Contacts of the helix formed by residues 121 - 133 (chain A) in PDB entry 2DNP
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 LYS 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A TRP* 4.4 0.4 - - - -
104A ARG* 5.2 11.0 + - + +
119A MET* 4.4 4.2 - - - +
120A GLU* 1.3 95.1 + - + +
122A GLU* 1.3 64.4 + - - +
123A ALA* 4.6 4.0 - - + +
124A ASP* 3.3 32.3 + - + +
125A ALA* 3.1 20.1 + - - +
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Residues in contact with GLU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A TRP* 3.0 52.5 - - + +
120A GLU 3.3 5.5 + - - -
121A LYS* 1.3 67.7 - - - +
123A ALA* 1.3 70.5 + - - +
125A ALA* 2.8 20.7 + - - +
126A LYS* 3.1 30.2 + - + +
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Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A LYS* 5.1 3.6 - - + -
122A GLU* 1.3 82.2 - - - +
124A ASP* 1.3 66.9 + - - +
126A LYS* 3.6 4.5 + - - +
127A ALA* 3.1 22.3 + - - +
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Residues in contact with ASP 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ARG 3.9 18.1 - - - +
103A GLY* 4.0 8.6 - - - -
104A ARG 4.3 3.5 + - - +
119A MET* 3.6 20.4 - - + +
121A LYS* 3.3 31.2 + - + +
122A GLU 3.2 0.4 - - - -
123A ALA* 1.3 77.7 - - - +
125A ALA* 1.3 66.3 + - - +
127A ALA* 3.4 7.3 + - - +
128A ALA* 3.0 25.5 + - - +
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Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A TRP* 4.6 16.6 - - + -
81A ILE* 4.1 11.3 - - + +
119A MET* 3.6 24.4 - - + +
121A LYS 3.1 12.8 + - - +
122A GLU* 2.8 20.4 + - - +
124A ASP* 1.3 75.0 - - - +
126A LYS* 1.3 68.4 + - + +
128A ALA* 3.2 9.7 + - - +
129A ILE* 3.2 19.3 + - - +
146A LEU* 5.5 1.8 - - + -
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Residues in contact with LYS 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A TRP* 3.2 28.1 - - - -
122A GLU* 3.1 45.8 + - + +
123A ALA* 4.1 4.9 - - - +
125A ALA* 1.3 76.9 - - + +
127A ALA* 1.3 70.0 + - - +
129A ILE* 2.9 27.5 + - + +
130A ALA* 3.0 12.7 + - - +
146A LEU* 3.4 23.7 - - + +
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Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ARG* 5.3 4.7 - - + +
123A ALA 3.1 16.7 + - - +
124A ASP* 3.5 9.9 - - - +
126A LYS* 1.3 77.9 - - - +
128A ALA* 1.3 61.3 + - - +
130A ALA* 3.3 8.8 + - - +
131A GLN* 3.1 25.2 + - - +
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Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A PHE* 4.3 11.0 - - + -
102A ARG* 3.6 34.5 - - + +
119A MET* 4.7 4.0 - - - -
124A ASP 3.0 13.3 + - - +
125A ALA 3.4 9.4 - - - +
126A LYS 3.0 0.2 - - - -
127A ALA* 1.3 71.8 - - - +
129A ILE* 1.3 52.1 + - - +
130A ALA 2.9 4.7 - - - -
131A GLN 2.7 7.0 + - - +
132A LEU* 2.6 52.1 + - + +
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Residues in contact with ILE 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ILE* 3.7 30.3 - - + -
125A ALA 3.3 14.8 - - - +
126A LYS* 2.9 18.7 + - + +
128A ALA* 1.3 72.7 - - - +
130A ALA* 1.3 52.2 + - - +
132A LEU* 4.3 1.1 - - - +
133A ASN* 2.6 43.3 + - + +
144A VAL* 3.3 35.9 - - + +
145A GLU* 3.7 4.7 - - - -
146A LEU* 3.4 40.8 - - + +
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Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A LYS 3.0 8.3 + - - +
127A ALA* 3.3 12.8 - - - +
128A ALA 2.7 4.8 + - - -
129A ILE* 1.3 73.2 - - - +
131A GLN* 1.3 71.1 + - + +
132A LEU 3.1 4.3 + - - -
133A ASN* 4.1 12.4 + - - +
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Residues in contact with GLN 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ARG* 4.5 26.8 + - + +
127A ALA 3.1 11.1 + - - +
128A ALA* 2.7 10.8 + - - +
130A ALA* 1.3 83.4 + - + +
132A LEU* 1.3 59.9 + - - +
135A LYS* 3.8 20.7 - - - +
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU* 3.8 40.2 - - + -
99A PHE* 3.3 53.4 - - + +
102A ARG* 4.3 11.0 - - - +
128A ALA* 2.6 29.6 + - + +
131A GLN* 1.3 77.0 - - - +
133A ASN* 1.3 53.3 + - - +
134A GLY 2.6 19.8 + - - -
135A LYS* 2.6 29.0 + - + +
142A ILE* 4.0 12.4 - - + +
144A VAL* 3.8 14.6 - - + -
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Residues in contact with ASN 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ILE* 2.6 28.2 + - + +
130A ALA* 4.2 10.0 + - - +
132A LEU* 1.3 69.0 - - - +
134A GLY* 1.3 61.5 + - - +
135A LYS 3.8 0.5 + - - -
143A ASN* 4.2 13.0 + - - +
144A VAL* 3.4 36.9 + - - +
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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