Contacts of the helix formed by residues 92 - 119 (chain X) 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 X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37X PHE* 3.6 19.5 - - - -
44X LEU* 3.8 8.0 - - - +
47X VAL* 4.1 17.5 - - + +
91X ASN* 1.3 72.5 - - - +
93X LEU* 1.3 58.3 + - - +
95X ALA* 3.9 1.3 - - - +
96X MET* 3.0 38.4 + - + +
151X LEU* 4.1 8.1 - - + -
156X LEU* 4.0 7.6 - - - -
163X GLU* 2.8 30.2 + - + +
166X PHE* 3.8 34.3 - - + -
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Residues in contact with LEU 93 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91X ASN* 2.9 10.7 + - - +
92X THR* 1.3 75.1 - - - +
94X GLU* 1.3 61.4 + - - +
96X MET* 3.3 1.6 + - - +
97X GLN* 2.9 52.9 + - - +
148X ILE* 3.9 30.3 - - + +
151X LEU* 3.9 23.6 - - + -
152X LYS* 4.3 16.4 - - + -
156X LEU* 3.4 18.4 - - + +
157X PRO* 3.7 35.4 - - + -
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Residues in contact with GLU 94 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86X ARG* 3.0 39.5 + - - +
89X TRP 3.4 11.9 - - - +
90X GLY* 3.7 7.9 - - - -
91X ASN* 3.1 26.7 + - - +
92X THR 3.4 0.2 - - - -
93X LEU* 1.3 79.9 - - - +
95X ALA* 1.3 57.6 + - - +
97X GLN* 3.5 15.5 + - + +
98X ALA* 3.0 27.4 + - - +
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Residues in contact with ALA 95 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33X MET* 3.8 9.8 - - - +
37X PHE* 3.7 28.0 - - + -
51X PHE* 4.1 11.4 - - + -
89X TRP* 3.7 15.6 + - + -
91X ASN 3.0 17.3 + - - +
92X THR 3.9 2.7 - - - +
94X GLU* 1.3 75.6 - - - +
96X MET* 1.3 60.1 + - - +
98X ALA* 3.4 7.9 + - - +
99X ALA* 2.9 27.4 + - - +
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Residues in contact with MET 96 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47X VAL* 4.6 3.8 - - + -
50X PHE* 4.0 16.2 - - + -
51X PHE* 3.7 30.7 - - + -
92X THR* 3.0 26.8 + - + +
93X LEU 3.7 4.0 - - - +
95X ALA* 1.3 75.0 - - - +
97X GLN* 1.3 61.0 + - - +
99X ALA* 3.3 2.1 + - - -
100X LEU* 2.8 23.9 + - - +
144X ILE* 3.4 20.5 - - + +
147X PHE* 3.9 33.0 - - + -
148X ILE* 3.7 17.7 - - + +
151X LEU* 3.8 17.5 - - + -
166X PHE* 4.3 16.2 - - + -
171X VAL* 5.3 1.3 - - + -
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Residues in contact with GLN 97 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93X LEU* 2.9 43.8 + - + +
94X GLU* 3.8 15.5 - - + +
96X MET* 1.3 71.9 - - - +
98X ALA* 1.3 66.3 + - - +
100X LEU* 3.3 3.7 + - - +
101X GLN* 3.1 25.1 + - - +
148X ILE* 4.0 20.7 - - + +
152X LYS* 4.1 21.1 + - - -
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Residues in contact with ALA 98 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33X MET* 4.0 4.4 - - + +
85X GLU* 5.4 4.3 - - - +
86X ARG* 5.6 2.7 - - - +
89X TRP* 3.8 32.3 - - + -
94X GLU 3.0 15.9 + - - +
95X ALA 3.5 7.9 - - - +
97X GLN* 1.3 75.5 - - - +
99X ALA* 1.3 58.5 + - - +
101X GLN* 3.4 7.0 + - - +
102X LEU* 3.0 27.4 + - - +
