Contacts of the helix formed by residues 92 - 119 (chain P) in PDB entry 1MFR
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 92 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P PHE* 3.6 19.5 - - - -
44P LEU* 3.8 8.5 - - - +
47P VAL* 4.1 17.7 - - + +
91P ASN* 1.3 73.0 - - - +
93P LEU* 1.3 57.5 + - - +
95P ALA* 3.6 1.4 + - - +
96P MET* 3.0 37.2 + - + +
151P LEU* 4.1 7.9 - - + -
156P LEU* 4.0 7.9 - - - -
163P GLU* 2.8 30.4 + - - +
166P PHE* 3.8 35.2 - - + -
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Residues in contact with LEU 93 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91P ASN* 2.9 10.6 + - - +
92P THR* 1.3 74.3 - - - +
94P GLU* 1.3 62.1 + - - +
96P MET* 3.3 1.8 + - - +
97P GLN* 2.9 52.5 + - + +
148P ILE* 3.9 30.3 - - + +
151P LEU* 3.9 24.5 - - + -
152P LYS* 4.3 15.9 - - + -
156P LEU* 3.4 18.6 - - + +
157P PRO* 3.7 35.0 - - + -
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Residues in contact with GLU 94 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86P ARG* 3.0 40.0 + - - +
89P TRP 3.4 12.1 - - - +
90P GLY* 3.7 8.0 - - - -
91P ASN* 3.1 26.6 + - - +
93P LEU* 1.3 80.1 - - - +
95P ALA* 1.3 58.9 + - - +
97P GLN* 3.5 14.5 + - - +
98P ALA* 3.0 26.3 + - - +
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Residues in contact with ALA 95 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P MET* 3.8 10.2 - - - +
37P PHE* 3.7 27.8 - - + -
51P PHE* 4.1 11.2 - - + -
89P TRP* 3.7 17.2 + - + -
91P ASN 3.0 17.5 + - - +
92P THR 3.9 2.5 - - - +
94P GLU* 1.3 74.9 - - - +
96P MET* 1.3 60.3 + - - +
98P ALA* 3.4 7.3 + - - +
99P ALA* 2.9 27.4 + - - +
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Residues in contact with MET 96 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47P VAL* 4.6 3.8 - - + -
50P PHE* 4.0 17.0 - - + -
51P PHE* 3.7 29.8 - - + -
92P THR* 3.0 27.0 + - + +
93P LEU 3.3 3.8 + - - +
95P ALA* 1.3 74.3 - - - +
97P GLN* 1.3 62.1 + - - +
99P ALA* 3.3 2.3 + - - +
100P LEU* 2.8 23.7 + - - +
144P ILE* 3.4 20.4 - - + +
147P PHE* 3.9 33.4 - - + -
148P ILE* 3.7 18.3 - - + +
151P LEU* 3.8 16.8 - - + -
166P PHE* 4.3 16.4 - - + -
171P VAL* 5.3 1.1 - - + -
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Residues in contact with GLN 97 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93P LEU* 2.9 41.5 + - + +
94P GLU* 3.8 15.8 - - - +
96P MET* 1.3 74.0 - - - +
98P ALA* 1.3 64.3 + - - +
100P LEU* 3.3 3.6 + - - +
101P GLN* 3.1 25.1 + - - +
148P ILE* 4.0 21.7 - - + +
152P LYS* 4.1 21.7 + - - -
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Residues in contact with ALA 98 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P MET* 4.0 4.7 - - + -
85P GLU* 5.4 4.5 - - - +
86P ARG* 5.6 2.5 - - - +
89P TRP* 3.8 32.5 - - + -
94P GLU 3.0 15.3 + - - +
95P ALA 3.5 8.7 - - - +
97P GLN* 1.3 75.8 - - - +
99P ALA* 1.3 58.1 + - - +
101P GLN* 3.4 6.4 + - - +
102P LEU* 3.0 27.2 + - - +
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Residues in contact with ALA 99 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30P TYR* 3.9 28.2 + - + +
33P MET* 4.2 5.6 - - + +
51P PHE* 4.2 8.3 - - + -
95P ALA 2.9 17.9 + - - +
96P MET* 3.5 9.4 - - - +
97P GLN 3.2 0.2 - - - -
98P ALA* 1.3 73.8 - - - +
100P LEU* 1.3 60.1 + - - +
102P LEU* 3.2 5.6 + - - +
103P GLU* 2.9 34.2 + - - +
144P ILE* 4.1 12.8 - - + -
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Residues in contact with LEU 100 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K GLN* 3.8 37.7 - - + +
4K VAL* 5.0 0.9 - - + -
96P MET 2.8 20.0 + - - +
97P GLN* 3.3 6.0 + - - +
99P ALA* 1.3 72.2 - - - +
101P GLN* 1.3 59.5 + - + +
103P GLU* 3.4 4.0 + - - +
104P LYS* 3.0 42.6 + - + +
141P ILE* 3.9 41.5 - - + +
144P ILE* 3.9 11.6 - - + +
145P GLY* 4.5 3.6 - - - +
148P ILE* 3.7 22.7 - - + -
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Residues in contact with GLN 101 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97P GLN 3.1 12.5 + - - +
