Contacts of the helix formed by residues 119 - 128 (chain O) 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 THR 119 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117O LYS 4.0 2.4 + - - +
118O MET* 1.3 73.1 - - - +
120O GLU* 1.3 60.2 + - - +
121O GLU* 3.4 12.2 + - - +
122O GLU* 2.9 41.9 + - - +
123O VAL* 3.0 25.5 + - - +
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Residues in contact with GLU 120 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108O ARG* 3.7 32.5 + - - +
109O HIS* 5.1 6.4 - - - -
112O ALA* 3.7 21.9 - - + +
118O MET 3.6 1.0 + - - -
119O THR* 1.3 70.3 - - - +
121O GLU* 1.3 58.3 + - - +
123O VAL* 3.7 12.9 - - - +
124O GLU* 3.0 61.6 + - - +
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Residues in contact with GLU 121 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116N PHE* 5.0 13.9 - - - -
119O THR* 3.6 10.3 + - - +
120O GLU* 1.3 77.0 - - - +
122O GLU* 1.3 62.9 + - + +
124O GLU* 3.2 12.1 + - - +
125O GLU* 3.1 48.9 + - + +
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Residues in contact with GLU 122 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798M LEU* 3.4 33.1 - - + +
799M MET* 5.3 8.5 - - - +
802M GLU* 6.4 2.5 - - + -
118O MET* 4.0 9.1 - - + +
119O THR* 2.9 46.8 + - - +
121O GLU* 1.3 77.3 - - + +
123O VAL* 1.3 62.5 + - - +
125O GLU* 3.1 18.1 + - - +
126O LEU* 3.0 27.4 + - - +
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Residues in contact with VAL 123 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107O LEU 4.8 0.2 - - - +
108O ARG* 3.6 39.5 - - + +
111O LEU* 3.8 39.0 - - + -
112O ALA 4.3 0.4 - - - +
118O MET* 3.9 11.2 - - + +
119O THR 3.0 20.3 + - - +
120O GLU* 3.6 23.6 - - - +
121O GLU 3.3 0.2 - - - -
122O GLU* 1.3 74.3 - - - +
124O GLU* 1.3 62.2 + - - +
126O LEU* 3.1 9.6 + - - +
127O MET* 3.0 26.0 + - + +
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Residues in contact with GLU 124 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108O ARG* 5.3 7.0 - - - +
120O GLU* 3.0 50.5 + - - +
121O GLU* 3.2 8.2 + - - +
123O VAL* 1.3 75.3 - - - +
125O GLU* 1.3 59.1 + - + +
127O MET* 3.2 7.0 + - - +
128O LYS* 3.0 32.2 + - - +
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Residues in contact with GLU 125 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798M LEU* 6.0 0.3 - - - +
801M VAL* 5.6 7.7 - - + +
802M GLU* 4.9 18.0 - - - +
121O GLU* 3.1 35.8 + - + +
122O GLU* 3.1 29.1 + - - +
124O GLU* 1.3 76.7 - - + +
126O LEU* 1.3 64.8 + - + +
127O MET 3.8 0.2 + - - -
128O LYS* 4.1 35.6 + - - +
130O GLN* 5.3 0.2 - - - +
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Residues in contact with LEU 126 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794M CYS* 5.9 2.5 - - + -
797M PHE* 2.7 28.5 - - + -
798M LEU* 2.1 77.2 - - + +
801M VAL* 4.5 9.6 - - + -
111O LEU* 4.2 16.6 - - + -
122O GLU 3.0 11.3 + - - +
123O VAL* 3.1 5.8 + - - +
125O GLU* 1.3 84.7 - - + +
127O MET* 1.3 64.4 + - - +
128O LYS 3.5 0.4 - - - -
130O GLN* 3.1 24.2 + - - +
142O PHE* 3.2 14.2 - - + -
146O ILE* 4.4 3.4 - - + +
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Residues in contact with MET 127 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107O LEU* 3.9 22.0 - - + -
108O ARG* 4.4 13.0 - - + +
111O LEU* 5.3 1.3 - - - -
123O VAL* 3.0 29.9 + - + +
124O GLU* 3.2 5.1 + - - +
126O LEU* 1.3 85.0 - - - +
128O LYS* 1.3 57.9 + - - +
129O GLY 3.0 9.5 + - - -
130O GLN* 3.0 12.4 - - - +
131O GLU* 3.1 34.0 + - + +
137O ILE* 3.5 48.7 - - + -
142O PHE* 3.7 21.5 - - + -
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Residues in contact with LYS 128 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106N PRO* 6.6 0.2 - - + -
124O GLU 3.0 16.4 + - - +
125O GLU* 4.1 33.4 + - + +
126O LEU 3.5 0.8 - - - -
127O MET* 1.3 72.7 - - - +
129O GLY* 1.3 58.3 + - - +
130O GLN* 3.4 7.5 + - - +
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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