Contacts of the helix formed by residues 113 - 123 (chain Q) 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 LYS 113 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111Q SER 3.9 2.0 + - - +
112Q ILE* 1.3 75.6 - - + +
114Q LYS* 1.3 65.5 + - - +
115Q SER* 3.3 20.4 + - - +
116Q PHE* 3.1 27.6 + - + +
117Q LEU* 3.2 4.9 + - - +
146Q GLY 2.9 4.0 - - - -
147Q ASN* 3.0 11.8 - - - +
148Q VAL* 4.4 5.8 - - - -
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Residues in contact with LYS 114 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113Q LYS* 1.3 66.3 - - - +
115Q SER* 1.3 63.9 + - - +
118Q GLU* 3.1 36.8 + - - +
137Q TRP* 3.3 28.9 - - + +
146Q GLY* 1.8 31.5 + - - +
147Q ASN* 2.4 19.1 + - - -
148Q VAL* 4.3 6.7 - - + +
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Residues in contact with SER 115 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113Q LYS* 3.3 22.6 + - - +
114Q LYS* 1.3 79.7 - - - +
116Q PHE* 1.3 58.6 + - - +
118Q GLU* 3.2 15.0 - - - +
119Q GLU* 3.0 49.9 + - - +
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Residues in contact with PHE 116 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104Q LEU* 5.0 5.6 - - + -
112Q ILE* 3.5 31.4 - - + -
113Q LYS* 3.1 25.4 + - + +
115Q SER* 1.3 79.3 + - - +
117Q LEU* 1.3 58.9 + - + +
119Q GLU* 3.3 13.1 + - - +
120Q LEU* 2.9 60.3 + - + +
121R GLU* 4.7 16.2 - - - -
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Residues in contact with LEU 117 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101Q PHE* 5.2 11.2 - - + -
104Q LEU* 4.2 20.2 - - + -
112Q ILE* 3.5 32.3 - - + -
113Q LYS 3.2 2.0 + - - +
114Q LYS 3.3 0.2 + - - -
116Q PHE* 1.3 82.0 - - + +
118Q GLU* 1.3 54.7 + - - +
120Q LEU* 4.6 6.5 - - + -
121Q LEU* 3.0 33.9 + - - +
144Q VAL 5.0 0.4 - - - +
147Q ASN* 1.7 89.1 - - + +
150Q TYR* 5.7 1.1 - - + -
153Q ILE* 6.5 0.4 - - + -
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Residues in contact with GLU 118 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114Q LYS* 3.1 32.6 + - - +
115Q SER* 3.2 22.3 - - - +
116Q PHE 3.3 0.2 - - - -
117Q LEU* 1.3 76.6 - - - +
119Q GLU* 1.3 64.9 + - + +
122Q THR* 3.0 30.8 + - - -
133Q ILE* 3.5 32.4 - - + +
137Q TRP* 3.1 24.2 + - - +
147Q ASN* 4.1 3.6 - - - +
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Residues in contact with GLU 119 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115Q SER* 3.0 33.9 + - - +
116Q PHE* 3.7 12.2 - - - +
118Q GLU* 1.3 79.3 - - + +
120Q LEU* 1.3 56.9 + - - +
122Q THR* 3.8 1.5 - - - -
123Q THR* 2.8 45.0 + - + +
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Residues in contact with LEU 120 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809P ARG* 5.0 22.4 - - - +
813P ILE* 6.1 0.7 - - - +
104Q LEU* 3.7 31.2 - - + -
116Q PHE* 2.9 41.3 + - + +
117Q LEU* 4.2 6.7 - - + +
119Q GLU* 1.3 74.1 - - - +
121Q LEU* 1.3 66.3 + - - +
123Q THR* 3.7 9.0 - - - +
124Q GLY* 3.6 17.6 + - - +
128Q PHE* 4.5 1.6 - - - -
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Residues in contact with LEU 121 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117Q LEU 3.0 18.7 + - - +
118Q GLU 3.9 2.2 - - - +
120Q LEU* 1.3 74.7 - - - +
122Q THR* 1.3 60.5 + - - +
125Q GLY 2.9 12.6 + - - +
127Q ARG 4.3 5.2 - - - +
128Q PHE* 0.6 160.3 - - + +
132Q GLU* 5.9 1.6 - - + -
133Q ILE* 4.0 16.8 - - + +
136Q MET* 5.2 13.9 - - + -
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Residues in contact with THR 122 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118Q GLU 3.0 16.6 + - - -
119Q GLU* 3.8 3.4 - - - -
121Q LEU* 1.3 78.0 - - - +
123Q THR* 1.3 64.8 + - + +
124Q GLY 3.0 3.2 + - - -
125Q GLY 2.6 21.1 + - - +
128Q PHE 2.9 19.3 + - - -
129Q THR* 4.5 2.9 - - - -
130Q PRO* 3.9 22.7 - - + +
133Q ILE* 3.3 8.7 - - - +
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Residues in contact with THR 123 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119Q GLU* 2.8 39.8 + - + +
120Q LEU* 3.7 12.2 + - - +
122Q THR* 1.3 76.1 - - + +
124Q GLY* 1.2 58.3 + - - +
19R ARG* 4.2 25.4 + - - +
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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