Contacts of the helix formed by residues 172 - 184 (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 GLU 172 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137B LYS* 3.2 33.2 + - - +
170B VAL 3.6 2.2 + - - -
171B LEU* 1.3 69.2 - - - +
173B ASP* 1.3 63.6 + - - +
174B PHE 3.0 11.0 + - - -
175B ALA* 3.1 26.8 + - - +
178B ARG* 4.5 2.2 - - - +
398B ARG* 4.8 24.0 - - + +
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Residues in contact with ASP 173 (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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135B THR 4.3 1.0 - - - +
137B LYS* 3.5 38.4 - - - +
138B GLY* 4.0 11.5 + - - -
139B LYS* 2.9 44.4 + - - +
140B TYR* 3.5 27.7 + - - -
171B LEU* 3.3 4.1 - - + +
172B GLU* 1.3 79.9 - - - +
174B PHE* 1.3 70.8 + - + +
175B ALA 3.4 0.6 + - - -
176B LEU 4.9 0.2 + - - -
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Residues in contact with PHE 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LYS* 5.7 2.9 - - - -
140B TYR* 3.6 36.8 - + - -
141B ASN* 3.6 30.3 - - + -
143B TYR* 3.6 26.7 - + - -
144B GLY* 4.7 2.9 - - - -
167B THR* 3.9 8.1 - - - -
168B TRP* 3.6 40.2 - - + +
171B LEU* 3.1 33.7 + - + +
172B GLU 3.0 1.6 - - - -
173B ASP* 1.3 82.9 - - + +
175B ALA* 1.3 63.6 + - - +
176B LEU 3.3 2.9 - - - -
177B LEU* 3.1 15.3 + - + +
178B ARG* 3.0 26.4 + - - +
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Residues in contact with ALA 175 (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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137B LYS* 4.4 13.2 - - + +
171B LEU 3.9 1.0 + - - -
172B GLU* 3.1 25.9 + - - +
173B ASP 3.4 0.8 - - - -
174B PHE* 1.3 77.7 - - - +
176B LEU* 1.3 63.7 + - + +
178B ARG* 3.4 24.7 + - - +
179B GLU* 3.2 29.5 + - - +
240B GLY 4.7 1.2 - - - +
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Residues in contact with LEU 176 (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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134B SER 3.8 17.9 - - - +
135B THR* 3.8 21.5 - - - +
136B TRP 4.4 4.3 - - - +
137B LYS* 4.1 32.9 - - + +
173B ASP 4.9 0.8 + - - -
174B PHE 3.3 0.6 - - - -
175B ALA* 1.3 76.5 - - + +
177B LEU* 1.3 65.4 - - - +
179B GLU* 3.4 23.9 + - - +
180B PHE* 3.0 24.1 + - - +
183B ARG* 4.9 1.4 + - - -
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Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B THR* 3.8 18.1 + - + +
140B TYR* 3.6 25.6 - - + +
143B TYR* 5.0 0.9 - - + -
144B GLY* 3.9 26.9 - - - +
147B LEU* 4.0 25.8 - - + -
148B GLU 4.7 3.8 - - - +
168B TRP* 4.4 14.6 - - + -
174B PHE* 3.1 29.4 + - + +
176B LEU* 1.3 77.2 - - - +
178B ARG* 1.3 63.0 + - - +
180B PHE* 3.3 5.8 + - + +
181B LEU* 3.1 40.7 + - + +
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Residues in contact with ARG 178 (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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168B TRP* 2.8 36.9 + - + +
169B LEU* 3.5 12.9 + - - +
170B VAL 3.3 14.6 + - - -
171B LEU 2.5 38.0 + - - +
172B GLU* 4.5 1.2 - - - +
174B PHE 3.0 9.6 + - - +
175B ALA* 3.5 30.0 - - - +
177B LEU* 1.3 74.7 - - - +
179B GLU* 1.3 65.2 + - - +
181B LEU* 3.5 3.2 + - - -
182B ALA* 3.1 24.3 + - - +
238B TRP* 3.6 17.5 - - + -
240B GLY* 3.3 33.7 + - - +
241B GLU* 3.9 11.2 - - - +
242B ILE* 3.6 18.3 - - - +
243B ILE* 5.0 1.3 - - - -
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Residues in contact with GLU 179 (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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175B ALA* 3.2 17.8 + - - +
176B LEU* 3.4 23.8 + - - +
178B ARG* 1.3 75.8 - - - +
180B PHE* 1.3 65.3 + - - +
182B ALA* 3.2 3.1 + - - +
183B ARG* 3.0 42.3 + - - +
239B GLU 3.9 19.7 - - - +
240B GLY* 4.8 4.3 - - - +
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Residues in contact with PHE 180 (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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134B SER* 4.7 2.2 - - - -
135B THR* 3.6 20.2 - - + -
148B GLU* 3.7 29.8 - - + -
151B VAL* 3.6 39.3 - - + -
152B ARG* 3.4 37.5 - - + -
176B LEU 3.0 13.5 + - - +
177B LEU* 3.3 11.0 - - + +
179B GLU* 1.3 76.0 - - - +
181B LEU* 1.3 76.2 + - + +
183B ARG* 3.3 27.4 + - - +
184B GLU* 2.9 42.3 + - + +
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Residues in contact with LEU 181 (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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147B LEU* 4.8 7.6 - - + -
151B VAL* 4.0 20.9 - - + -
168B TRP* 4.1 22.9 - - + -
177B LEU* 3.1 34.3 + - + +
178B ARG* 3.9 4.0 - - - +
180B PHE* 1.3 96.4 - - + +
182B ALA* 1.3 63.6 + - - +
184B GLU* 3.2 0.4 + - - -
185B GLY 3.2 26.2 + - - +
187B THR* 4.0 17.6 + - - +
206B ILE* 4.1 22.9 - - + -
208B PHE* 3.4 16.5 - - + -
238B TRP* 4.3 6.1 - - + -
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Residues in contact with ALA 182 (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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178B ARG 3.1 16.3 + - - +
179B GLU 3.5 4.9 - - - +
181B LEU* 1.3 79.7 - - - +
183B ARG* 1.3 60.8 + - + +
185B GLY 3.6 12.4 - - - +
212B GLY* 5.8 0.7 - - - -
213B LYS 4.1 10.2 + - - +
214B GLY 6.0 0.2 - - - -
238B TRP* 3.6 25.4 - - + +
239B GLU* 3.5 33.2 - - - +
240B GLY 3.6 2.2 - - - +
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Residues in contact with ARG 183 (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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176B LEU 4.9 1.0 + - - -
179B GLU* 3.0 28.6 + - - +
180B PHE* 3.7 46.0 - - - +
182B ALA* 1.3 76.8 - - + +
184B GLU* 1.3 77.3 + - - +
185B GLY 3.5 0.2 - - - -
212B GLY* 5.5 2.7 - - - -
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Residues in contact with GLU 184 (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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151B VAL* 4.1 5.6 - - + +
152B ARG* 5.8 2.0 + - - -
180B PHE* 2.9 49.5 + - + +
181B LEU* 3.2 0.6 + - - +
183B ARG* 1.3 98.3 + - + +
185B GLY* 1.3 56.3 + - - +
208B PHE* 3.6 20.2 - - + -
210B LYS* 3.7 38.9 + - - +
212B GLY* 4.2 4.8 + - - -
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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