Contacts of the helix formed by residues 120 - 131 (chain B) in PDB entry 2W9M
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 120 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B GLY* 4.3 13.9 - - - -
98B ASP* 5.6 1.6 - - - -
99B LEU* 4.1 8.2 - - - +
118B ILE* 3.7 1.1 - - - +
119B ASP* 1.3 86.8 + - - +
121B LEU* 1.3 59.8 + - - +
122B GLU 3.8 2.5 + - - -
123B ARG* 3.2 22.3 + - - +
124B LEU* 2.8 30.3 + - - +
164B ARG* 3.9 35.1 + - - -
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Residues in contact with LEU 121 (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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98B ASP* 3.7 43.5 + - + +
99B LEU* 3.7 17.7 - - + -
102B VAL* 3.7 20.6 - - + -
120B SER* 1.3 72.7 - - - +
122B GLU* 1.3 58.2 + - - +
124B LEU* 3.2 8.0 + - + +
125B ARG* 2.9 29.1 + - - +
151B VAL* 4.0 18.2 - - + +
154B LEU* 4.3 25.1 - - + -
155B PHE* 3.9 17.9 - - + -
158B ARG* 4.4 14.6 - - - +
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Residues in contact with GLU 122 (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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120B SER* 3.2 1.8 + - - -
121B LEU* 1.3 78.0 - - - +
123B ARG* 1.3 58.5 + - - +
125B ARG* 2.5 42.2 + - - +
126B GLU* 2.6 47.4 + - - +
155B PHE* 4.2 6.8 - - + -
162B SER* 5.6 0.7 - - - +
164B ARG* 3.5 40.8 - - + +
165B ALA* 3.8 24.9 - - + +
168B ALA* 2.9 16.4 - - + +
169B VAL* 5.0 1.0 - - - +
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Residues in contact with ARG 123 (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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116B ALA 4.9 2.0 + - - -
117B GLY 3.7 17.5 + - - +
118B ILE* 3.9 24.0 - - - +
119B ASP* 4.0 10.3 - - - +
120B SER* 3.2 20.5 + - - +
122B GLU* 1.3 77.0 - - - +
124B LEU* 1.3 60.5 + - - +
126B GLU* 3.5 21.0 + - - +
127B ALA* 3.1 34.0 + - - +
132B GLU* 2.9 42.0 + - - -
164B ARG* 5.8 1.1 - - - -
521B GLY* 5.8 6.3 - - - -
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 3.8 22.9 - - + -
102B VAL* 4.4 4.3 - - + -
105B LEU* 4.2 13.7 - - + -
113B LEU* 4.4 10.1 - - + -
118B ILE* 3.6 19.0 - - + +
120B SER 2.8 16.8 + - - +
121B LEU* 3.4 6.5 - - + +
123B ARG* 1.3 74.6 - - - +
125B ARG* 1.3 65.4 + - - +
127B ALA* 3.2 2.1 + - + +
128B ALA* 3.0 21.0 + - + +
133B LEU* 3.6 31.4 - - + -
147B ILE* 3.8 24.5 - - + -
151B VAL* 3.9 15.5 - - + -
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Residues in contact with ARG 125 (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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121B LEU 2.9 13.8 + - - +
122B GLU* 2.5 49.3 + - - +
124B LEU* 1.3 77.2 - - - +
126B GLU* 1.3 72.5 + - - +
128B ALA* 3.5 3.9 + - - +
129B GLU* 3.1 34.4 + - - +
148B LEU* 3.8 19.2 - - + +
151B VAL* 4.4 12.3 - - + +
155B PHE* 4.2 15.5 - - + -
168B ALA* 4.4 4.0 + - - +
169B VAL* 4.3 19.1 - - - +
172B GLU* 2.6 37.4 + - - +
228B TYR* 4.0 3.6 - - - -
229B GLU* 2.8 34.9 + - + +
231B VAL* 5.6 0.4 - - - -
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Residues in contact with GLU 126 (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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122B GLU* 2.6 39.4 + - - +
123B ARG* 3.7 31.7 + - - +
124B LEU 3.2 0.2 - - - -
125B ARG* 1.3 83.3 - - - +
127B ALA* 1.3 67.0 + - - +
129B GLU* 3.1 9.6 + - - +
130B SER* 3.0 26.5 + - - -
168B ALA* 3.8 10.4 - - - +
171B GLU* 5.0 5.2 - - - +
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Residues in contact with ALA 127 (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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118B ILE* 3.5 32.3 - - + -
123B ARG* 3.1 24.3 + - - +
124B LEU* 3.2 6.0 + - - +
126B GLU* 1.3 77.2 - - - +
128B ALA* 1.3 62.9 + - - +
130B SER* 4.0 6.5 - - - -
131B GLY 3.4 2.6 + - - -
132B GLU* 3.1 17.5 + - + +
133B LEU* 2.9 31.1 + - + +
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Residues in contact with ALA 128 (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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124B LEU* 3.0 12.6 + - + +
125B ARG 3.6 8.7 - - - +
127B ALA* 1.3 79.0 - - - +
129B GLU* 1.3 62.2 + - - +
130B SER 3.3 0.5 + - - -
131B GLY* 3.5 7.8 + - - -
133B LEU* 3.8 16.5 - - + +
144B ALA* 3.7 27.4 - - - +
148B LEU* 3.9 25.6 - - + +
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Residues in contact with GLU 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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125B ARG* 3.1 20.7 + - - +
126B GLU* 3.2 14.1 - - - +
128B ALA* 1.3 79.3 - - - +
130B SER* 1.3 60.1 + - - +
131B GLY 3.6 0.5 + - - -
148B LEU* 4.2 8.4 - - - +
172B GLU* 2.7 33.0 - - - +
228B TYR* 2.8 17.1 + - - -
229B GLU* 2.6 30.5 - - - +
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Residues in contact with SER 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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126B GLU 3.0 16.7 + - - -
127B ALA* 4.0 0.7 - - - -
129B GLU* 1.3 75.7 - - - +
131B GLY* 1.3 58.9 + - - +
132B GLU* 3.2 28.5 + - - +
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Residues in contact with GLY 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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127B ALA 3.4 3.8 + - - -
128B ALA 3.5 5.6 + - - -
129B GLU 3.4 3.6 + - - -
130B SER* 1.3 77.8 - - - +
132B GLU* 1.3 64.6 + - - +
133B LEU 3.2 2.9 - - - -
134B ALA* 3.3 12.2 + - - +
135B GLY* 3.1 19.2 + - - -
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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