98P ALA* 3.7 9.4 - - - +
100P LEU* 1.3 76.9 - - + +
102P LEU* 1.3 61.9 + - - +
104P LYS* 3.2 10.7 + - - +
105P THR* 2.9 34.1 + - - +
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Residues in contact with LEU 102 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22P LEU* 5.4 2.0 - - + -
25P TYR* 4.1 27.1 - - + -
26P ALA* 3.9 25.8 - - + +
29P THR* 3.7 29.2 - - + -
30P TYR* 3.9 32.5 - - + +
33P MET* 5.2 0.2 - - + -
98P ALA 3.0 17.6 + - - +
99P ALA* 3.2 6.0 + - - +
101P GLN* 1.3 76.4 - - - +
103P GLU* 1.3 58.8 + - + +
105P THR* 3.4 10.2 + - + -
106P VAL* 3.1 35.7 + - + +
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Residues in contact with GLU 103 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P ALA* 6.5 0.4 - - - -
30P TYR* 2.8 28.9 + - - +
54P HIS* 3.6 14.4 + - - -
58P GLU* 3.4 12.3 - - - +
99P ALA 2.9 13.2 + - - +
100P LEU* 3.8 5.2 - - - +
102P LEU* 1.3 77.2 - - - +
104P LYS* 1.3 59.7 + - - +
106P VAL* 3.3 5.4 + - - +
107P ASN* 2.8 25.6 + - - +
137P GLN* 3.0 28.5 + - - +
140P ASP* 4.4 7.2 - - + -
141P ILE* 3.9 15.0 - - + -
144P ILE* 3.9 14.6 - - + -
177P MG 2.9 26.8 - - - -
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Residues in contact with LYS 104 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2K SER 5.0 0.6 + - - -
3K GLN* 2.9 30.6 + - - +
4K VAL 4.5 4.9 - - - +
5K ARG 3.5 17.0 + - - -
6K GLN* 3.1 44.2 + - + +
100P LEU* 3.0 29.9 + - + +
101P GLN* 3.7 9.4 - - - +
103P GLU* 1.3 75.7 - - - +
105P THR* 1.3 57.3 + - - +
107P ASN* 4.1 0.4 - - - -
108P GLN* 2.9 26.0 + - - +
141P ILE* 4.2 11.7 - - + -
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Residues in contact with THR 105 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22P LEU* 4.6 19.5 - - + -
25P TYR* 6.5 0.4 - - + -
101P GLN* 2.9 20.3 + - - +
102P LEU* 3.5 13.0 - - + +
103P GLU 3.2 0.2 - - - -
104P LYS* 1.3 77.5 - - - +
106P VAL* 1.3 62.0 + - - +
108P GLN* 3.4 6.6 + - - +
109P ALA* 3.1 21.7 + - - +
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Residues in contact with VAL 106 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19P MET* 5.1 1.6 - - - -
22P LEU* 3.9 29.6 - - + +
23P GLU* 4.0 10.3 - - - +
26P ALA* 4.2 23.8 - - + -
58P GLU* 4.9 0.9 - - - +
102P LEU* 3.1 19.9 + - + +
103P GLU* 3.7 9.9 - - - +
105P THR* 1.3 73.0 - - - +
107P ASN* 1.3 65.5 + - - +
109P ALA* 3.2 2.9 + - - +
110P LEU* 3.0 31.8 + - + +
137P GLN* 3.9 11.2 - - - +
176P MG 3.8 22.2 - - - -
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Residues in contact with ASN 107 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K GLN* 3.1 39.0 + - - +
103P GLU 2.8 20.8 + - - +
104P LYS 3.6 0.7 - - - +
105P THR 3.3 0.2 - - - -
106P VAL* 1.3 73.4 - - - +
108P GLN* 1.3 57.8 + - - +
110P LEU* 3.1 8.8 + - - +
111P LEU* 2.9 42.9 + - - +
134P LEU* 4.8 8.7 - - - +
137P GLN* 3.6 23.7 - - - +
138P VAL* 5.0 9.7 - - - +
141P ILE* 3.9 16.4 - - + +
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Residues in contact with GLN 108 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K GLN* 3.6 21.2 + - - +
7K ASN* 5.9 2.2 - - - +
104P LYS 2.9 17.5 + - - +
105P THR* 3.6 7.0 - - - +
107P ASN* 1.3 78.7 - - - +
109P ALA* 1.3 56.8 + - - +
111P LEU* 3.4 16.3 + - - +
112P ASP* 2.9 63.2 + - - +
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Residues in contact with ALA 109 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19P MET* 3.1 20.8 - - + +
22P LEU* 3.7 22.2 - - + -
105P THR 3.1 13.1 + - - +
106P VAL 3.4 9.0 - - - +
108P GLN* 1.3 77.9 - - - +
110P LEU* 1.3 58.0 + - - +
112P ASP* 3.4 10.0 + - - +
113P LEU* 2.9 22.5 + - - +
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Residues in contact with LEU 110 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19P MET* 3.7 24.5 - - + -
23P GLU* 4.9 2.0 - - - +
65P PHE* 4.0 20.9 - - + -
106P VAL* 3.0 25.1 + - + +
107P ASN* 3.1 7.4 + - - +
