Contacts of the helix formed by residues 179 - 187 (chain A) in PDB entry 1MNG
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 ARG 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A TYR* 4.7 0.2 - - - -
175A LYS 4.3 4.6 + - - -
176A TYR* 3.0 58.5 + - + +
177A GLN* 3.2 19.3 + - - +
178A ASN* 1.3 95.3 + - - +
180A ARG* 1.3 64.2 + - - +
181A ALA* 3.1 3.4 - - + +
182A ASP* 3.0 40.8 + - + +
183A TYR 3.4 7.6 + - - -
31B LYS* 6.0 5.2 - - - +
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Residues in contact with ARG 180 (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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124A ALA 2.5 38.0 + - - -
125A MET* 3.9 28.7 + - + +
127A ARG 2.8 20.0 + - - -
128A PHE* 5.3 0.2 - - - +
129A GLY 3.3 26.1 + - - +
167A VAL* 3.5 28.2 + - + +
169A GLU* 5.6 2.2 - - - +
172A TYR* 3.2 44.7 + - + +
178A ASN 2.9 11.2 + - - +
179A ARG* 1.3 73.3 - - - +
181A ALA* 1.3 61.9 + - - +
183A TYR* 3.2 7.0 + - + +
184A LEU* 3.0 27.3 + - + +
168B TRP* 6.0 2.2 - - - -
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Residues in contact with ALA 181 (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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121A THR* 6.4 1.3 - - + -
125A MET* 3.7 27.6 - - + +
179A ARG* 3.1 2.1 - - + -
180A ARG* 1.3 79.6 - - - +
182A ASP* 1.3 64.9 - - - +
184A LEU* 3.4 5.2 + - - +
185A GLN* 3.1 26.7 + - + +
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Residues in contact with ASP 182 (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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176A TYR* 3.8 20.9 - - + -
179A ARG* 3.0 44.2 + - + +
181A ALA* 1.3 81.3 - - - +
183A TYR* 1.3 61.2 + - - +
185A GLN* 3.4 9.8 + - - +
186A ALA* 3.1 23.0 + - - +
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Residues in contact with TYR 183 (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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19A HIS 5.5 0.4 - - - -
20A ILE* 4.9 13.2 - - + -
86A PHE* 3.6 25.6 - - - -
165A ILE* 4.4 7.3 - - + +
167A VAL* 4.4 12.7 + - + -
171A ALA* 3.7 32.8 - - + +
172A TYR* 3.5 44.2 - + + -
176A TYR* 3.9 24.3 - + + -
179A ARG 3.4 6.0 + - - +
180A ARG* 3.2 10.5 + - + +
182A ASP* 1.3 77.6 - - - +
184A LEU* 1.3 78.4 + - + +
186A ALA* 3.2 3.3 + - + +
187A ILE* 3.0 47.3 + - + +
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Residues in contact with LEU 184 (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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121A THR* 4.3 18.4 - - + +
124A ALA* 3.7 30.1 - - + -
125A MET* 3.4 40.8 - - + -
165A ILE* 4.1 22.4 - - + -
167A VAL* 4.3 3.6 - - + -
180A ARG* 3.0 13.4 + - + +
181A ALA* 3.8 6.3 - - - +
182A ASP 3.3 0.2 - - - -
183A TYR* 1.3 89.4 - - + +
185A GLN* 1.3 64.8 + - - +
186A ALA 3.3 0.3 + - - -
187A ILE* 3.3 12.2 + - + +
188A TRP* 3.0 29.1 + - + +
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Residues in contact with GLN 185 (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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117A LYS* 6.0 3.8 - - - +
121A THR* 5.2 9.5 + - - +
181A ALA* 3.1 17.8 + - + +
182A ASP* 3.7 10.8 - - - +
184A LEU* 1.3 77.3 - - - +
186A ALA* 1.3 61.6 + - - +
188A TRP* 3.6 26.1 + - - +
189A ASN* 4.0 9.6 + - - -
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Residues in contact with ALA 186 (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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19A HIS* 4.0 27.0 - - + +
20A ILE* 6.1 0.7 - - + -
176A TYR* 3.3 26.5 - - + +
182A ASP 3.1 8.2 + - - +
183A TYR* 3.6 7.6 - - + +
184A LEU 3.2 0.2 - - - -
185A GLN* 1.3 79.8 - - - +
187A ILE* 1.3 64.3 + - - +
189A ASN* 3.0 28.6 + - - +
190A VAL* 3.9 2.4 + - - +
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Residues in contact with ILE 187 (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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20A ILE* 3.9 26.5 - - + -
86A PHE* 4.2 10.1 - - + -
90A LEU* 4.2 13.7 - - + -
165A ILE* 4.3 27.8 - - + -
183A TYR* 3.0 49.7 + - + +
184A LEU* 3.3 10.5 + - + +
186A ALA* 1.3 75.1 - - - +
188A TRP* 1.3 69.7 + - + +
190A VAL* 3.0 28.7 + - + +
191A LEU* 3.2 21.9 + - + +
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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