Contacts of the helix formed by residues 92 - 119 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C PHE* 3.6 20.5 - - - -
44C LEU* 3.8 8.0 - - - +
47C VAL* 4.1 17.7 - - + +
91C ASN* 1.3 71.9 - - - +
93C LEU* 1.3 57.2 + - - +
95C ALA* 3.9 1.0 - - - +
96C MET* 3.0 38.7 + - + +
151C LEU* 4.1 7.2 - - + -
156C LEU* 4.0 7.0 - - - -
163C GLU* 2.8 30.9 + - - +
166C PHE* 3.8 35.2 - - + -
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Residues in contact with LEU 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C ASN* 2.9 10.5 + - - +
92C THR* 1.3 75.2 - - - +
94C GLU* 1.3 63.1 + - - +
96C MET* 3.3 1.4 + - - +
97C GLN* 2.9 53.0 + - + +
148C ILE* 3.9 29.8 - - + +
151C LEU* 3.9 23.6 - - + -
152C LYS* 4.3 15.7 - - + -
156C LEU* 3.4 19.7 - - + +
157C PRO* 3.7 35.4 - - + -
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Residues in contact with GLU 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ARG* 3.0 39.3 + - - +
89C TRP 3.4 11.7 - - - +
90C GLY* 3.7 7.7 - - - -
91C ASN* 3.1 27.5 + - - +
92C THR 3.4 0.2 - - - -
93C LEU* 1.3 79.4 - - - +
95C ALA* 1.3 57.2 + - - +
97C GLN* 3.5 14.3 + - - +
98C ALA* 3.0 26.9 + - - +
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Residues in contact with ALA 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C MET* 3.8 10.4 - - - +
37C PHE* 3.7 27.6 - - + -
51C PHE* 4.1 12.1 - - + -
89C TRP* 3.7 17.0 + - + -
91C ASN 3.0 17.3 + - - +
92C THR 3.9 2.0 - - - +
94C GLU* 1.3 75.9 - - - +
96C MET* 1.3 59.6 + - - +
98C ALA* 3.4 7.3 + - - +
99C ALA* 2.9 27.4 + - - +
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Residues in contact with MET 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C VAL* 4.6 3.8 - - + -
50C PHE* 4.0 16.8 - - + -
51C PHE* 3.7 31.9 - - + -
92C THR* 3.0 25.2 + - + +
93C LEU 3.7 3.8 - - - +
95C ALA* 1.3 73.2 - - - +
97C GLN* 1.3 61.9 + - - +
99C ALA* 3.3 3.0 + - - +
100C LEU* 2.8 23.7 + - - +
144C ILE* 3.4 20.3 - - + +
147C PHE* 3.9 32.8 - - + -
148C ILE* 3.7 17.9 - - + +
151C LEU* 3.8 17.3 - - + -
166C PHE* 4.3 16.6 - - + -
171C VAL* 5.3 1.6 - - + -
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Residues in contact with GLN 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C LEU* 2.9 43.0 + - + +
94C GLU* 3.8 14.5 - - - +
96C MET* 1.3 72.3 - - - +
98C ALA* 1.3 66.2 + - - +
100C LEU* 3.3 3.7 + - - +
101C GLN* 3.1 25.6 + - - +
148C ILE* 4.0 20.7 - - + +
152C LYS* 4.1 20.8 + - - -
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Residues in contact with ALA 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C MET* 4.0 4.3 - - + -
85C GLU* 5.4 3.8 - - - +
86C ARG* 5.6 2.2 - - - +
89C TRP* 3.8 32.5 - - + -
94C GLU 3.0 15.4 + - - +
95C ALA 3.5 8.3 - - - +
96C MET 3.3 0.2 - - - -
97C GLN* 1.3 76.7 - - - +
99C ALA* 1.3 58.0 + - - +
101C GLN* 3.4 6.4 + - - +
102C LEU* 3.0 27.8 + - - +
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Residues in contact with ALA 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C TYR* 3.9 27.6 - - + +
33C MET* 4.2 5.6 - - + +
51C PHE* 4.2 9.0 - - + -
95C ALA 2.9 17.5 + - - +
96C MET* 3.5 9.0 - - - +
97C GLN 3.2 0.2 - - - -
98C ALA* 1.3 74.1 - - - +
100C LEU* 1.3 59.6 + - - +
102C LEU* 3.2 6.1 + - - +
103C GLU* 2.9 34.2 + - - +
144C ILE* 4.1 13.0 - - + -
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Residues in contact with LEU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C MET 2.8 20.4 + - - +
97C GLN* 3.3 5.8 + - - +
99C ALA* 1.3 72.1 - - - +
101C GLN* 1.3 59.2 + - + +
103C GLU* 3.4 3.7 + - - +
104C LYS* 3.0 42.7 + - + +
141C ILE* 3.9 41.1 - - + +
144C ILE* 3.9 12.1 - - + +
145C GLY* 4.5 3.4 - - - +
148C ILE* 3.7 22.7 - - + -
3S GLN* 3.8 37.7 - - + +
4S VAL* 5.0 0.4 - - + -
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Residues in contact with GLN 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C GLN 3.1 12.9 + - - +
