Contacts of the helix formed by residues 108 - 133 (chain M) in PDB entry 5MS0
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 GLN 108 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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906C PHE 2.8 18.5 - - - +
907C GLY* 3.9 4.9 - - - -
908C GLU 5.7 0.4 - - - +
909C LYS* 3.9 25.1 - - + +
910C ALA* 4.9 4.7 - - + -
106M THR* 3.0 11.6 + - - +
107M THR* 1.3 77.5 - - - +
109M THR* 1.3 57.0 + - - +
110M ALA 3.1 1.7 - - - +
111M LYS* 2.7 30.0 + - + +
112M GLN 3.2 4.2 + - - -
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Residues in contact with THR 109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905C ILE 3.8 2.6 - - - +
906C PHE* 3.2 17.2 + - - -
910C ALA* 5.7 0.8 - - - +
30M ALA* 5.4 4.9 - - - +
106M THR* 4.7 14.3 - - - -
108M GLN* 1.3 74.3 - - - +
110M ALA* 1.3 58.2 + - - -
113M VAL* 3.0 34.0 + - - +
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Residues in contact with ALA 110 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5M ILE* 6.0 5.8 - - + -
30M ALA* 5.5 7.2 - - + +
107M THR* 4.5 15.9 - - - +
108M GLN 4.0 1.0 - - - +
109M THR* 1.3 77.8 - - - +
111M LYS* 1.4 62.7 - - - +
113M VAL* 3.2 4.2 + - - +
114M ILE* 2.9 25.1 + - - +
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Residues in contact with LYS 111 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908C GLU* 5.1 13.2 - - + +
5M ILE* 6.5 0.7 - - - -
107M THR 4.7 3.1 + - - +
108M GLN* 2.7 24.8 + - + +
110M ALA* 1.4 74.1 - - - +
112M GLN* 1.3 59.8 + - + +
114M ILE* 3.3 9.7 - - - +
115M VAL* 3.1 20.3 + - - +
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Residues in contact with GLN 112 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903C ARG 5.4 1.1 - - - +
904C ALA* 2.9 32.8 - - - +
905C ILE 3.1 12.2 - - - +
906C PHE 3.5 2.0 + - - +
907C GLY* 3.5 33.0 - - - +
908C GLU 4.6 1.6 - - - +
108M GLN 3.2 5.7 + - - -
111M LYS* 1.3 75.8 - - - +
113M VAL* 1.3 61.7 + - - +
115M VAL* 3.6 13.2 - - + -
116M GLN* 3.0 12.1 + - - +
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Residues in contact with VAL 113 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905C ILE* 3.2 6.0 + - + +
26M ALA* 5.2 8.3 - - + +
30M ALA* 4.6 20.2 - - + -
109M THR 3.0 22.9 + - - +
110M ALA* 3.9 2.5 - - - +
112M GLN* 1.3 78.3 - - - +
114M ILE* 1.3 58.7 + - - +
116M GLN* 3.3 8.1 + - + +
117M LYS* 2.9 28.2 + - - +
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Residues in contact with ILE 114 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9M VAL* 5.7 10.1 - - + -
26M ALA* 5.9 2.9 - - - +
110M ALA 2.9 13.4 + - - +
111M LYS* 3.3 12.8 - - - +
113M VAL* 1.3 75.0 - - - +
115M VAL* 1.3 63.7 + - - +
117M LYS* 3.2 6.6 + - - +
118M VAL* 3.0 26.0 + - - +
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Residues in contact with VAL 115 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904C ALA* 4.4 6.1 - - + +
111M LYS 3.1 9.1 + - - +
112M GLN* 3.7 22.2 - - + +
113M VAL 3.4 0.4 - - - -
114M ILE* 1.3 76.0 - - - +
116M GLN* 1.3 62.1 + - - +
118M VAL* 4.4 4.1 - - - +
119M ARG* 3.5 19.8 + - - +
