Contacts of the helix formed by residues 81 - 111 (chain C) in PDB entry 1M7L
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 81 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C LEU* 1.3 66.6 + - - -
83C PRO* 3.5 5.8 - - - -
84C ASP* 3.4 19.0 + - - +
85C VAL* 3.1 24.7 + - - +
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Residues in contact with LEU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C GLY* 1.3 67.7 - - - -
83C PRO* 1.4 68.9 - - + +
85C VAL* 2.8 41.2 + - + +
86C ALA* 3.3 4.3 + - - +
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Residues in contact with PRO 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C GLY* 3.7 4.0 - - - -
82C LEU* 1.4 95.5 - - + +
84C ASP* 1.3 53.1 + - - +
86C ALA* 3.2 9.6 + - + +
87C SER* 2.6 36.1 + - - +
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Residues in contact with ASP 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C GLY 3.4 21.4 + - - +
82C LEU 3.2 0.8 - - - -
83C PRO* 1.3 76.2 - - - +
85C VAL* 1.3 66.7 + - - +
87C SER* 3.3 13.1 - - - -
88C LEU* 2.9 25.3 + - - +
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Residues in contact with VAL 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 5.8 0.2 - - - +
81C GLY 3.1 18.2 - - - +
82C LEU* 2.8 22.9 + - + +
84C ASP* 1.3 81.6 - - + +
86C ALA* 1.3 58.2 + - - +
88C LEU* 3.1 4.2 + - - -
89C ARG* 2.7 57.5 + - - +
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Residues in contact with ALA 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C LEU 3.3 3.5 + - - +
83C PRO* 3.2 9.3 + - + +
85C VAL* 1.3 80.9 - - + +
87C SER* 1.3 56.8 + - - +
89C ARG* 3.0 34.3 + - + +
90C GLN* 3.5 6.8 + - - +
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Residues in contact with SER 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C PRO* 2.6 26.0 + - - +
84C ASP* 3.0 20.0 + - - -
86C ALA* 1.3 72.4 - - - +
88C LEU* 1.3 62.9 + - - +
89C ARG 3.1 1.8 - - - -
90C GLN* 2.8 41.0 + - - +
91C GLN* 3.1 10.6 + - - +
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Residues in contact with LEU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 4.0 31.0 - - + +
12A VAL* 4.7 13.5 - - + -
84C ASP* 2.9 13.1 + - - +
85C VAL* 3.1 12.5 + - - +
87C SER* 1.3 78.4 - - - +
89C ARG* 1.3 74.8 + - - +
91C GLN* 3.4 33.2 + - + +
92C VAL* 2.9 43.5 + - + +
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Residues in contact with ARG 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 3.6 25.1 - - - +
45B VAL* 5.9 0.2 - - - +
48B LEU* 4.0 26.3 - - + +
49B ARG* 3.7 16.1 - - - +
85C VAL* 2.7 52.5 + - - +
86C ALA* 3.0 18.7 + - + +
88C LEU* 1.3 105.2 - - - +
90C GLN* 1.3 57.7 + - - +
91C GLN 3.2 0.2 - - - -
92C VAL* 2.9 30.4 - - + +
93C GLU* 3.0 16.7 + - - +
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Residues in contact with GLN 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ALA 3.5 3.0 + - - +
87C SER* 2.8 43.4 + - - +
89C ARG* 1.3 75.6 - - - +
91C GLN* 1.3 60.9 + - - +
93C GLU* 3.1 22.2 + - - +
94C ALA* 3.0 24.8 + - - +
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Residues in contact with GLN 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 5.4 2.2 - - - +
13A GLU* 6.1 0.2 - - - +
16A GLN* 3.9 24.2 + - - +
87C SER 3.1 13.9 + - - +
88C LEU* 3.5 32.1 - - - +
89C ARG 3.2 0.2 - - - -
90C GLN* 1.3 78.7 - - - +
92C VAL* 1.3 56.7 + - - +
94C ALA* 3.1 13.0 - - + +
95C LEU* 3.1 22.9 + - - +
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Residues in contact with VAL 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 5.0 17.9 - - + -
48B LEU* 4.8 20.0 - - + -
51B GLN* 5.8 0.9 - - - +