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Residues in contact with ALA 99 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30X TYR* 3.9 27.1 - - + +
33X MET* 4.2 4.9 - - + +
51X PHE* 4.2 8.3 - - + -
95X ALA 2.9 17.5 + - - +
96X MET* 3.5 9.9 - - - +
98X ALA* 1.3 74.9 - - - +
100X LEU* 1.3 59.3 + - - +
102X LEU* 3.2 6.2 + - - +
103X GLU* 2.9 34.4 + - - +
144X ILE* 4.1 12.6 - - + -
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Residues in contact with LEU 100 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H GLN* 3.8 37.9 - - + +
4H VAL* 4.9 0.7 - - + -
96X MET 2.8 20.4 + - - +
97X GLN* 3.3 6.5 + - + +
99X ALA* 1.3 72.5 - - - +
101X GLN* 1.3 59.3 + - + +
103X GLU* 3.4 3.1 + - - +
104X LYS* 3.0 41.9 + - + +
141X ILE* 3.9 41.5 - - + +
144X ILE* 3.9 12.7 - - + +
145X GLY* 4.5 2.9 - - - +
148X ILE* 3.7 22.4 - - + -
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Residues in contact with GLN 101 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97X GLN 3.1 12.0 + - - +
98X ALA* 3.7 8.7 - - - +
99X ALA 3.3 0.2 - - - -
100X LEU* 1.3 76.9 - - + +
102X LEU* 1.3 60.9 + - - +
104X LYS* 3.2 10.7 + - - +
105X THR* 2.9 34.5 + - - +
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Residues in contact with LEU 102 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22X LEU* 5.4 1.6 - - + -
25X TYR* 4.1 27.4 - - + -
26X ALA* 3.9 25.1 - - + +
29X THR* 3.7 28.3 - - + -
30X TYR* 3.9 32.8 - - + +
33X MET* 5.2 0.2 - - + -
98X ALA 3.0 17.2 + - - +
99X ALA* 3.2 5.4 + - - +
101X GLN* 1.3 76.7 - - - +
103X GLU* 1.3 59.7 + - + +
105X THR* 3.4 10.5 + - + -
106X VAL* 3.1 36.2 + - + +
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Residues in contact with GLU 103 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26X ALA* 6.5 0.4 - - - -
30X TYR* 2.8 28.9 + - - +
54X HIS* 3.6 14.4 + - - -
58X GLU* 3.4 12.4 - - - +
99X ALA 2.9 14.5 + - - +
100X LEU* 3.8 5.4 - - - +
102X LEU* 1.3 75.7 - - - +
104X LYS* 1.3 59.6 + - - +
106X VAL* 3.3 6.2 + - - +
107X ASN* 2.8 26.2 + - - +
137X GLN* 3.0 29.0 + - - +
140X ASP* 4.4 7.2 - - + -
141X ILE* 3.9 14.4 - - + -
144X ILE* 3.9 14.6 - - + -
177X MG 2.9 27.8 - - - -
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Residues in contact with LYS 104 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H SER 5.0 0.6 + - - -
3H GLN* 2.9 30.3 + - - +
4H VAL 4.4 5.4 - - - +
5H ARG 3.6 16.6 + - - -
6H GLN* 3.1 44.5 + - + +
100X LEU* 3.0 29.3 + - + +
101X GLN* 3.7 9.2 - - - +
103X GLU* 1.3 75.3 - - - +
105X THR* 1.3 57.0 + - - +
107X ASN* 4.1 0.4 - - - -
108X GLN* 2.9 25.5 + - - +
141X ILE* 4.2 11.9 - - + -
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Residues in contact with THR 105 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22X LEU* 4.6 19.5 - - + -
25X TYR* 6.5 0.2 - - + -
101X GLN* 2.9 21.0 + - - +
102X LEU* 3.5 12.5 - - + +
103X GLU 3.2 0.2 - - - -
104X LYS* 1.3 77.5 - - - +
106X VAL* 1.3 63.8 + - + +
