Contacts of the helix formed by residues 92 - 119 (chain H) 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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H PHE* 3.6 19.3 - - - -
44H LEU* 3.8 8.1 - - - +
47H VAL* 4.1 17.1 - - + +
91H ASN* 1.3 73.0 - - - +
93H LEU* 1.3 56.7 + - - +
95H ALA* 3.9 1.4 - - - +
96H MET* 3.0 38.5 + - + +
151H LEU* 4.1 7.9 - - + -
156H LEU* 4.0 7.2 - - - -
163H GLU* 2.8 30.5 + - - +
166H PHE* 3.8 34.8 - - + -
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Residues in contact with LEU 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H ASN* 2.9 10.5 + - - +
92H THR* 1.3 74.7 - - - +
94H GLU* 1.3 62.5 + - - +
96H MET* 3.3 1.2 + - - +
97H GLN* 2.9 52.2 + - - +
148H ILE* 3.9 29.6 - - + +
151H LEU* 3.9 24.7 - - + -
152H LYS* 4.3 16.2 - - + -
156H LEU* 3.4 18.5 - - + +
157H PRO* 3.7 35.7 - - + -
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Residues in contact with GLU 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H ARG* 3.0 40.0 + - - +
89H TRP 3.4 11.7 - - - +
90H GLY* 3.7 8.1 - - - -
91H ASN* 3.1 27.3 + - - +
92H THR 3.4 0.2 - - - -
93H LEU* 1.3 80.2 - - - +
95H ALA* 1.3 57.9 + - - +
97H GLN* 3.5 14.3 + - - +
98H ALA* 3.0 26.2 + - - +
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Residues in contact with ALA 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H MET* 3.8 10.3 - - - +
37H PHE* 3.7 27.4 - - + -
51H PHE* 4.1 11.9 - - + -
89H TRP* 3.7 16.3 + - + -
91H ASN 3.0 17.1 + - - +
92H THR 3.9 2.7 - - - +
94H GLU* 1.3 76.0 - - - +
96H MET* 1.3 59.6 + - - +
98H ALA* 3.4 7.6 + - - +
99H ALA* 2.9 27.2 + - - +
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Residues in contact with MET 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H VAL* 4.6 4.5 - - + -
50H PHE* 4.0 16.8 - - + -
51H PHE* 3.7 31.0 - - + -
92H THR* 3.0 27.0 + - + +
93H LEU 3.3 4.2 + - - +
95H ALA* 1.3 73.4 - - - +
97H GLN* 1.3 62.3 + - - +
99H ALA* 3.3 2.6 + - - +
100H LEU* 2.8 23.7 + - - +
144H ILE* 3.4 19.6 - - + +
147H PHE* 3.9 32.3 - - + -
148H ILE* 3.7 18.1 - - + +
151H LEU* 3.8 16.6 - - + -
166H PHE* 4.3 16.8 - - + -
171H VAL* 5.3 1.3 - - + -
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Residues in contact with GLN 97 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93H LEU* 2.9 43.4 + - + +
94H GLU* 3.8 14.7 - - - +
95H ALA 3.3 0.2 - - - -
96H MET* 1.3 71.9 - - - +
98H ALA* 1.3 64.0 + - - +
100H LEU* 3.3 4.3 + - + +
101H GLN* 3.1 25.8 + - - +
148H ILE* 4.0 21.1 - - + +
152H LYS* 4.1 21.8 + - - -
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Residues in contact with ALA 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H MET* 4.0 4.0 - - + -
85H GLU* 5.4 4.3 - - - +
86H ARG* 5.6 2.5 - - - +
89H TRP* 3.8 32.8 - - + -
94H GLU 3.0 15.3 + - - +
95H ALA 3.5 8.1 - - - +
97H GLN* 1.3 77.2 - - - +
99H ALA* 1.3 57.6 + - - +
101H GLN* 3.4 6.9 + - - +
102H LEU* 3.0 27.9 + - - +