52B VAL* 5.2 13.2 - - + -
55B LEU* 4.1 8.2 - - + +
88C LEU* 2.9 38.2 + - + +
89C ARG* 2.9 29.3 + - + +
91C GLN* 1.3 74.0 - - - +
93C GLU* 1.3 64.0 + - + +
94C ALA 3.1 1.3 - - - -
95C LEU* 3.2 14.1 + - + +
96C GLN* 3.0 31.7 + - - +
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Residues in contact with GLU 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ARG* 3.0 17.2 + - - +
90C GLN* 3.1 28.4 + - - +
92C VAL* 1.3 78.3 - - + +
94C ALA* 1.3 58.0 + - - +
96C GLN* 2.9 39.0 + - - +
97C GLY* 3.0 12.1 + - - -
100C GLN* 5.0 0.5 + - - -
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Residues in contact with ALA 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C GLN 3.0 11.7 + - - +
91C GLN* 3.1 17.7 - - + +
93C GLU* 1.3 76.4 - - - +
95C LEU* 1.3 60.1 + - - +
97C GLY* 3.0 15.7 + - - +
98C GLN* 3.0 21.7 + - + +
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Residues in contact with LEU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 4.2 13.5 - - + +
15A LEU* 3.9 33.0 - - + +
16A GLN* 3.5 26.7 - - + +
19A VAL* 3.4 34.1 - - + -
55B LEU* 3.9 11.9 - - + -
91C GLN 3.1 9.2 + - - +
92C VAL* 3.2 15.2 + - + +
94C ALA* 1.3 80.3 - - - +
96C GLN* 1.3 60.1 + - - +
98C GLN* 3.3 8.9 + - + +
99C VAL* 3.3 20.6 + - - +
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Residues in contact with GLN 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B GLN* 4.0 22.1 + - - +
55B LEU* 3.5 21.0 - - + +
92C VAL* 3.0 13.4 + - - +
93C GLU* 2.9 49.8 - - - +
95C LEU* 1.3 74.5 - - - +
97C GLY* 1.3 59.6 + - - +
99C VAL* 3.1 11.8 - - + +
100C GLN* 3.0 37.3 + - - +
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Residues in contact with GLY 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C GLU 3.0 13.4 + - - -
94C ALA* 3.0 7.0 + - - -
96C GLN* 1.3 80.1 - - - +
98C GLN* 1.3 56.9 + - - +
100C GLN* 3.0 33.5 - - - +
101C HIS* 2.9 17.7 + - - +
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Residues in contact with GLN 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A VAL* 4.1 18.2 - - + -
23A GLN* 5.2 6.9 - - - +
94C ALA* 3.0 17.9 + - - +
95C LEU* 3.5 12.6 - - + +
97C GLY* 1.3 77.6 - - - +
99C VAL* 1.3 58.6 + - - +
101C HIS* 2.7 48.0 + - - -
102C LEU* 3.0 21.2 + - + +
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Residues in contact with VAL 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL* 4.2 10.5 - - + +
55B LEU* 3.4 29.4 - - + -
58B GLN* 4.2 22.0 - - + -
59B VAL* 4.2 21.1 - - + +
62B LEU* 4.0 17.9 - - + +
95C LEU 3.3 4.8 + - - +
96C GLN* 3.1 17.9 - - + +
98C GLN* 1.3 81.0 - - - +
100C GLN* 1.3 59.3 + - + +
102C LEU* 3.8 6.1 - - + +
103C GLN* 3.0 27.4 + - - +
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Residues in contact with GLN 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C GLU 5.0 0.6 + - - -
96C GLN* 3.0 22.4 + - - +
97C GLY* 3.0 38.1 - - - +
99C VAL* 1.3 80.1 - - + +
101C HIS* 1.3 58.8 + - + +
103C GLN* 3.4 7.7 + - - +
104C ALA* 3.0 23.4 + - - +
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Residues in contact with HIS 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLN* 5.3 2.6 - - - +
97C GLY 2.9 15.8 + - - +
98C GLN* 2.7 56.6 + - - -
100C GLN* 1.3 80.9 - - + +
102C LEU* 1.3 75.3 + - + +
103C GLN 3.3 0.2 - - - -
104C ALA* 3.0 12.3 - - + +
105C ALA* 3.0 26.6 + - + +
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Residues in contact with LEU 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL* 4.0 20.9 - - + +
22A LEU* 4.6 4.7 - - + -
23A GLN* 3.7 46.2 - - + +
26A PHE* 3.2 30.2 - - + -
62B LEU* 4.6 7.4 - - + -
98C GLN* 3.0 14.7 + - + +
99C VAL* 3.8 6.5 - - - +