98C ALA* 3.7 9.0 - - - +
100C LEU* 1.3 76.5 - - + +
102C LEU* 1.3 60.7 + - - +
104C LYS* 3.2 10.6 + - - +
105C THR* 2.9 34.0 + - - +
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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
----------------------------------------------------------
22C LEU* 5.4 1.8 - - + -
25C TYR* 4.1 27.1 - - + -
26C ALA* 3.9 25.4 - - + +
29C THR* 3.7 28.3 - - + -
30C TYR* 3.9 34.1 - - + +
33C MET* 5.2 0.2 - - + -
98C ALA 3.0 17.6 + - - +
99C ALA* 3.2 5.6 + - - +
101C GLN* 1.3 75.9 - - - +
103C GLU* 1.3 57.9 + - + +
105C THR* 3.4 10.0 + - + -
106C VAL* 3.1 35.9 + - + +
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Residues in contact with GLU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ALA* 6.5 0.2 - - - -
30C TYR* 2.8 29.4 + - - +
54C HIS* 3.6 14.0 + - - -
58C GLU* 3.4 12.2 - - - +
99C ALA 2.9 15.1 + - - +
100C LEU* 3.8 5.4 - - - +
102C LEU* 1.3 75.5 - - - +
104C LYS* 1.3 59.7 + - - +
106C VAL* 3.3 5.9 + - - +
107C ASN* 2.8 26.3 + - - +
137C GLN* 3.0 29.3 + - - +
140C ASP* 4.4 6.5 - - + -
141C ILE* 3.9 14.8 - - + -
144C ILE* 3.9 14.4 - - + -
177C MG 2.9 28.5 - - - -
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Residues in contact with LYS 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C LEU* 3.0 28.8 + - + +
101C GLN* 3.7 9.6 - - - +
103C GLU* 1.3 74.0 - - - +
105C THR* 1.3 58.0 + - - +
107C ASN* 4.1 0.7 - - - -
108C GLN* 2.9 26.7 + - - +
141C ILE* 4.2 11.4 - - + -
2S SER 5.0 0.4 + - - -
3S GLN* 3.0 30.0 + - - +
4S VAL 4.5 6.1 - - - +
5S ARG 3.5 17.2 + - - -
6S GLN* 3.1 44.2 + - + +
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Residues in contact with THR 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LEU* 4.6 19.1 - - + -
25C TYR* 6.5 0.9 - - + -
101C GLN* 2.9 21.0 + - - +
102C LEU* 3.5 12.3 - - + +
104C LYS* 1.3 76.8 - - - +
106C VAL* 1.3 64.4 + - - +
108C GLN* 3.4 6.6 + - - +
109C ALA* 3.1 21.7 + - - +
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Residues in contact with VAL 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C MET* 5.1 1.3 - - - -
22C LEU* 3.9 29.2 - - + +
23C GLU* 4.0 10.8 - - - +
26C ALA* 4.2 24.7 - - + -
58C GLU* 4.9 0.7 - - - +
102C LEU* 3.1 19.5 + - + +
103C GLU* 3.7 9.4 - - - +
105C THR* 1.3 72.5 - - - +
107C ASN* 1.3 65.7 + - - +
109C ALA* 3.2 3.6 + - - +
110C LEU* 3.0 30.9 + - + +
137C GLN* 3.9 12.6 - - - +
176C MG 3.8 22.0 - - - -
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Residues in contact with ASN 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C GLU 2.8 21.7 + - - +
104C LYS 3.6 0.2 - - - +
105C THR 3.3 0.2 - - - -
106C VAL* 1.3 72.6 - - - +
108C GLN* 1.3 58.6 + - - +
110C LEU* 3.1 10.1 + - - +
111C LEU* 2.9 42.9 + - - +
134C LEU* 4.8 8.5 - - - +
137C GLN* 3.6 23.3 - - - +
138C VAL* 5.0 9.5 - - - +
141C ILE* 3.9 16.4 - - + +
6S GLN* 3.1 39.3 + - - +
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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
----------------------------------------------------------
104C LYS 2.9 19.0 + - - +
105C THR* 3.6 7.0 - - - +
107C ASN* 1.3 78.4 - - - +
109C ALA* 1.3 57.8 + - - +
111C LEU* 3.4 17.0 + - - +
112C ASP* 2.9 63.6 + - - +
6S GLN* 3.6 19.9 + - - +
7S ASN* 5.9 2.2 - - - +
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Residues in contact with ALA 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C MET* 3.1 21.6 - - + +
22C LEU* 3.7 22.2 - - + -
105C THR 3.1 13.7 + - - +
106C VAL 3.4 8.5 - - - +
108C GLN* 1.3 77.5 - - - +
110C LEU* 1.3 57.2 + - - +
112C ASP* 3.4 9.9 + - - +
113C LEU* 2.9 22.2 + - - +
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Residues in contact with LEU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C MET* 3.7 25.6 - - + -
23C GLU* 4.9 2.0 - - - +
65C PHE* 4.0 20.9 - - + -
106C VAL* 3.0 24.8 + - + +
