Contacts of the helix formed by residues 181 - 191 (chain A) in PDB entry 1MMM
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 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A ALA 2.9 29.4 + - - -
121A ALA* 3.5 15.1 + - - +
123A ARG 2.9 22.0 + - - -
125A GLY 3.3 25.3 + - - +
168A VAL* 3.5 23.2 + - - +
170A GLU* 5.2 3.0 - - - +
173A TYR* 3.0 50.2 + - + +
179A ASN 2.8 12.8 + - - +
180A ARG* 1.3 72.1 - - - +
182A PRO* 1.3 63.1 - - + +
184A TYR* 3.0 10.0 + - + +
185A ILE* 2.9 41.4 + - + +
169B TRP* 5.7 3.0 - - - -
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Residues in contact with PRO 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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121A ALA* 5.2 12.3 - - + -
179A ASN 4.4 1.8 - - - +
180A ARG* 3.2 9.2 - - + -
181A ARG* 1.3 94.8 - - + +
183A ASP* 1.3 59.9 + - - +
185A ILE* 3.4 12.0 + - + +
186A LYS* 3.0 36.5 + - + +
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Residues in contact with ASP 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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177A PHE* 4.0 16.2 - - + -
180A ARG* 3.1 41.1 + - + +
182A PRO* 1.3 79.1 - - - +
184A TYR* 1.3 64.5 + - - +
186A LYS* 3.3 11.6 + - - +
187A GLU* 3.1 27.5 + - - +
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Residues in contact with TYR 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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18A PHE* 3.4 28.2 - + - -
84A PHE* 4.0 10.7 - - - -
166A LEU* 3.5 24.4 - - + +
167A ASP 2.9 29.2 + - - -
168A VAL* 4.6 1.6 - - + -
172A ALA* 3.5 28.6 + - + +
173A TYR* 3.3 43.5 - + + -
177A PHE* 3.8 29.3 - + + -
180A ARG 3.4 2.0 + - - -
181A ARG* 3.0 17.9 + - + +
183A ASP* 1.3 79.4 - - - +
185A ILE* 1.3 66.5 + - + +
187A GLU* 3.3 3.5 + - - +
188A PHE* 3.1 18.9 + - - +
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Residues in contact with ILE 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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116A PHE* 5.3 3.8 - - + -
117A GLU* 4.0 37.9 - - + +
120A ALA* 3.4 28.0 - - + -
121A ALA* 3.6 20.2 - - + +
166A LEU* 4.0 19.5 - - + -
168A VAL* 5.0 0.4 - - + -
181A ARG* 2.9 37.5 + - + +
182A PRO* 3.7 8.7 - - + +
184A TYR* 1.3 75.9 - - + +
186A LYS* 1.3 65.0 + - + +
188A PHE* 3.2 21.5 - - + +
189A TRP* 3.7 10.5 + - + +
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Residues in contact with LYS 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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117A GLU* 2.9 35.1 + - - +
182A PRO* 3.0 28.2 + - - +
183A ASP* 3.5 13.2 - - - +
184A TYR 3.2 0.2 - - - -
185A ILE* 1.3 77.4 - - + +
187A GLU* 1.3 63.7 + - + +
189A TRP* 3.1 28.9 + - + +
190A ASN* 4.0 6.0 + - - -
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Residues in contact with GLU 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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16A PRO 4.9 1.3 - - - -
17A HIS* 2.7 47.1 + - - +
18A PHE* 4.1 14.4 - - + -
176A LYS* 4.8 4.0 - - - +
177A PHE* 3.7 22.7 - - + -
183A ASP 3.1 17.6 + - - +
184A TYR 3.3 8.9 + - - +
186A LYS* 1.3 73.8 - - + +
188A PHE* 1.3 57.0 + - - +
190A ASN* 2.7 40.4 + - - +
191A VAL* 3.5 6.2 + - - +
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Residues in contact with PHE 188 (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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18A PHE* 4.0 13.2 - + + -
84A PHE* 4.4 0.7 - + - -
87A GLY 4.9 1.3 - - - -
88A LEU* 3.8 23.6 - - + -
116A PHE* 3.6 33.9 - + - -
164A MET* 4.1 8.7 - - + -
165A GLY 3.7 23.1 - - - -
166A LEU* 3.5 33.7 - - + -
184A TYR 3.1 12.8 + - - +
185A ILE* 3.2 15.5 - - + +
187A GLU* 1.3 76.3 - - - +
189A TRP* 1.3 68.5 + + - +
191A VAL* 3.0 7.2 + - - -
192A VAL* 2.9 58.8 + - + +
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Residues in contact with TRP 189 (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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112A PHE* 3.8 28.7 - + - -
113A LYS* 3.7 57.2 + - + +
116A PHE* 3.5 30.7 - + + -
117A GLU* 3.0 30.9 + - + +
164A MET* 5.1 1.3 - - + -
185A ILE* 4.0 9.2 + - + -
186A LYS* 3.4 21.8 - - + +
187A GLU 3.1 0.8 - - - -
188A PHE* 1.3 91.3 - + - +
190A ASN* 1.3 62.7 + - - +
191A VAL 3.6 0.5 + - - -
192A VAL* 3.8 23.0 - - + +
194A TRP* 4.1 16.0 + + - -
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Residues in contact with ASN 190 (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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17A HIS* 3.4 34.5 + - + +
89A LYS 4.2 0.5 - - - +
90A LYS* 4.1 14.2 - - - +
91A GLY 4.8 2.3 + - - -
186A LYS 4.0 5.0 + - - -
187A GLU* 2.7 46.0 + - - +
189A TRP* 1.3 74.9 - - - +
191A VAL* 1.3 60.0 + - - +
192A VAL 3.8 0.9 - - - -
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Residues in contact with VAL 191 (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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14A LEU* 4.1 31.6 - - + +
17A HIS* 3.6 30.5 - - + -
18A PHE* 3.6 37.2 - - + -
88A LEU* 3.2 12.8 - - + -
89A LYS 2.8 33.8 + - - -
90A LYS* 4.1 3.4 - - + -
187A GLU 3.8 5.2 - - - +
188A PHE* 3.5 9.4 - - - +
190A ASN* 1.3 85.5 - - - +
192A VAL* 1.3 60.3 + - - +
193A ASN 3.1 0.5 + - - -
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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