Contacts of the helix formed by residues 122 - 132 (chain B) in PDB entry 2P2L
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 122 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118B ASP 4.1 3.8 + - - +
119B LEU* 2.9 36.9 + - + +
121B ASP* 1.3 71.0 + - - +
123B LYS* 1.3 60.6 + - - +
124B ASP* 3.8 11.9 + - - +
125B THR* 2.2 67.4 + - - +
126B ILE* 3.0 7.3 + - - +
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Residues in contact with LYS 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 ASP 3.3 8.8 + - - +
122B ASP* 1.3 70.8 + - - +
124B ASP* 1.3 66.2 + - - +
125B THR 2.9 1.2 + - - -
126B ILE* 3.1 36.4 + - + +
127B GLU* 2.9 54.8 + - + +
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Residues in contact with ASP 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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122B ASP* 3.3 14.1 + - - +
123B LYS* 1.3 76.3 - - - +
125B THR* 1.3 58.7 + - + +
127B GLU* 4.4 4.8 - - - +
128B LYS* 3.2 41.3 + - + +
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Residues in contact with THR 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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85B VAL* 4.9 10.8 - - + -
119B LEU* 3.2 40.5 + - + -
122B ASP* 2.2 62.5 + - - +
124B ASP* 1.3 72.7 - - + +
126B ILE* 1.3 56.7 + - - -
128B LYS* 3.6 5.0 + - - +
129B LEU* 3.0 35.3 + - - +
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Residues in contact with ILE 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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119B LEU 4.5 0.4 - - - +
120B ARG 3.8 13.7 - - - +
121B ASP* 3.0 46.0 - - + +
122B ASP 3.0 15.0 + - - +
123B LYS* 3.7 31.6 - - + +
125B THR* 1.3 74.2 + - - +
127B GLU* 1.3 62.0 - - - +
129B LEU* 3.4 10.5 + - - +
130B LYS* 2.9 33.5 + - + +
134B LEU 4.8 0.3 - - - +
136B PRO* 4.3 17.2 - - + +
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Residues in contact with GLU 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 LYS* 2.9 47.1 + - + +
124B ASP* 4.4 4.9 - - - +
126B ILE* 1.3 74.1 - - - +
128B LYS* 1.3 65.2 + - + +
130B LYS* 3.1 10.2 + - - +
131B GLU* 3.0 30.6 + - - +
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Residues in contact with LYS 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 ASP* 3.2 28.9 + - + +
125B THR* 3.9 5.4 - - - +
127B GLU* 1.3 79.5 - - + +
129B LEU* 1.3 61.0 + - - +
131B GLU* 3.6 25.6 - - - +
132B LYS* 3.5 34.0 - - - +
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Residues in contact with LEU 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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85B VAL* 3.6 35.2 - - + +
87B PRO* 4.3 5.2 - - + -
125B THR* 3.0 26.5 + - - +
126B ILE* 3.5 6.3 - - - +
127B GLU 3.2 0.2 - - - -
128B LYS* 1.3 74.9 - - - +
130B LYS* 1.3 59.8 + - - +
132B LYS* 3.0 19.9 + - + +
134B LEU* 2.8 61.0 + - + +
135B THR* 4.2 2.7 - - - -
136B PRO* 3.7 37.0 - - + -
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Residues in contact with LYS 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 ILE* 2.9 20.7 + - + +
127B GLU* 3.1 12.3 + - - +
129B LEU* 1.3 77.4 - - - +
131B GLU* 1.3 56.6 + - - +
133B LYS* 2.9 30.3 + - - +
134B LEU 3.5 13.1 + - - +
135B THR* 5.1 9.7 + - - -
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Residues in contact with GLU 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 GLU* 3.0 20.7 + - - +
128B LYS* 3.6 28.7 + - - +
129B LEU 3.2 0.2 - - - -
130B LYS* 1.3 76.5 - - - +
132B LYS* 1.3 64.5 + - + +
133B LYS* 3.3 13.3 + - - +
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Residues in contact with LYS 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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128B LYS* 3.5 27.0 - - - +
129B LEU* 3.0 11.2 + - + +
131B GLU* 1.3 81.1 - - + +
133B LYS* 1.3 73.3 - - - +
134B LEU* 3.2 27.6 + - + +
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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