75B ASP* 3.3 28.5 - - - -
106B ASP* 6.1 0.7 - - + -
135B SER* 2.8 18.3 + - - +
138B HIS* 1.3 82.8 - - + +
140B PRO* 1.3 55.2 - - - +
141B GLN 3.3 2.2 - - - -
142B ILE* 3.2 30.7 + - + -
143B SER* 2.7 31.9 + - - -
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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