Contacts of the helix formed by residues 109 - 116 (chain A) in PDB entry 1MUG
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 LYS 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A GLY* 1.3 69.1 - - - -
110A GLN* 1.3 64.8 + - - +
112A TYR* 3.1 4.9 + - - +
113A GLU* 2.9 45.1 + - - +
121A ALA* 3.5 32.5 + - + +
122A GLN* 4.5 1.0 - - - +
123A TRP* 3.1 58.9 - - + +
137A VAL* 3.8 11.4 - - + -
170A SO4 2.8 19.0 + - - +
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Residues in contact with GLN 110 (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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82A LYS* 3.2 22.2 + - - +
85A LEU* 4.4 9.2 - - + -
109A LYS* 1.3 71.8 - - - +
111A ALA* 1.3 64.0 + - - +
113A GLU* 3.2 14.8 + - - +
114A GLN* 2.9 49.4 + - - +
170A SO4 2.7 22.9 + - - +
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Residues in contact with ALA 111 (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 GLY 5.6 1.3 - - - -
17A ILE* 3.6 36.2 - - + +
69A LEU* 3.5 24.4 - - + +
85A LEU* 4.3 9.6 - - + +
106A ILE* 3.9 11.9 - - + -
108A GLY* 3.4 11.0 + - - +
109A LYS 3.3 0.4 - - - -
110A GLN* 1.3 77.8 - - - +
112A TYR* 1.3 57.4 + - - +
115A GLY* 2.9 26.7 + - - -
116A PHE* 5.0 0.3 - - - -
170A SO4 5.3 0.2 + - - -
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Residues in contact with TYR 112 (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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106A ILE* 3.6 13.2 - - + +
108A GLY 3.2 7.5 + - - +
109A LYS 3.1 8.1 + - - +
111A ALA* 1.3 79.4 - - - +
113A GLU* 1.3 59.5 + - - +
116A PHE* 2.9 63.7 + + + +
118A GLN* 3.7 23.0 + - + +
121A ALA* 3.8 21.1 - - + -
126A GLN* 3.6 32.2 + - + +
128A LEU* 3.5 28.6 - - + +
135A ILE* 3.8 21.3 - - + -
137A VAL* 3.5 27.1 - - + -
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Residues in contact with GLU 113 (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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109A LYS* 2.9 34.1 + - - +
110A GLN* 3.7 18.1 + - - +
112A TYR* 1.3 75.3 - - + +
114A GLN* 1.3 65.6 + - - +
117A SER* 3.0 10.2 + - - -
118A GLN* 2.9 49.7 + - - +
119A ARG* 4.4 12.9 + - - -
120A GLY* 3.4 12.7 + - - -
121A ALA* 3.1 38.0 + - + +
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Residues in contact with GLN 114 (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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82A LYS* 3.5 51.6 + - + +
85A LEU* 3.4 24.8 - - + +
86A HIS* 3.3 25.6 - - + +
110A GLN* 2.9 50.4 + - - +
113A GLU* 1.3 82.8 + - - +
115A GLY* 1.3 66.5 + - - +
116A PHE 3.3 0.3 + - - -
117A SER* 3.4 2.1 + - - +
119A ARG* 4.7 14.7 + - - -
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Residues in contact with GLY 115 (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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69A LEU* 4.3 7.0 - - - -
85A LEU* 3.4 22.1 + - - +
86A HIS* 4.3 8.0 + - - +
89A GLY* 3.4 22.9 + - - -
93A ILE* 5.7 1.2 - - - +
111A ALA 2.9 17.4 + - - -
112A TYR 4.0 0.2 - - - -
114A GLN* 1.3 78.4 - - - +
116A PHE* 1.3 67.5 + - - +
117A SER* 3.5 0.4 + - - -
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Residues in contact with PHE 116 (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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69A LEU* 5.1 3.6 - - + -
89A GLY* 4.9 2.5 - - - -
92A LEU* 3.7 33.7 - - + -
93A ILE* 3.7 33.7 - - + -
104A LEU* 4.0 12.6 - - + -
106A ILE* 4.2 15.7 - - + -
111A ALA 5.5 0.4 - - - -
112A TYR* 2.9 40.1 + + + +
115A GLY* 1.3 82.2 - - - +
117A SER* 1.3 72.9 + - - +
118A GLN* 2.9 26.5 + - + -
128A LEU* 4.2 17.7 - - + +
130A ILE* 3.8 14.1 - - + -
135A ILE* 4.3 6.1 - - + -
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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