107C ASN* 3.4 6.7 - - - +
109C ALA* 1.3 75.6 - - - +
111C LEU* 1.3 60.7 + - - +
113C LEU* 3.4 3.0 + - - +
114C HIS* 2.9 26.9 + - - +
129C LEU* 4.2 14.5 - - + +
133C TYR* 3.9 31.6 - - + -
134C LEU* 3.9 16.3 - - + +
137C GLN* 3.7 31.0 - - + -
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Residues in contact with LEU 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C ASN* 2.9 43.0 + - - +
108C GLN* 3.7 20.2 - - - +
110C LEU* 1.3 74.8 - - - +
112C ASP* 1.3 60.0 + - - +
114C HIS* 3.2 6.3 + - - +
115C LYS* 3.0 26.9 + - - +
134C LEU* 4.6 16.2 - - + -
6S GLN* 4.6 4.3 - - + -
7S ASN* 3.8 33.0 - - + +
123S PRO* 3.7 35.4 - - + +
124S HIS* 5.4 3.1 - - + +
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Residues in contact with ASP 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C GLN* 2.9 47.5 + - - +
109C ALA* 3.4 8.9 - - - +
111C LEU* 1.3 76.7 - - - +
113C LEU* 1.3 62.3 + - - +
115C LYS* 3.3 8.2 + - - +
116C LEU* 3.0 26.2 + - - +
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Residues in contact with LEU 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C CYS* 4.3 9.0 - - - +
15C ALA* 3.5 31.6 - - + +
16C VAL* 4.3 17.0 - - + -
19C MET* 3.7 35.2 - - + -
65C PHE* 4.5 2.2 - - + -
109C ALA 2.9 16.7 + - - +
110C LEU* 3.7 5.4 - - + +
111C LEU 3.3 0.2 - - - -
112C ASP* 1.3 75.4 - - - +
114C HIS* 1.3 59.9 + - - +
116C LEU* 3.4 10.1 + - + +
117C ALA* 3.0 25.8 + - - +
125C LEU* 4.4 9.9 - - + -
129C LEU* 3.9 25.8 - - + -
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Residues in contact with HIS 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C LEU 2.9 14.5 + - - +
111C LEU* 3.3 12.6 - - - +
112C ASP 3.1 0.2 - - - -
113C LEU* 1.3 75.1 - - - +
115C LYS* 1.3 61.2 + - - +
117C ALA* 3.3 4.6 + - - +
118C THR* 2.9 42.6 + - - -
126C CYS* 3.6 31.1 + - - +
129C LEU* 3.8 17.7 - - + +
130C GLU* 2.9 25.9 + - - -
134C LEU* 4.2 7.2 - - + -
121S VAL* 6.1 1.2 - - - +
123S PRO* 3.6 36.9 - - + +
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Residues in contact with LYS 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C LEU 3.0 13.2 + - - +
112C ASP* 3.5 11.2 - - - +
114C HIS* 1.3 75.3 + - - +
116C LEU* 1.3 61.5 + - - +
118C THR* 3.2 9.7 + - + +
119C ASP* 2.9 29.5 + - - +
121S VAL* 4.4 24.2 - - + -
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Residues in contact with LEU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ASP* 3.6 41.1 - - + +
12C CYS* 4.0 11.2 - - - -
15C ALA* 3.7 19.7 - - + -
18C ARG* 5.4 2.0 - - - +
112C ASP 3.0 14.2 + - - +
113C LEU* 3.6 11.0 - - + +
115C LYS* 1.3 76.8 - - - +
117C ALA* 1.3 57.0 + - - +
119C ASP* 3.3 5.0 + - + +
120C LYS* 2.9 50.2 + - + +
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Residues in contact with ALA 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C CYS* 4.3 10.7 - - - -
113C LEU 3.0 13.7 + - - +
114C HIS* 3.5 10.3 - - - +
116C LEU* 1.3 73.4 - - - +
118C THR* 1.3 63.9 + - - +
120C LYS 3.5 0.9 + - - +
121C VAL 3.1 3.6 + - - -
122C ASP* 2.9 35.0 + - + +
125C LEU* 3.9 28.5 - - + -
126C CYS* 3.6 17.5 - - - +
129C LEU* 5.1 0.2 - - + -
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Residues in contact with THR 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C HIS* 2.9 32.1 + - - -
115C LYS* 3.2 11.0 + - + +
117C ALA* 1.3 76.4 - - - +
119C ASP* 1.3 62.9 + - - +
121C VAL* 3.1 17.8 + - - +
126C CYS* 3.5 15.4 - - - -
121S VAL* 6.5 1.6 - - + -
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Residues in contact with ASP 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C LYS 2.9 16.5 + - - +
116C LEU* 3.6 8.7 - - + +
118C THR* 1.3 79.3 - - - +
120C LYS* 1.3 72.8 + - + +
121C VAL* 3.2 10.0 + - - +
----------------------------------------------------------
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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