109P ALA* 1.3 74.7 - - - +
111P LEU* 1.3 60.7 + - - +
113P LEU* 3.4 2.8 + - - +
114P HIS* 2.9 26.7 + - - +
129P LEU* 4.2 14.3 - - + +
133P TYR* 3.9 31.9 - - + -
134P LEU* 3.9 16.3 - - + +
137P GLN* 3.7 30.3 - - + -
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Residues in contact with LEU 111 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K GLN* 4.6 4.3 - - + -
7K ASN* 3.8 32.5 - - + +
123K PRO* 3.7 34.1 - - + +
124K HIS* 5.4 4.5 - - + +
107P ASN* 2.9 43.3 + - - +
108P GLN* 3.7 20.2 - - - +
110P LEU* 1.3 75.0 - - - +
112P ASP* 1.3 61.1 + - - +
114P HIS* 3.2 6.7 + - - +
115P LYS* 3.0 26.5 + - - +
134P LEU* 4.6 16.2 - - + -
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Residues in contact with ASP 112 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108P GLN* 2.9 48.1 + - - +
109P ALA* 3.4 9.6 - - - +
111P LEU* 1.3 76.0 - - - +
113P LEU* 1.3 59.8 - - - +
115P LYS* 3.3 8.2 + - - +
116P LEU* 3.0 25.5 + - - +
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Residues in contact with LEU 113 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12P CYS 4.3 8.7 - - - +
15P ALA* 3.5 31.9 - - + +
16P VAL* 4.3 16.8 - - + -
19P MET* 3.7 34.8 - - + -
65P PHE* 4.5 2.0 - - + -
109P ALA 2.9 16.3 + - - +
110P LEU* 3.7 4.9 - - + +
112P ASP* 1.3 76.0 - - - +
114P HIS* 1.3 59.3 + - - +
116P LEU* 3.4 9.9 + - + +
117P ALA* 3.0 26.2 + - - +
125P LEU* 4.4 10.3 - - + -
129P LEU* 3.9 27.4 - - + -
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Residues in contact with HIS 114 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121K VAL* 6.1 1.0 - - - +
123K PRO* 3.6 34.9 - - + +
110P LEU 2.9 14.5 + - - +
111P LEU* 3.3 12.8 - - - +
112P ASP 3.1 0.4 - - - -
113P LEU* 1.3 75.2 - - - +
115P LYS* 1.3 61.3 + - - +
117P ALA* 3.3 4.2 + - - +
118P THR* 2.9 43.5 + - - -
126P CYS* 3.6 30.9 + - - +
129P LEU* 3.8 18.3 - - + +
130P GLU* 2.9 26.6 + - - -
134P LEU* 4.2 7.0 - - + -
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Residues in contact with LYS 115 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121K VAL* 4.4 23.8 - - + -
111P LEU 3.0 13.0 + - - +
112P ASP* 3.3 11.4 + - - +
114P HIS* 1.3 74.6 + - - +
116P LEU* 1.3 62.5 + - - +
118P THR* 3.2 9.3 + - + +
119P ASP* 2.9 29.3 + - - +
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Residues in contact with LEU 116 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11P ASP* 3.6 39.5 - - + +
12P CYS* 4.0 11.9 - - - -
15P ALA* 3.7 20.0 - - + -
18P ARG* 5.4 2.2 - - - +
112P ASP 3.0 14.7 + - - +
113P LEU* 3.6 10.3 - - + +
115P LYS* 1.3 77.2 - - - +
117P ALA* 1.3 57.0 + - - +
119P ASP* 3.3 5.2 + - + +
120P LYS* 2.9 50.4 + - + +
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Residues in contact with ALA 117 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12P CYS* 4.3 11.2 - - - -
113P LEU 3.0 14.3 + - - +
114P HIS* 3.5 10.5 - - - +
116P LEU* 1.3 73.9 - - - +
118P THR* 1.3 63.9 + - - +
120P LYS 3.5 0.9 + - - -
121P VAL 3.1 3.3 + - - -
122P ASP* 2.9 34.3 + - + +
125P LEU* 3.9 28.0 - - + -
126P CYS* 3.6 18.4 - - - +
129P LEU* 5.1 0.2 - - + -
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Residues in contact with THR 118 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121K VAL* 6.4 1.8 - - + -
114P HIS* 2.9 30.9 + - - -
115P LYS* 3.5 11.4 - - + +
117P ALA* 1.3 77.0 - - - +
119P ASP* 1.3 62.3 + - - +
121P VAL* 3.1 18.6 + - - +
126P CYS* 3.5 15.0 - - - -
----------------------------------------------------------
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Residues in contact with ASP 119 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115P LYS 2.9 15.2 + - - +
116P LEU* 3.3 10.1 + - + +
118P THR* 1.3 79.2 - - - +
120P LYS* 1.3 73.0 + - + +
121P VAL* 3.2 9.6 + - - +
----------------------------------------------------------
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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