Contacts of the helix formed by residues 150 - 161 (chain B) in PDB entry 2AOT
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 150 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148B VAL* 3.8 3.1 - - - +
149B LYS* 1.3 80.8 - - + +
151B ILE* 1.3 60.6 + - - +
152B PRO* 3.4 12.1 - - - +
153B ALA* 3.2 33.1 + - + +
154B THR* 2.9 27.9 + - - -
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Residues in contact with ILE 151 (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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145B LEU* 3.7 28.9 - - + +
148B VAL* 4.0 18.2 - - + +
149B LYS 3.8 1.6 + - - -
150B ASP* 1.3 70.7 - - - +
152B PRO* 1.3 70.6 - - + +
154B THR* 3.1 6.1 + - - -
155B LEU* 2.8 55.1 + - + +
197B GLN* 3.8 12.3 - - - +
199B ILE* 3.6 41.5 - - + -
204B LEU* 3.9 7.9 - - + -
207B MET* 3.8 18.6 - - + -
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Residues in contact with PRO 152 (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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150B ASP* 3.4 11.9 - - - +
151B ILE* 1.3 93.9 - - + +
153B ALA* 1.3 55.7 + - - +
155B LEU* 4.5 2.7 - - + -
156B LYS* 3.0 30.4 + - - +
207B MET* 3.7 24.9 - - + -
211B LEU* 3.7 26.2 - - + +
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Residues in contact with ALA 153 (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 GLN* 4.0 12.6 + - - +
150B ASP* 3.2 31.2 + - + +
152B PRO* 1.3 79.9 - - - +
154B THR* 1.3 57.4 + - - +
156B LYS* 3.8 5.1 - - - +
157B PHE* 2.9 31.9 + - - +
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Residues in contact with THR 154 (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* 4.4 6.2 + - - +
121B SER* 5.9 2.1 + - - -
124B GLN* 4.2 14.3 + - - -
141B MET* 3.3 33.4 - - + -
145B LEU* 4.4 5.6 - - + -
148B VAL* 3.2 23.3 - - + +
150B ASP 2.9 20.4 + - - -
151B ILE* 3.1 6.1 + - - -
153B ALA* 1.3 74.9 - - - +
155B LEU* 1.3 65.9 + - - +
157B PHE* 4.6 0.2 - - - -
158B PHE* 3.0 43.6 + - + +
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Residues in contact with LEU 155 (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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141B MET* 4.9 6.3 - - - -
145B LEU* 4.4 12.8 - - + -
151B ILE* 2.8 40.3 + - + +
154B THR* 1.3 73.6 - - - +
156B LYS* 1.3 61.4 + - - +
158B PHE* 5.2 0.2 - - - -
159B HIS* 3.0 28.2 + - - +
168B MET* 4.0 7.6 - - + +
170B ILE* 3.3 34.1 - - + -
204B LEU* 4.7 7.0 - - + -
207B MET* 4.3 15.9 - - + -
208B LEU* 4.0 27.1 - - + -
211B LEU* 3.7 21.5 - - + -
213B LEU* 4.4 2.1 - - + +
290B ILE* 4.9 1.8 - - + -
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Residues in contact with LYS 156 (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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152B PRO 3.0 17.9 + - - +
153B ALA* 3.9 5.4 - - - +
155B LEU* 1.3 78.5 - - - +
157B PHE* 1.3 61.9 + - - +
159B HIS* 3.5 7.7 + - - +
160B SER* 3.0 22.6 + - - -
211B LEU* 4.2 28.0 + - + +
213B LEU* 5.0 6.2 - - + +
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Residues in contact with PHE 157 (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 TYR* 4.7 2.5 - + - -
124B GLN* 3.5 58.3 - - + +
127B MET* 4.2 11.7 - - + -
128B LEU* 4.1 26.0 - - + -
133B LEU* 4.1 9.2 - - + -
153B ALA 2.9 19.2 + - - +
154B THR 3.9 1.8 - - - +
156B LYS* 1.3 74.9 - - - +
158B PHE* 1.3 87.9 + + - +
160B SER* 2.5 29.8 + - - -
161B LEU* 3.3 42.6 + - + +
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Residues in contact with PHE 158 (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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57B LEU* 3.8 17.0 - - + -
59B ILE* 3.7 25.4 - - + -
120B SER* 4.0 25.1 - - - -
123B TYR* 4.0 15.3 - + - -
124B GLN* 4.6 3.4 - - - -
139B ILE* 3.4 29.3 - - + +
141B MET* 4.0 8.1 - - + -
154B THR* 3.0 47.9 + - + +
155B LEU 4.5 0.2 - - - +
157B PHE* 1.3 104.2 - + - +
159B HIS* 1.3 63.9 + - - +
161B LEU* 3.0 21.8 + - + -
162B LEU* 3.7 1.6 + - - +
168B MET* 3.7 22.4 - - - -
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Residues in contact with HIS 159 (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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155B LEU 3.0 20.7 + - - +
156B LYS* 3.8 5.9 + - - +
158B PHE* 1.3 75.8 - - - +
160B SER* 1.3 66.1 + - - +
161B LEU 3.1 0.9 + - - -
162B LEU* 3.1 30.3 + - + +
168B MET* 3.8 14.4 - - + +
213B LEU* 3.8 32.4 - - + +
290B ILE* 3.9 12.1 - - + -
291B GLU 3.2 19.9 + - - -
292B ALA* 2.8 28.5 + - - -
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Residues in contact with SER 160 (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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133B LEU* 4.5 8.2 - - - +
135B LYS* 3.6 20.6 + - - -
156B LYS* 3.0 15.1 + - - -
157B PHE* 2.5 29.1 + - - -
159B HIS* 1.3 82.5 + - - +
161B LEU* 1.3 65.8 + - - +
162B LEU 3.4 1.4 + - - +
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Residues in contact with LEU 161 (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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57B LEU* 4.4 4.5 - - + -
123B TYR* 4.5 6.5 - - + -
127B MET* 5.6 2.5 - - + -
133B LEU* 4.0 18.4 - - + -
134B GLN* 3.6 19.7 - - + +
135B LYS* 3.1 8.2 - - - -
136B TRP* 2.7 54.8 + - + +
139B ILE* 3.9 7.6 - - + -
157B PHE* 3.6 43.1 - - + +
158B PHE* 3.0 26.0 + - + +
160B SER* 1.3 89.5 - - - +
162B LEU* 1.3 53.6 + - - +
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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