Contacts of the helix formed by residues 171 - 178 (chain A) in PDB entry 1ASC
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 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A LEU* 3.2 19.1 + - + +
170A ASP* 1.3 75.3 + - - +
172A ASP* 1.3 64.1 + - - +
174A LEU* 3.4 8.5 + - + +
175A ILE* 3.1 47.9 + - + +
205A GLN* 3.3 61.9 - - + +
208A THR* 3.8 21.8 - - + -
209A LEU* 3.9 25.8 - - + -
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Residues in contact with ASP 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A ASP* 3.3 17.3 - - - +
171A PHE* 1.3 79.1 + - - +
173A ALA* 1.3 60.6 + - - +
175A ILE* 3.4 3.7 + - - +
176A ASN* 2.8 44.4 + - - +
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Residues in contact with ALA 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ALA* 3.3 20.8 - - + +
170A ASP* 3.3 32.6 + - + +
171A PHE 3.4 0.2 - - - -
172A ASP* 1.3 78.5 - - - +
174A LEU* 1.3 53.2 + - - +
176A ASN* 4.0 3.8 - - - +
177A SER* 2.8 35.3 + - - -
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Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A TYR* 3.9 13.2 - - + -
160A ALA 3.4 24.2 - - - +
161A TYR* 3.9 11.4 - - + -
169A LEU* 3.5 27.8 - - + -
170A ASP 3.0 15.9 + - - +
171A PHE* 3.4 13.5 - - + +
173A ALA* 1.3 72.5 - - - +
175A ILE* 1.3 68.1 + - - +
177A SER* 2.7 18.4 + - - -
178A LEU* 2.9 37.5 + - + +
189A PHE* 5.1 2.5 - - + -
201A PRO* 6.0 0.2 - - + -
209A LEU* 4.0 34.8 - - + -
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Residues in contact with ILE 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A PHE* 3.1 43.6 + - + +
172A ASP* 3.8 3.8 - - - +
174A LEU* 1.3 75.5 - - - +
176A ASN* 1.3 73.9 + - - +
178A LEU* 3.1 14.2 + - - +
179A ASN* 2.8 32.6 + - - +
208A THR* 4.2 11.9 - - + -
209A LEU* 3.9 22.2 - - + -
212A LEU* 4.4 20.2 - - + -
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Residues in contact with ASN 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ASP* 2.8 36.7 + - - +
173A ALA* 4.0 3.8 - - - +
175A ILE* 1.3 84.4 - - - +
177A SER* 1.3 59.7 + - - +
179A ASN* 4.1 23.0 + - - +
180A GLU* 4.9 2.1 + - - +
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Residues in contact with SER 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A TRP* 3.7 12.7 - - - -
158A GLU 5.2 1.6 - - - -
159A TYR* 3.4 8.6 - - - +
160A ALA* 3.1 28.5 + - - -
173A ALA 2.8 16.2 + - - -
174A LEU 2.7 18.0 + - - -
176A ASN* 1.3 77.6 - - - +
178A LEU* 1.3 62.7 + - - +
179A ASN 3.3 0.9 - - - -
180A GLU* 3.5 19.6 - - - +
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Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A TRP* 4.0 27.4 - - + -
159A TYR* 3.9 15.0 - - + -
174A LEU* 2.9 37.6 + - + +
175A ILE* 3.1 5.3 + - - +
177A SER* 1.3 75.3 + - - +
179A ASN* 1.3 55.2 - - - +
180A GLU 3.1 5.2 - - - -
181A ALA* 2.8 25.4 + - + +
187A VAL* 3.9 31.9 - - + -
189A PHE* 4.8 6.1 - - + -
209A LEU* 5.3 2.7 - - + -
212A LEU* 5.6 0.2 - - + -
218A TRP* 2.9 47.4 - - + -
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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