Contacts of the helix formed by residues 104 - 114 (chain R) in PDB entry 1MVW
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 GLY 104 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102R VAL 3.4 1.2 + - - -
103R MET* 1.3 72.2 - - - +
105R ALA* 1.3 61.6 + - - +
106R GLU 3.1 0.9 + - - -
107R LEU* 3.1 13.2 + - - +
108R ARG* 3.2 24.7 + - - +
131R GLU* 3.1 26.4 + - - -
135R GLY* 2.9 13.5 + - - -
137R ILE* 3.6 10.6 - - - +
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Residues in contact with ALA 105 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103R MET* 3.2 2.0 + - + +
104R GLY* 1.3 72.3 - - - +
106R GLU* 1.3 62.3 + - + +
108R ARG* 3.7 27.1 - - - +
109R HIS* 3.0 51.8 + - + +
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Residues in contact with GLU 106 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94R PHE* 3.8 34.0 - - + +
95R ASP* 5.1 4.2 - - - +
96R LYS* 5.8 1.0 + - - -
102R VAL* 3.8 5.2 - - - +
103R MET* 2.9 56.2 + - + +
105R ALA* 1.3 77.3 - - + +
107R LEU* 1.3 58.3 + - - +
109R HIS* 4.0 1.8 - - - +
110R VAL* 3.0 34.5 + - - +
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Residues in contact with LEU 107 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91R LEU* 4.7 14.1 - - + -
94R PHE* 4.4 4.3 - - + -
102R VAL* 3.6 30.5 - - + -
103R MET 3.6 0.6 + - - -
104R GLY 3.1 1.8 + - - -
106R GLU* 1.3 78.6 - - - +
108R ARG* 1.3 59.2 + - - +
110R VAL* 3.9 3.4 - - + +
111R LEU* 2.9 45.0 + - + +
127R MET* 3.9 22.4 - - + -
137R ILE* 3.8 27.4 - - + -
142R PHE* 3.9 29.4 - - + -
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Residues in contact with ARG 108 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104R GLY* 3.2 14.2 + - - +
105R ALA* 3.4 32.9 + - - +
106R GLU 3.3 0.2 - - - -
107R LEU* 1.3 79.0 - - + +
109R HIS* 1.3 68.1 + - + +
111R LEU* 3.4 1.7 + - - +
112R ALA* 3.1 24.9 + - - +
120R GLU* 3.7 25.4 + - - +
123R VAL* 3.6 20.2 - - + +
124R GLU* 5.3 7.2 - - - +
127R MET* 4.4 17.0 - - + -
131R GLU* 3.5 25.4 + - - +
137R ILE* 5.6 0.7 - - + -
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Residues in contact with HIS 109 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105R ALA* 3.0 39.1 + - + +
106R GLU* 4.2 2.4 - - - +
108R ARG* 1.3 83.7 + - + +
110R VAL* 1.3 59.5 + - + +
112R ALA* 3.3 3.5 + - + +
113R THR* 2.8 44.0 + - + +
120R GLU* 5.1 6.5 - - - -
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Residues in contact with VAL 110 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787P ILE* 6.3 1.6 - - + -
94R PHE* 3.7 27.8 - - + -
106R GLU* 3.0 20.5 + - - +
107R LEU* 3.9 5.2 - - + +
109R HIS* 1.3 78.0 - - + +
111R LEU* 1.3 58.6 + - - +
114R LEU* 2.9 68.1 + - + +
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Residues in contact with LEU 111 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791P GLN* 5.7 7.1 + - + +
794P CYS* 4.7 21.8 - - + -
107R LEU* 2.9 33.3 + - + +
108R ARG 3.9 3.6 - - - +
110R VAL* 1.3 78.4 - - + +
112R ALA* 1.3 58.7 + - - +
114R LEU 4.9 1.7 + - - +
116R GLU 4.0 4.4 - - - +
118R MET* 3.2 45.0 + - + +
123R VAL* 3.8 28.3 - - + -
126R LEU* 4.2 25.8 - - + -
127R MET* 5.3 1.6 - - - -
142R PHE* 5.9 2.2 - - + -
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Residues in contact with ALA 112 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108R ARG 3.1 16.1 + - - +
109R HIS* 4.0 3.8 - - + +
111R LEU* 1.3 80.3 - - - +
113R THR* 1.3 67.0 + - + +
114R LEU 3.8 0.4 - - - -
117R LYS* 3.3 29.7 - - - +
118R MET 3.1 19.8 + - - +
120R GLU* 3.7 19.7 - - + +
123R VAL* 4.4 1.8 - - + -
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Residues in contact with THR 113 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109R HIS* 2.8 27.1 + - + +
112R ALA* 1.3 87.2 - - + +
114R LEU* 1.3 77.4 + - - +
115R GLY 3.7 2.5 + - - -
117R LYS* 3.2 29.0 + - - +
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Residues in contact with LEU 114 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787P ILE* 4.6 13.9 - - + +
791P GLN* 2.1 29.6 + - - -
110R VAL* 2.9 52.7 + - + +
111R LEU* 4.8 1.6 + - - +
112R ALA 3.8 0.8 - - - -
113R THR* 1.3 95.2 - - - +
115R GLY* 1.3 52.5 - - - +
116R GLU 4.5 1.9 + - - +
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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