108X GLN* 3.4 6.6 + - - +
109X ALA* 3.1 21.7 + - - +
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Residues in contact with VAL 106 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19X MET* 5.1 1.8 - - - -
22X LEU* 3.9 29.2 - - + +
23X GLU* 4.0 11.2 - - + +
26X ALA* 4.2 24.5 - - + -
58X GLU* 4.9 0.7 - - - +
102X LEU* 3.1 19.2 + - + +
103X GLU* 3.7 9.6 - - - +
105X THR* 1.3 72.8 - - - +
107X ASN* 1.3 66.5 + - - +
109X ALA* 3.2 3.5 + - - +
110X LEU* 3.0 30.8 + - + +
137X GLN* 3.9 11.9 - - - +
176X MG 3.8 21.8 - - - -
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Residues in contact with ASN 107 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H GLN* 3.1 39.4 + - - +
103X GLU 2.8 21.8 + - - +
104X LYS 3.6 0.2 - - - +
106X VAL* 1.3 71.1 - - - +
108X GLN* 1.3 58.2 + - - +
110X LEU* 3.1 10.5 + - - +
111X LEU* 2.9 42.7 + - - +
134X LEU* 4.8 8.8 - - - +
137X GLN* 3.6 23.0 - - - +
138X VAL* 5.0 9.3 - - - +
141X ILE* 3.9 16.8 - - + +
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Residues in contact with GLN 108 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H GLN* 3.5 21.5 + - - +
7H ASN* 5.9 1.8 - - - +
104X LYS 2.9 18.3 + - - +
105X THR* 3.6 7.0 - - - +
107X ASN* 1.3 78.1 - - - +
109X ALA* 1.3 56.5 + - - +
111X LEU* 3.4 16.2 + - - +
112X ASP* 2.9 63.4 + - - +
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Residues in contact with ALA 109 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19X MET* 3.1 20.8 - - + +
22X LEU* 3.7 22.4 - - + -
105X THR 3.1 13.6 + - - +
106X VAL 3.2 9.2 + - - +
108X GLN* 1.3 77.3 - - - +
110X LEU* 1.3 57.0 + - - +
112X ASP* 3.4 9.4 + - - +
113X LEU* 2.9 23.4 + - - +
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Residues in contact with LEU 110 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19X MET* 3.7 25.1 - - + -
23X GLU* 4.9 2.0 - - - +
65X PHE* 4.0 21.1 - - + -
106X VAL* 3.0 25.3 + - + +
107X ASN* 3.1 6.9 + - - +
109X ALA* 1.3 74.8 - - - +
111X LEU* 1.3 61.1 + - - +
113X LEU* 3.4 3.0 + - - +
114X HIS* 2.9 26.5 + - - +
129X LEU* 4.2 13.9 - - + +
133X TYR* 3.9 31.4 - - + -
134X LEU* 3.9 15.1 - - + +
137X GLN* 3.7 30.7 - - + +
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Residues in contact with LEU 111 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H GLN* 4.5 4.0 - - + -
7H ASN* 3.8 33.4 - - + +
123H PRO* 3.7 34.0 - - + +
124H HIS* 5.4 4.3 - - + +
107X ASN* 2.9 43.5 + - - +
108X GLN* 3.7 20.4 - - - +
110X LEU* 1.3 75.0 - - - +
112X ASP* 1.3 60.4 + - - +
114X HIS* 3.2 6.2 + - - +
115X LYS* 3.0 27.4 + - - +
134X LEU* 4.6 15.5 - - + -
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Residues in contact with ASP 112 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108X GLN* 2.9 49.2 + - - +
109X ALA* 3.4 9.4 - - - +
110X LEU 3.2 0.2 - - - -
111X LEU* 1.3 76.1 - - - +
113X LEU* 1.3 60.8 - - - +
115X LYS* 3.3 8.3 + - - +
116X LEU* 3.0 26.2 + - - +