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Residues in contact with GLN 116 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904C ALA* 3.8 12.0 + - - +
905C ILE* 4.8 7.4 - - + -
112M GLN 3.0 16.0 + - - +
113M VAL* 3.5 11.4 - - - +
114M ILE 3.2 0.2 - - - -
115M VAL* 1.3 77.1 - - - +
117M LYS* 1.3 57.6 + - - +
119M ARG* 3.2 7.6 + - - +
120M GLU* 3.0 27.6 + - - +
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Residues in contact with LYS 117 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22M LYS* 5.6 7.6 - - + +
23M ILE* 6.3 0.7 - - + -
26M ALA* 4.6 17.7 - - + -
113M VAL 2.9 16.3 + - - +
114M ILE* 3.2 5.8 + - - +
116M GLN* 1.3 76.9 - - - +
118M VAL* 1.3 58.8 + - - +
120M GLU* 3.9 4.5 - - - +
121M ALA* 2.9 30.1 + - - +
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Residues in contact with VAL 118 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M VAL* 6.2 4.0 - - + -
114M ILE 3.0 15.2 + - - +
115M VAL* 4.5 4.9 - - - +
117M LYS* 1.3 78.0 - - - +
119M ARG* 1.3 57.6 + - - +
121M ALA* 3.8 5.4 - - - +
122M GLU* 3.0 27.5 + - - +
71N LEU* 5.4 10.8 - - + +
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Residues in contact with ARG 119 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115M VAL 3.5 12.5 + - - +
116M GLN* 3.2 10.8 + - - +
118M VAL* 1.3 79.1 - - - +
120M GLU* 1.3 56.1 + - - +
122M GLU* 3.3 8.9 - - - +
123M ARG* 2.9 25.1 + - - +
191M ARG* 6.0 6.1 - - + -
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Residues in contact with GLU 120 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116M GLN 3.0 15.7 + - - +
117M LYS* 4.3 4.3 - - - +
119M ARG* 1.3 74.8 - - - +
121M ALA* 1.3 60.0 + - - +
123M ARG* 3.4 11.7 + - + +
124M ALA* 2.9 24.9 + - - +
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Residues in contact with ALA 121 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22M LYS* 6.2 4.5 - - + -
117M LYS 2.9 18.4 + - - +
118M VAL* 3.8 6.7 - - - +
119M ARG 3.3 0.2 - - - -
120M GLU* 1.3 76.1 - - - +
122M GLU* 1.3 64.6 + - - +
124M ALA* 3.0 18.8 + - - +
125M MET* 3.0 14.7 + - - +
67N ILE* 5.7 0.4 - - - +
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Residues in contact with GLU 122 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118M VAL 3.0 15.8 + - - +
119M ARG* 3.3 13.5 - - - +
121M ALA* 1.3 75.2 - - - +
123M ARG* 1.3 56.0 + - - +
125M MET* 3.4 2.4 + - - +
126M VAL* 3.0 30.3 + - - +
64N HIS* 5.4 0.7 - - - +
67N ILE* 5.1 15.1 - - + +
68N GLU* 6.1 1.1 - - - -
71N LEU* 4.7 17.3 - - + -
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Residues in contact with ARG 123 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119M ARG 2.9 15.7 + - - +
120M GLU* 3.4 14.6 - - - +
121M ALA 3.2 0.2 - - - -
122M GLU* 1.3 75.5 - - - +
124M ALA* 1.3 57.1 + - - +
126M VAL* 3.5 6.6 + - - +
127M VAL* 2.9 30.0 + - - +
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Residues in contact with ALA 124 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120M GLU 2.9 14.2 + - - +
121M ALA* 3.0 14.1 + - - +
123M ARG* 1.3 76.7 - - - +
125M MET* 1.3 58.0 + - - +
127M VAL* 3.2 8.9 + - - +
128M ASP* 2.9 23.0 + - - +
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Residues in contact with MET 125 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M LYS* 6.2 3.6 - - + -
