Contacts of the helix formed by residues 122 - 133 (chain B) in PDB entry 2NO5
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 ASN 122 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60B ASP* 3.1 23.6 + - + +
61B PHE* 3.4 3.1 + - - +
62B TRP* 3.0 37.9 + - - +
120B ASN 3.7 1.8 + - - -
121B GLY* 1.3 75.0 - - - +
123B ASP* 1.3 66.1 + - - +
124B GLU* 3.0 5.2 + - - +
125B MET* 3.3 19.6 + - - +
126B LEU* 3.2 14.7 + - - +
144B SER* 3.5 6.3 - - - -
146B ASP* 3.2 27.4 - - - +
1003B SO4 3.1 24.0 + - - +
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Residues in contact with ASP 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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121B GLY 3.9 0.8 + - - -
122B ASN* 1.3 71.0 - - - +
124B GLU* 1.3 53.9 + - - +
126B LEU* 4.3 4.4 - - - +
127B GLN* 2.5 78.8 + - + +
142B CYS* 3.6 20.8 - - - +
144B SER* 4.2 13.1 + - - -
146B ASP* 4.9 1.2 + - - +
147B ASP* 5.8 2.7 - - - +
1003B SO4 3.1 12.8 + - - +
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Residues in contact with GLU 124 (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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93B LYS* 3.4 31.5 + - - -
122B ASN* 3.0 6.1 + - - +
123B ASP* 1.3 72.5 - - - +
125B MET* 1.3 63.1 + - - +
127B GLN* 3.9 4.3 - - - +
128B ALA* 3.1 25.1 + - + +
1003B SO4 2.8 35.1 + - - +
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Residues in contact with MET 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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13B TYR* 3.5 20.9 + - + +
61B PHE* 3.8 17.9 - - + -
62B TRP* 3.5 45.8 - - + -
65B THR* 3.7 15.0 - - - +
92B TYR* 3.6 28.9 - - + -
93B LYS* 3.9 13.7 - - + +
121B GLY* 4.3 2.2 - - - -
122B ASN* 3.3 36.6 + - - +
124B GLU* 1.3 77.7 + - - +
126B LEU* 1.3 66.2 + - - +
128B ALA* 3.5 5.8 + - - +
129B ALA* 3.2 23.2 + - - +
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Residues in contact with LEU 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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12B ALA* 4.1 16.8 - - + -
13B TYR* 3.9 11.2 - - + +
17B LEU* 4.4 8.3 - - + -
117B ILE* 4.1 4.3 - - + -
119B SER* 3.6 33.9 - - - +
121B GLY 4.1 10.8 - - - +
122B ASN 3.2 13.8 + - - +
123B ASP* 3.6 8.3 - - - +
125B MET* 1.3 82.5 - - - +
127B GLN* 1.3 57.4 + - - +
129B ALA* 3.1 2.8 + - - -
130B LEU* 2.9 57.5 + - + +
142B CYS* 3.6 24.0 - - - -
143B LEU 5.1 2.5 - - - +
144B SER* 5.5 0.9 - - - -
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Residues in contact with GLN 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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123B ASP* 2.5 64.5 + - - +
124B GLU* 4.0 4.5 - - - +
126B LEU* 1.3 70.4 - - - +
128B ALA* 1.3 61.1 + - - +
130B LEU* 3.4 13.4 + - - +
131B LYS* 2.7 37.7 + - + +
136B ASP* 5.7 4.9 - - - +
142B CYS* 3.6 23.0 - - - +
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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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93B LYS* 3.7 35.0 - - + +
94B GLU* 4.0 11.5 - - - +
124B GLU 3.1 17.5 + - - +
125B MET 3.8 4.3 - - - +
127B GLN* 1.3 76.4 - - - +
129B ALA* 1.3 57.8 + - - +
131B LYS* 3.8 5.1 - - - +
132B ALA* 2.8 30.8 + - - +
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Residues in contact with ALA 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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13B TYR* 4.5 5.6 - - + +
17B LEU* 3.8 27.4 - - + +
92B TYR 4.9 1.8 - - - +
93B LYS 3.5 18.8 - - - +
94B GLU* 4.6 1.6 - - - +
95B LEU* 4.3 10.4 - - + +
125B MET 3.2 11.3 + - - +
126B LEU 3.1 4.7 + - - +
128B ALA* 1.3 78.5 - - - +
130B LEU* 1.3 66.2 + - - +
132B ALA* 4.0 4.2 - - - +
133B SER* 2.9 28.1 + - - -
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Residues in contact with LEU 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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16B LEU* 5.4 0.4 - - + -
17B LEU* 4.4 12.1 - - + -
117B ILE* 3.8 22.0 - - + -
126B LEU* 2.9 39.6 + - + +
127B GLN* 4.0 17.3 - - - +
129B ALA* 1.3 74.8 - - - +
131B LYS* 1.3 61.2 + - - +
133B SER* 3.9 2.5 - - - -
134B LYS 2.9 22.9 + - - -
135B LEU* 2.9 31.2 + - + -
136B ASP* 3.3 19.4 + - + +
139B LEU* 3.8 20.9 - - + -
142B CYS* 4.1 16.2 - - + -
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Residues in contact with LYS 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 GLN* 2.7 24.9 + - + +
128B ALA* 3.8 5.6 - - - +
130B LEU* 1.3 77.0 - - - +
132B ALA* 1.3 63.1 + - - +
134B LYS* 3.0 19.4 + - - +
136B ASP* 3.5 20.9 - - + +
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Residues in contact with ALA 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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94B GLU* 3.7 41.7 - - + +
95B LEU 5.3 1.1 - - - +
128B ALA 2.8 17.9 + - - +
129B ALA 3.5 3.6 + - - +
130B LEU 3.4 0.2 - - - -
131B LYS* 1.3 78.2 - - - +
133B SER* 1.3 57.2 + - - +
134B LYS* 3.7 10.9 + - - +
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Residues in contact with SER 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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17B LEU* 4.0 2.5 - - - +
95B LEU 4.3 6.5 - - - -
96B SER* 5.0 0.9 - - - -
97B ALA* 4.0 30.9 - - - +
102B ALA* 5.5 1.0 - - - +
129B ALA 2.9 18.7 + - - -
130B LEU* 3.7 1.9 + - - -
132B ALA* 1.3 75.1 - - - +
134B LYS* 1.3 74.4 + - - +
135B LEU* 3.2 30.3 + - - +
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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