Contacts of the helix formed by residues 104 - 114 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102L VAL 3.4 1.4 + - - -
103L MET* 1.3 73.1 - - - +
105L ALA* 1.3 60.8 + - - +
106L GLU 3.1 0.5 + - - -
107L LEU* 3.1 13.2 + - - +
108L ARG* 3.2 25.3 + - - +
131L GLU* 3.1 26.2 - - - -
135L GLY* 2.9 13.8 + - - -
137L ILE* 3.6 9.3 - - - +
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Residues in contact with ALA 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103L MET* 3.4 1.8 - - + +
104L GLY* 1.3 74.8 - - - +
106L GLU* 1.3 62.9 + - + +
108L ARG* 3.7 26.5 - - - +
109L HIS* 3.0 52.5 + - + +
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Residues in contact with GLU 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94L PHE* 3.8 32.5 - - + +
95L ASP* 5.1 3.5 - - - +
96L LYS* 5.8 1.8 + - - -
102L VAL* 3.8 5.6 - - + +
103L MET* 2.9 55.9 + - + +
105L ALA* 1.3 76.9 - - + +
107L LEU* 1.3 58.6 + - - +
109L HIS* 4.1 2.3 - - - +
110L VAL* 3.0 33.9 + - - +
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Residues in contact with LEU 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91L LEU* 4.7 13.9 - - + -
94L PHE* 4.4 5.2 - - + -
102L VAL* 3.6 30.3 - - + -
103L MET 3.5 0.8 + - - -
104L GLY 3.1 1.4 + - - -
106L GLU* 1.3 78.1 - - - +
108L ARG* 1.3 58.7 + - - +
110L VAL* 3.4 5.0 + - + +
111L LEU* 2.9 45.7 + - + +
127L MET* 3.9 22.9 - - + -
137L ILE* 3.8 26.9 - - + -
139L TYR* 5.6 0.2 - - + -
142L PHE* 3.9 29.6 - - + -
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Residues in contact with ARG 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104L GLY* 3.2 14.4 + - - +
105L ALA* 3.7 32.8 - - - +
106L GLU 3.3 0.2 - - - -
107L LEU* 1.3 79.1 - - + +
109L HIS* 1.3 70.1 + - + +
111L LEU* 3.9 1.9 - - - +
112L ALA* 3.1 24.6 + - - +
120L GLU* 3.7 25.7 + - - +
123L VAL* 3.6 18.8 - - + +
124L GLU* 5.3 8.1 - - - +
127L MET* 4.4 17.0 - - + -
131L GLU* 3.5 25.6 + - - +
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Residues in contact with HIS 109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105L ALA* 3.0 40.7 + - + +
106L GLU* 4.2 2.0 - - - +
108L ARG* 1.3 84.2 + - + +
110L VAL* 1.3 59.2 + - + +
112L ALA* 3.3 3.7 + - + -
113L THR* 2.8 43.6 + - + +
120L GLU* 5.1 7.0 - - - -
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Residues in contact with VAL 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94L PHE* 3.7 26.7 - - + -
106L GLU* 3.0 19.6 + - - +
107L LEU* 3.9 5.2 - - + +
109L HIS* 1.3 79.2 - - + +
111L LEU* 1.3 59.2 + - + +
114L LEU* 2.9 66.3 + - + +
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Residues in contact with LEU 111 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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794J CYS* 4.6 22.4 - - + -
797J PHE* 5.9 0.2 - - + -
798J LEU* 4.7 3.4 - - + -
107L LEU* 2.9 33.0 + - + +
108L ARG 3.9 3.1 - - - +
110L VAL* 1.3 79.0 - - + +
112L ALA* 1.3 59.2 + - - +
114L LEU 4.8 1.4 + - - +
116L GLU 4.0 4.6 - - - +
118L MET* 3.2 40.4 + - + +
123L VAL* 3.8 28.7 - - + -
126L LEU* 4.2 25.8 - - + -
127L MET* 5.3 1.1 - - - -
142L PHE* 5.9 2.7 - - + -
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Residues in contact with ALA 112 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108L ARG 3.1 16.9 + - - +
109L HIS* 4.0 3.8 - - + +
111L LEU* 1.3 79.8 - - - +
113L THR* 1.3 65.5 - - + +
114L LEU 3.8 0.2 - - - -
117L LYS* 3.3 29.5 - - - +
118L MET 3.1 20.1 + - - +
120L GLU* 3.7 19.7 - - + +
123L VAL* 4.4 1.6 - - + -
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Residues in contact with THR 113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109L HIS* 2.8 28.4 + - + +
112L ALA* 1.3 87.1 - - + +
114L LEU* 1.3 76.6 + - - +
115L GLY 3.7 2.6 + - - -
117L LYS* 3.2 28.2 + - - +
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Residues in contact with LEU 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787J ILE* 6.1 1.1 - - - +
791J GLN* 4.2 2.9 + - - +
110L VAL* 2.9 53.5 + - + +
111L LEU 4.8 1.5 - - - +
112L ALA 3.8 1.0 - - - -
113L THR* 1.3 93.4 - - - +
115L GLY* 1.3 61.5 + - - +
116L GLU 3.7 6.0 + - - +
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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