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Residues in contact with ALA 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H TYR* 3.9 27.6 - - + +
33H MET* 4.2 5.4 - - + +
51H PHE* 4.2 8.5 - - + -
95H ALA 2.9 17.3 + - - +
96H MET* 3.5 9.9 - - - +
97H GLN 3.2 0.2 - - - -
98H ALA* 1.3 76.7 - - - +
100H LEU* 1.3 59.7 + - - +
102H LEU* 3.2 5.8 + - - +
103H GLU* 2.9 34.6 + - - +
144H ILE* 4.1 12.1 - - + -
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Residues in contact with LEU 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLN* 3.8 39.3 - - + +
4A VAL* 4.9 0.2 - - + -
96H MET 2.8 19.7 + - - +
97H GLN* 3.3 5.8 + - - +
99H ALA* 1.3 72.4 - - - +
101H GLN* 1.3 60.4 + - + +
103H GLU* 3.4 3.3 + - - +
104H LYS* 3.0 43.3 + - + +
141H ILE* 3.9 41.5 - - + +
144H ILE* 3.9 11.6 - - + +
145H GLY* 4.5 3.6 - - - +
148H ILE* 3.7 22.2 - - + -
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Residues in contact with GLN 101 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H GLN 3.1 12.7 + - - +
98H ALA* 3.7 8.5 - - - +
100H LEU* 1.3 76.9 - - + +
102H LEU* 1.3 60.7 + - - +
104H LYS* 3.2 9.9 + - - +
105H THR* 2.9 34.5 + - - +
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Residues in contact with LEU 102 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H LEU* 5.4 1.3 - - + -
25H TYR* 4.1 27.4 - - + -
26H ALA* 3.9 24.2 - - + +
29H THR* 3.7 28.3 - - + -
30H TYR* 3.9 33.2 - - + +
33H MET* 5.2 0.2 - - + -
98H ALA 3.0 17.8 + - - +
99H ALA* 3.2 5.6 + - - +
101H GLN* 1.3 76.4 - - - +
103H GLU* 1.3 58.8 + - + +
105H THR* 3.4 10.6 + - + -
106H VAL* 3.1 36.7 + - + +
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Residues in contact with GLU 103 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H ALA* 6.2 0.6 - - - +
30H TYR* 2.8 29.7 + - - +
54H HIS* 3.6 14.2 + - - -
58H GLU* 3.4 12.4 - - - +
99H ALA 2.9 14.3 + - - +
100H LEU* 3.8 5.4 - - - +
101H GLN 3.2 0.2 - - - -
102H LEU* 1.3 75.3 - - - +
104H LYS* 1.3 60.8 + - - +
106H VAL* 3.3 6.0 + - - +
107H ASN* 2.8 25.5 + - - +
137H GLN* 3.0 30.6 + - - +
140H ASP* 4.4 7.2 - - + -
141H ILE* 3.9 14.8 - - + -
144H ILE* 3.9 13.9 - - + -
177H MG 2.9 27.7 - - - -
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Residues in contact with LYS 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER 4.9 0.8 + - - -
3A GLN* 2.9 30.4 + - - +
4A VAL 4.4 5.8 - - - +
5A ARG 3.5 17.2 + - - -
6A GLN* 3.1 43.3 + - + +
100H LEU* 3.0 31.0 + - + +
101H GLN* 3.7 9.4 - - - +
103H GLU* 1.3 74.1 - - - +
105H THR* 1.3 57.1 + - - +
107H ASN* 4.1 0.4 - - - -
108H GLN* 2.9 26.3 + - - +
141H ILE* 4.2 11.4 - - + -
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Residues in contact with THR 105 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H LEU* 4.6 19.5 - - + -
25H TYR* 6.5 0.4 - - + -
101H GLN* 2.9 21.3 + - - +
102H LEU* 3.5 12.3 - - + +
104H LYS* 1.3 78.0 - - - +
106H VAL* 1.3 62.9 + - - +
108H GLN* 3.4 6.5 + - - +
109H ALA* 3.1 22.2 + - - +