121M ALA 3.0 13.5 + - - +
122M GLU 4.3 0.9 - - - +
124M ALA* 1.3 73.9 - - - +
126M VAL* 1.3 61.3 + - - +
128M ASP* 3.0 24.7 + - + +
129M GLN 3.0 12.0 + - - -
63N TYR 5.1 3.4 - - - +
64N HIS* 3.4 17.3 + - + +
67N ILE* 4.3 23.1 - - + -
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Residues in contact with VAL 126 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122M GLU 3.0 19.0 + - - +
123M ARG* 3.8 7.4 - - - +
125M MET* 1.3 76.3 - - - +
127M VAL* 1.3 55.2 + - - +
129M GLN* 3.4 5.7 + - - +
130M PHE* 3.0 25.3 + - - +
192M GLY 5.2 3.8 - - - +
193M ALA* 4.5 21.3 - - + -
64N HIS* 3.8 14.1 - - + +
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Residues in contact with VAL 127 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123M ARG 2.9 18.2 + - - +
124M ALA* 3.4 8.7 - - - +
126M VAL* 1.3 75.5 - - - +
128M ASP* 1.3 57.1 + - - +
130M PHE* 3.0 11.3 + - + +
131M ARG* 2.8 27.7 + - - +
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Residues in contact with ASP 128 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124M ALA 2.9 12.7 + - - +
125M MET* 3.0 15.6 + - + +
127M VAL* 1.3 73.4 - - - +
129M GLN* 1.3 63.2 + - - +
131M ARG* 3.2 9.5 + - - +
132M GLU* 3.0 21.3 + - - +
63N TYR* 6.1 4.5 - - + -
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Residues in contact with GLN 129 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125M MET 3.0 11.5 + - - +
126M VAL* 3.8 7.2 - - - +
128M ASP* 1.3 75.3 - - - +
130M PHE* 1.3 59.1 + - - +
132M GLU* 2.9 23.1 + - - +
133M HIS* 3.2 16.9 + - + +
62N GLU* 6.1 0.9 - - - -
63N TYR* 5.1 10.2 - - - +
64N HIS* 4.6 18.1 - - + +
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Residues in contact with PHE 130 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126M VAL 3.0 15.4 + - - +
127M VAL* 3.0 15.0 + - - +
129M GLN* 1.3 76.2 - - - +
131M ARG* 1.3 56.8 + - - +
133M HIS 5.9 0.2 - - - -
134M GLU* 3.4 25.6 - - - +
186M VAL* 5.3 13.7 - - + -
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Residues in contact with ARG 131 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127M VAL 2.8 10.6 + - - +
128M ASP* 3.5 11.0 - - - +
129M GLN 3.1 0.2 - - - -
130M PHE* 1.3 79.2 - - - +
132M GLU* 1.3 63.3 + - - +
133M HIS 3.3 1.4 + - - -
134M GLU* 4.0 10.3 + - - +
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Residues in contact with GLU 132 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128M ASP 3.0 13.6 + - - +
129M GLN* 2.9 10.3 + - - +
131M ARG* 1.3 77.5 - - - +
133M HIS* 1.3 58.5 + - + +
134M GLU 3.8 0.2 - - - -
50N SER 5.2 6.2 - - - +
51N ALA* 5.4 6.8 - - - +
60N VAL* 5.3 15.8 - - + +
63N TYR* 6.3 2.5 - - + -
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Residues in contact with HIS 133 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129M GLN* 3.2 12.2 + - + +
130M PHE* 5.9 0.2 - - - -
132M GLU* 1.3 79.9 - - + +
134M GLU* 1.3 60.3 + - - +
135M GLY* 3.3 0.7 - - - -
136M GLU* 2.8 37.3 + - + +
138M ILE* 6.5 1.1 - - + -
183M LEU* 4.1 10.6 - - + +
51N ALA* 6.3 0.7 - - - -
61N ALA 6.2 0.2 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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