100C GLN 3.2 0.2 - - - -
101C HIS* 1.3 113.6 - - + +
103C GLN* 1.3 61.1 + - - +
104C ALA 3.2 0.2 - - - -
105C ALA* 4.8 1.8 - - + -
106C PHE* 2.9 27.9 + - - +
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Residues in contact with GLN 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLN* 5.2 8.1 - - - +
61B HIS* 5.3 1.8 - - - +
62B LEU* 3.7 30.9 - - + +
99C VAL 3.0 17.3 + - - +
100C GLN* 3.6 7.6 - - - +
102C LEU* 1.3 74.5 - - - +
104C ALA* 1.3 60.3 + - - +
106C PHE* 3.3 7.4 - - - +
107C SER* 2.9 21.9 + - - -
110C LYS* 2.8 34.7 + - - +
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Residues in contact with ALA 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C GLN 3.0 14.8 + - - +
101C HIS* 3.0 19.3 - - + +
103C GLN* 1.3 75.5 - - - +
105C ALA* 1.3 63.5 + - - +
107C SER* 3.0 22.6 + - - -
108C GLN* 4.1 4.3 + - - +
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Residues in contact with ALA 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PHE* 4.4 7.0 - - + -
30A LYS* 6.2 3.6 - - + -
101C HIS* 3.0 12.1 + - + +
102C LEU* 4.1 4.9 - - + +
104C ALA* 1.3 79.3 - - - +
106C PHE* 1.3 62.3 + - - +
108C GLN* 3.0 18.8 + - - +
109C TYR* 2.9 36.3 - - + +
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Residues in contact with PHE 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PHE* 3.5 22.4 - + - -
62B LEU* 3.2 49.8 - - + -
65B ALA* 4.5 3.8 - - + -
66B PHE* 3.5 40.4 - + - -
69B TYR* 3.3 37.9 - + + -
102C LEU* 2.9 19.1 + - + +
103C GLN* 3.3 13.2 - - - +
104C ALA 3.2 0.2 - - - -
105C ALA* 1.3 77.3 - - - +
107C SER* 1.3 52.0 + - - +
109C TYR* 3.6 7.2 - - + -
110C LYS* 2.5 45.2 + - + +
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Residues in contact with SER 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C GLN* 2.9 13.9 + - - -
104C ALA* 3.0 17.0 + - - -
106C PHE* 1.3 75.9 - - - +
108C GLN* 1.3 62.3 + - - +
110C LYS* 3.4 31.0 + - - +
111C LYS* 3.6 12.3 - - - +
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Residues in contact with GLN 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLU* 3.2 31.0 + - - +
104C ALA 4.7 5.2 - - - +
105C ALA* 3.0 14.8 + - - +
107C SER* 1.3 76.1 - - - +
109C TYR* 1.3 69.0 + - + +
110C LYS 3.1 5.1 + - - -
111C LYS* 3.2 43.1 + - - +
112C VAL* 3.3 1.6 - - - +
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Residues in contact with TYR 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PHE* 3.2 28.9 - + + -
29A TYR* 3.3 17.3 - - + +
30A LYS* 2.8 46.1 + - + +
32A VAL* 5.0 0.7 - - + -
33A GLU* 4.0 26.9 - - + -
69B TYR* 3.3 17.6 - - + +
105C ALA* 2.9 42.6 - - + +
106C PHE* 3.1 14.3 + - + +
108C GLN* 1.3 79.4 - - + +
110C LYS* 1.3 60.7 + - - +
111C LYS 3.3 0.7 - - - -
112C VAL* 3.0 27.2 + - + +
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Residues in contact with LYS 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ALA* 6.2 3.4 - - + -
69B TYR* 2.8 45.8 + - + +
103C GLN* 2.8 36.0 + - - +
106C PHE* 2.5 28.3 + - + +
107C SER* 3.4 24.5 + - - +
108C GLN 3.1 0.4 - - - -
109C TYR* 1.3 74.9 - - - +
111C LYS* 1.3 57.7 + - + +
112C VAL 3.2 1.1 + - - -
113C GLU 4.3 3.8 + - - +
114C LEU* 5.0 0.5 - - - +
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Residues in contact with LYS 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLU* 2.6 29.3 + - - +
107C SER 3.6 10.5 - - - +
108C GLN* 3.2 35.7 - - - +
109C TYR 3.3 0.2 - - - -
110C LYS* 1.3 77.0 - - + +
112C VAL* 1.3 57.6 - - - +
114C LEU* 3.2 34.8 - - + +
115C PHE* 4.6 5.2 - - - -
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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