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Residues in contact with VAL 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H MET* 5.1 2.0 - - - -
22H LEU* 3.9 29.2 - - + +
23H GLU* 4.0 9.9 - - - +
26H ALA* 4.2 23.8 - - + -
58H GLU* 4.9 0.7 - - - +
102H LEU* 3.1 19.7 + - + +
103H GLU* 3.3 9.6 + - - +
105H THR* 1.3 73.0 - - - +
107H ASN* 1.3 67.0 + - - +
109H ALA* 3.2 3.6 + - - +
110H LEU* 3.0 31.3 + - + +
137H GLN* 3.9 11.4 - - - +
176H MG 3.8 22.4 - - - -
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Residues in contact with ASN 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLN* 3.1 39.4 + - - +
103H GLU 2.8 21.2 + - - +
104H LYS 3.6 0.2 - - - +
106H VAL* 1.3 72.7 - - - +
108H GLN* 1.3 58.6 + - - +
110H LEU* 3.1 9.5 + - - +
111H LEU* 2.9 42.6 + - - +
134H LEU* 4.8 9.2 - - - +
137H GLN* 3.6 22.8 - - - +
138H VAL* 5.0 9.0 - - - +
141H ILE* 3.9 16.8 - - + +
----------------------------------------------------------
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Residues in contact with GLN 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLN* 3.6 21.2 + - - +
7A ASN* 5.8 3.0 - - - +
104H LYS 2.9 18.2 + - - +
105H THR* 3.6 7.0 - - - +
107H ASN* 1.3 78.7 - - - +
109H ALA* 1.3 57.4 + - - +
111H LEU* 3.4 15.6 + - - +
112H ASP* 2.9 63.2 + - - +
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Residues in contact with ALA 109 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H MET* 3.1 21.0 - - + +
22H LEU* 3.7 22.0 - - + -
105H THR* 3.1 14.1 + - + +
106H VAL 3.2 9.2 + - - +
108H GLN* 1.3 79.1 - - - +
110H LEU* 1.3 57.2 + - - +
112H ASP* 3.4 10.2 + - - +
113H LEU* 2.9 22.3 + - - +
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Residues in contact with LEU 110 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H MET* 3.7 23.8 - - + -
23H GLU* 4.9 1.8 - - - +
65H PHE* 4.0 21.5 - - + -
106H VAL* 3.0 26.0 + - + +
107H ASN* 3.4 6.3 - - - +
109H ALA* 1.3 75.2 - - - +
111H LEU* 1.3 60.3 + - - +
113H LEU* 3.4 3.2 + - - +
114H HIS* 2.9 27.2 + - - +
129H LEU* 4.2 14.1 - - + +
133H TYR* 3.9 31.9 - - + -
134H LEU* 3.9 15.9 - - + +
137H GLN* 3.7 30.5 - - + +
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Residues in contact with LEU 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLN* 4.5 4.3 - - + -
7A ASN* 3.8 33.0 - - + +
123A PRO* 3.7 34.3 - - + +
124A HIS* 5.3 4.3 - - + +
107H ASN* 2.9 42.4 + - - +
108H GLN* 3.7 19.1 - - - +
110H LEU* 1.3 75.2 - - - +
112H ASP* 1.3 60.9 + - - +
114H HIS* 3.2 5.9 + - - +
115H LYS* 3.0 27.4 + - - +
134H LEU* 4.6 15.9 - - + -
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Residues in contact with ASP 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108H GLN* 2.9 49.4 + - - +
109H ALA* 3.4 10.0 - - - +
110H LEU 3.2 0.2 - - - -
111H LEU* 1.3 76.3 - - - +
113H LEU* 1.3 62.0 + - - +
115H LYS* 3.3 8.6 + - - +
116H LEU* 3.0 26.0 + - - +
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Residues in contact with LEU 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H CYS* 4.3 9.0 - - - +