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Residues in contact with LEU 113 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12X CYS 4.3 8.3 - - - +
15X ALA* 3.5 32.1 - - + +
16X VAL* 4.3 17.9 - - + -
19X MET* 3.7 34.5 - - + -
65X PHE* 4.5 2.2 - - + -
109X ALA 2.9 16.9 + - - +
110X LEU* 3.7 5.2 - - + +
111X LEU 3.3 0.2 - - - -
112X ASP* 1.3 75.8 - - - +
114X HIS* 1.3 59.0 + - - +
116X LEU* 3.4 10.2 + - + +
117X ALA* 3.0 26.2 + - - +
125X LEU* 4.4 10.3 - - + -
129X LEU* 3.9 26.2 - - + -
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Residues in contact with HIS 114 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H VAL* 6.1 1.2 - - - +
123H PRO* 3.5 35.5 - - + +
110X LEU 2.9 15.0 + - - +
111X LEU* 3.3 12.8 - - - +
112X ASP 3.1 0.2 - - - -
113X LEU* 1.3 75.1 - - - +
115X LYS* 1.3 61.5 + - - +
117X ALA* 3.3 4.2 + - - +
118X THR* 2.9 43.5 + - - -
126X CYS* 3.6 30.7 + - + +
129X LEU* 3.8 17.4 - - + +
130X GLU* 2.9 25.5 + - - -
134X LEU* 4.2 7.2 - - + -
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Residues in contact with LYS 115 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H VAL* 4.3 25.1 - - + -
111X LEU 3.0 12.9 + - - +
112X ASP* 3.6 11.7 - - - +
114X HIS* 1.3 74.3 + - - +
116X LEU* 1.3 60.6 + - - +
118X THR* 3.2 9.8 + - + +
119X ASP* 2.9 29.3 + - - +
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Residues in contact with LEU 116 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11X ASP* 3.6 39.5 - - + +
12X CYS* 4.0 11.0 - - - -
15X ALA* 3.7 20.0 - - + -
18X ARG* 5.4 2.2 - - - +
112X ASP 3.0 14.2 + - - +
113X LEU* 3.6 11.4 - - + +
115X LYS* 1.3 77.5 - - - +
117X ALA* 1.3 57.9 + - - +
119X ASP* 3.3 5.9 + - + +
120X LYS* 2.9 50.4 + - + +
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Residues in contact with ALA 117 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12X CYS* 4.3 10.9 - - - -
113X LEU 3.0 14.5 + - - +
114X HIS* 3.5 10.5 - - - +
116X LEU* 1.3 74.0 - - - +
118X THR* 1.3 64.8 + - - +
120X LYS 3.5 0.7 + - - -
121X VAL 3.1 3.3 + - - -
122X ASP* 2.9 34.4 + - + +
125X LEU* 3.9 28.0 - - + -
126X CYS* 3.6 17.7 - - - +
129X LEU* 5.1 0.2 - - + -
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Residues in contact with THR 118 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H VAL* 6.3 2.7 - - + -
114X HIS* 2.9 30.8 + - - -
115X LYS* 3.2 10.7 + - + +
117X ALA* 1.3 76.2 - - - +
119X ASP* 1.3 63.0 + - - +
121X VAL* 3.1 18.2 + - - +
122X ASP 5.1 0.2 - - - +
126X CYS* 3.5 15.8 - - - -
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Residues in contact with ASP 119 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115X LYS 2.9 15.8 + - - +
116X LEU* 3.6 9.9 - - + +
118X THR* 1.3 78.4 - - - +
120X LYS* 1.3 72.4 + - + +
121X VAL* 3.2 9.2 + - - +
----------------------------------------------------------
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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