Contacts of the helix formed by residues 173 - 180 (chain B) in PDB entry 3ASZ
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 VAL 173 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B GLY 3.7 22.4 - - - +
14B GLY* 4.1 0.7 - - - -
60B ASP* 5.2 4.0 - - + +
113B ILE* 3.2 39.0 - - + +
114B LEU* 3.8 18.2 - - + -
130B PHE* 3.7 8.7 - - + -
168B MET 3.4 4.0 + - - +
169B HIS* 3.2 38.1 + - + +
172B PHE* 1.3 73.9 - - + +
174B GLU* 1.3 67.9 + - - +
176B THR* 2.6 27.1 + - - -
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Residues in contact with GLU 174 (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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130B PHE* 4.0 13.9 - - - -
132B ASP* 4.3 6.8 - - - +
169B HIS* 2.7 54.9 + - + +
170B LEU* 4.4 11.9 - - + +
173B VAL* 1.3 72.5 - - - +
175B PRO* 1.3 68.2 - - + +
177B LYS* 3.1 54.0 + - - +
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Residues in contact with PRO 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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170B LEU 3.5 20.4 - - - +
171B HIS 3.7 12.3 - - - +
172B PHE 3.7 11.7 - - - +
173B VAL 3.5 4.9 - - - -
174B GLU* 1.3 93.4 - - + +
176B THR* 1.3 57.2 - - + +
177B LYS 3.0 5.2 + - - -
178B ARG* 3.1 30.9 + - + +
179B TYR* 5.0 2.9 - - - -
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Residues in contact with THR 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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12B ALA* 4.8 1.0 - - - +
113B ILE 4.7 4.3 + - - +
114B LEU* 5.0 1.8 - - + -
116B LEU* 3.8 30.6 + - - +
117B TYR* 3.9 33.7 - - + +
130B PHE* 3.8 10.3 - - - -
172B PHE 3.2 20.6 - - - +
173B VAL* 2.6 21.1 + - - +
175B PRO* 1.3 73.3 - - + +
177B LYS* 1.3 62.9 - - - +
178B ARG 3.0 2.7 - - - -
179B TYR* 3.0 31.3 + - + +
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Residues in contact with LYS 177 (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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132A ASP* 5.5 5.6 + - - -
185A PRO* 5.5 2.9 - - - +
130B PHE* 3.7 44.8 - - + -
132B ASP* 3.1 22.4 + - - +
174B GLU* 3.1 35.8 + - - +
175B PRO 3.0 0.4 - - - -
176B THR* 1.3 79.5 + - - +
178B ARG* 1.3 68.1 + - + +
179B TYR 3.1 0.7 - - - -
180B ALA* 3.1 17.4 + - - +
183B ILE* 3.8 32.6 - - + +
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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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134A ASP* 3.4 32.3 + - - -
137A GLU* 4.7 9.2 + - - -
185A PRO* 6.5 0.4 - - - -
186A ARG* 4.2 19.2 + - - -
175B PRO* 3.1 22.6 - - + +
176B THR 3.0 0.6 - - - -
177B LYS* 1.3 84.2 - - + +
179B TYR* 1.3 67.0 + - + +
180B ALA 3.4 1.3 - - - -
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Residues in contact with TYR 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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186A ARG* 4.6 3.3 + - - -
116B LEU* 3.5 22.0 - - + -
117B TYR 4.9 1.1 - - - -
122B ARG* 3.5 52.6 + - - -
128B LYS* 3.3 23.2 - - + +
175B PRO 5.0 2.7 - - - -
176B THR* 3.0 30.2 + - + +
178B ARG* 1.3 84.1 - - + +
180B ALA* 1.3 65.3 + - - +
181B ASP* 3.7 3.8 + - - +
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Residues in contact with ALA 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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185A PRO* 3.6 11.1 - - - +
186A ARG* 3.2 16.7 + - - -
116B LEU* 4.5 3.5 - - + +
128B LYS* 3.6 11.2 - - - +
129B VAL 4.4 1.3 - - - -
130B PHE* 3.7 28.7 - - + +
176B THR 3.9 1.0 + - - -
177B LYS* 3.1 17.6 + - - +
178B ARG 4.5 0.9 - - - +
179B TYR* 1.3 79.5 - - - +
181B ASP* 1.3 63.0 + - - +
182B VAL 3.8 14.4 - - - +
183B ILE* 4.5 5.4 - - + -
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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