Contacts of the helix formed by residues 122 - 132 (chain B) in PDB entry 2ADM
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 PHE 122 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111B VAL* 3.2 48.2 - - + +
112B GLY* 3.7 24.2 - - - -
121B VAL* 1.3 89.6 - - + +
123B LYS* 1.3 53.5 + - - +
125B VAL* 3.1 3.6 + - - +
126B LYS* 2.7 35.3 + - - +
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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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111B VAL* 4.1 3.3 - - - +
121B VAL 3.6 0.6 - - - +
122B PHE* 1.3 79.1 - - - +
124B ALA* 1.3 75.6 + - - +
126B LYS* 3.4 17.5 + - - +
127B ASP* 3.0 49.7 + - - +
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Residues in contact with ALA 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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121B VAL* 2.8 20.2 + - - +
123B LYS* 1.3 90.4 - - - +
125B VAL* 1.3 61.5 + - + +
127B ASP* 3.3 16.6 + - - +
128B LEU* 3.0 21.4 - - + +
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ASP* 4.8 1.6 - - - +
92B LEU* 4.5 13.2 - - + -
121B VAL* 2.7 47.2 + - + +
122B PHE* 3.7 3.6 - - - +
124B ALA* 1.3 70.5 - - + +
126B LYS* 1.3 67.4 + - - +
128B LEU* 2.8 24.9 + - + +
129B TYR* 3.0 45.6 + - + +
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Residues in contact with LYS 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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110B ILE* 4.8 8.1 - - + +
111B VAL* 3.7 31.3 - - + +
122B PHE 2.7 21.4 + - - +
123B LYS* 3.5 17.8 - - - +
124B ALA 3.3 0.2 - - - -
125B VAL* 1.3 73.0 - - - +
127B ASP* 1.3 58.8 - - - +
129B TYR* 3.1 13.7 + - + +
130B LYS* 2.8 53.9 + - + +
136B TRP* 4.2 18.6 - - + +
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Residues in contact with ASP 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* 3.0 42.0 + - - +
124B ALA* 3.4 10.0 - - - +
125B VAL 3.1 0.6 - - - -
126B LYS* 1.3 80.2 - - - +
128B LEU* 1.3 62.8 + - + +
130B LYS* 3.3 8.7 + - - +
131B LYS* 3.0 48.7 + - + +
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Residues in contact with LEU 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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92B LEU* 4.3 29.6 - - + +
124B ALA* 3.0 32.8 - - + +
125B VAL* 2.8 12.2 + - + +
127B ASP* 1.3 80.2 - - + +
129B TYR* 1.3 58.7 + - + +
131B LYS* 3.3 6.1 + - - +
132B ALA* 2.9 31.9 + - - +
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Residues in contact with TYR 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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89B ASP* 2.9 32.7 + - - -
91B LEU* 3.7 28.3 - - + +
92B LEU* 4.0 12.3 - - + -
111B VAL* 6.1 3.8 - - - -
112B GLY 6.1 1.6 - - - -
125B VAL* 3.0 35.0 + - + +
126B LYS* 3.3 13.9 - - - +
128B LEU* 1.3 78.4 - - - +
130B LYS* 1.3 54.0 + - - +
132B ALA* 2.8 6.1 + - - -
133B PHE* 2.7 54.3 + + + +
136B TRP* 3.6 34.5 - + + -
142B LEU* 4.1 13.8 - - + +
500B SAM 4.1 6.6 + - - -
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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 LYS* 2.8 42.2 + - + +
127B ASP* 3.3 11.6 + - - +
129B TYR* 1.3 72.5 - - - +
131B LYS* 1.3 76.4 + - - +
133B PHE 3.7 12.9 - - - +
136B TRP* 3.3 45.8 - - + +
138B GLY 5.1 4.3 - - - -
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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 ASP* 3.0 47.9 + - - +
128B LEU* 3.9 5.4 - - - +
129B TYR 3.0 0.8 - - - -
130B LYS* 1.3 97.9 - - + +
132B ALA* 1.3 60.4 + - - +
133B PHE 5.1 0.8 - - - -
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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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91B LEU 5.3 1.6 - - - +
92B LEU* 5.0 11.0 - - + -
128B LEU 2.9 17.4 + - - +
129B TYR* 2.8 8.2 + - - +
131B LYS* 1.3 80.4 - - - +
133B PHE* 1.3 76.1 + - + +
134B SER 3.9 2.1 + - - -
148B GLU* 4.3 3.3 - - - +
152B ARG* 5.5 1.7 + - - -
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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