15H ALA* 3.5 31.2 - - + +
16H VAL* 4.3 16.8 - - + -
19H MET* 3.7 34.3 - - + -
65H PHE* 4.5 2.2 - - + -
109H ALA 2.9 17.4 + - - +
110H LEU* 3.7 5.8 - - + +
111H LEU 3.3 0.2 - - - -
112H ASP* 1.3 75.8 - - - +
114H HIS* 1.3 59.1 + - - +
116H LEU* 3.4 10.4 + - + +
117H ALA* 3.0 26.0 + - - +
125H LEU* 4.4 10.1 - - + -
129H LEU* 3.9 26.0 - - + -
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Residues in contact with HIS 114 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A VAL* 6.2 0.8 - - - +
123A PRO* 3.5 36.9 - - + +
110H LEU 2.9 15.0 + - - +
111H LEU* 3.3 12.8 - - - +
112H ASP 3.1 0.2 - - - -
113H LEU* 1.3 76.0 - - - +
115H LYS* 1.3 62.3 + - - +
117H ALA* 3.3 3.7 + - - +
118H THR* 2.9 42.4 + - - -
126H CYS* 3.6 31.5 + - - +
129H LEU* 3.8 17.9 - - + +
130H GLU* 2.9 25.4 + - - -
134H LEU* 4.2 7.0 - - + -
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Residues in contact with LYS 115 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A VAL* 4.3 24.9 - - + -
111H LEU 3.0 12.6 + - - +
112H ASP* 3.3 11.9 + - - +
114H HIS* 1.3 74.4 + - - +
116H LEU* 1.3 60.5 + - - +
118H THR* 3.2 10.3 + - + +
119H ASP* 2.9 29.2 + - - +
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Residues in contact with LEU 116 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H ASP* 3.6 40.2 - - + +
12H CYS* 4.0 10.5 - - - -
15H ALA* 3.7 20.0 - - + -
18H ARG* 5.4 1.8 - - - +
112H ASP 3.0 14.4 + - - +
113H LEU* 3.6 11.4 - - + +
114H HIS 3.3 0.2 - - - -
115H LYS* 1.3 76.6 - - - +
117H ALA* 1.3 57.0 + - - +
119H ASP* 3.3 5.6 + - + +
120H LYS* 2.9 50.1 + - + +
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Residues in contact with ALA 117 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H CYS* 4.3 11.0 - - - -
113H LEU 3.0 14.1 + - - +
114H HIS* 3.3 10.7 + - - +
116H LEU* 1.3 73.6 - - - +
118H THR* 1.3 64.1 + - - +
120H LYS 3.5 0.5 + - - -
121H VAL 3.1 3.3 + - - -
122H ASP* 2.9 33.5 + - + +
125H LEU* 3.9 27.8 - - + -
126H CYS* 3.6 17.7 - - - +
129H LEU* 5.1 0.2 - - + -
----------------------------------------------------------
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Residues in contact with THR 118 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A VAL* 6.4 1.8 - - + -
114H HIS* 2.9 30.5 + - - -
115H LYS* 3.2 10.7 + - + +
117H ALA* 1.3 76.4 - - - +
119H ASP* 1.3 63.5 + - - +
121H VAL* 3.1 18.6 + - - +
126H CYS* 3.5 15.0 - - - -
----------------------------------------------------------
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Residues in contact with ASP 119 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115H LYS* 2.9 17.5 + - + +
116H LEU* 3.6 9.2 - - + +
118H THR* 1.3 78.6 - - - +
120H LYS* 1.3 73.4 + - + +
121H VAL* 3.2 9.1 + - - +
----------------------------------------------------------
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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