Contacts of the helix formed by residues 92 - 119 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37S PHE* 3.6 19.6 - - - -
44S LEU* 3.8 8.1 - - - +
47S VAL* 4.1 17.1 - - + +
91S ASN* 1.3 71.0 - - - +
93S LEU* 1.3 58.0 + - - +
95S ALA* 3.6 1.0 + - - +
96S MET* 3.0 38.9 + - + +
151S LEU* 4.1 8.3 - - + -
156S LEU* 4.0 7.4 - - - -
163S GLU* 2.8 31.2 + - - +
166S PHE* 3.8 34.5 - - + -
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Residues in contact with LEU 93 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91S ASN* 2.9 10.5 + - - +
92S THR* 1.3 75.6 - - - +
94S GLU* 1.3 62.2 + - - +
96S MET* 3.3 1.8 + - - +
97S GLN* 2.9 52.3 + - - +
148S ILE* 3.9 29.2 - - + +
151S LEU* 3.9 23.8 - - + -
152S LYS* 4.3 16.2 - - + -
156S LEU* 3.4 18.6 - - + +
157S PRO* 3.7 35.0 - - + -
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Residues in contact with GLU 94 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86S ARG* 3.0 40.0 + - - +
89S TRP 3.4 12.3 - - - +
90S GLY* 3.7 8.3 - - - -
91S ASN* 3.1 27.7 + - - +
92S THR 3.4 0.2 - - - -
93S LEU* 1.3 80.1 - - - +
95S ALA* 1.3 57.9 + - - +
97S GLN* 3.5 14.3 + - + +
98S ALA* 3.0 26.9 + - - +
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Residues in contact with ALA 95 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33S MET* 3.8 9.7 - - - +
37S PHE* 3.7 26.7 - - + -
51S PHE* 4.1 11.9 - - + -
89S TRP* 3.7 16.9 + - + -
91S ASN 3.0 18.2 + - - +
92S THR 3.9 2.2 - - - +
94S GLU* 1.3 75.4 - - - +
96S MET* 1.3 59.8 + - - +
98S ALA* 3.4 7.7 + - - +
99S ALA* 2.9 27.5 + - - +
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Residues in contact with MET 96 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47S VAL* 4.6 3.6 - - + -
50S PHE* 4.0 16.8 - - + -
51S PHE* 3.7 30.7 - - + -
92S THR* 3.0 26.6 + - + +
93S LEU 3.3 4.2 + - - +
95S ALA* 1.3 73.8 - - - +
97S GLN* 1.3 61.0 + - - +
99S ALA* 3.3 1.9 + - - +
100S LEU* 2.8 23.7 + - - +
144S ILE* 3.4 20.9 - - + +
147S PHE* 3.9 32.5 - - + -
148S ILE* 3.7 18.3 - - + +
151S LEU* 3.8 16.8 - - + -
166S PHE* 4.3 16.8 - - + -
171S VAL* 5.3 1.3 - - + -
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Residues in contact with GLN 97 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93S LEU* 2.9 42.2 + - + +
94S GLU* 3.8 14.7 - - - +
96S MET* 1.3 71.8 - - - +
98S ALA* 1.3 66.0 + - - +
100S LEU* 3.3 3.3 + - + +
101S GLN* 3.1 25.5 + - - +
148S ILE* 4.0 22.0 - - + +
152S LYS* 4.1 21.3 + - - -
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Residues in contact with ALA 98 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33S MET* 4.0 4.4 - - + +
85S GLU* 5.4 4.0 - - - +
86S ARG* 5.6 2.5 - - - +
89S TRP* 3.8 32.3 - - + -
94S GLU 3.0 15.1 + - - +
95S ALA 3.5 8.7 - - - +
97S GLN* 1.3 76.7 - - - +
99S ALA* 1.3 57.7 + - - +
101S GLN* 3.4 7.0 + - - +
102S LEU* 3.0 26.9 + - - +
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Residues in contact with ALA 99 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30S TYR* 3.9 27.3 + - + +
33S MET* 4.2 5.1 - - + +
51S PHE* 4.2 9.2 - - + -
95S ALA 2.9 17.3 + - - +
96S MET* 3.5 9.2 - - - +
98S ALA* 1.3 75.1 - - - +
100S LEU* 1.3 58.8 + - - +
102S LEU* 3.2 6.0 + - - +
103S GLU* 2.9 35.2 + - - +
144S ILE* 4.1 12.6 - - + -
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Residues in contact with LEU 100 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3R GLN* 3.7 38.6 - - + +
4R VAL* 4.9 0.7 - - + -
96S MET 2.8 19.9 + - - +
97S GLN* 3.3 6.3 + - - +
99S ALA* 1.3 72.2 - - - +
101S GLN* 1.3 60.2 + - + +
103S GLU* 3.4 4.0 + - + +
104S LYS* 3.0 42.1 + - + +
141S ILE* 3.9 41.3 - - + +
144S ILE* 3.9 12.1 - - + +
145S GLY* 4.5 3.4 - - - +
148S ILE* 3.7 22.2 - - + -
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Residues in contact with GLN 101 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97S GLN 3.1 12.3 + - - +
98S ALA* 3.7 8.7 - - - +
99S ALA 3.3 0.2 - - - -
100S LEU* 1.3 77.1 - - + +
102S LEU* 1.3 61.0 + - - +
104S LYS* 3.2 10.1 + - - +
105S THR* 2.9 34.5 + - - +
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Residues in contact with LEU 102 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22S LEU* 5.4 1.3 - - + -
25S TYR* 4.1 27.6 - - + -
26S ALA* 3.9 25.6 - - + +
29S THR* 3.7 28.0 - - + -
30S TYR* 3.9 33.4 - - + +
98S ALA 3.0 17.4 + - - +
99S ALA* 3.2 5.4 + - - +
101S GLN* 1.3 74.8 - - - +
103S GLU* 1.3 60.1 + - + +
105S THR* 3.4 10.3 + - + -
106S VAL* 3.1 35.5 + - + +
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Residues in contact with GLU 103 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26S ALA* 6.5 0.4 - - - -
30S TYR* 2.8 29.3 + - - +
54S HIS* 3.6 14.2 + - - -
58S GLU* 3.4 12.9 - - - +
99S ALA 2.9 14.9 + - - +
100S LEU* 3.8 5.6 - - - +
102S LEU* 1.3 76.6 - - - +
104S LYS* 1.3 59.3 + - - +
106S VAL* 3.3 6.0 + - - +
107S ASN* 2.8 26.0 + - - +
137S GLN* 3.0 29.5 + - - +
140S ASP* 4.4 6.3 - - + -
141S ILE* 3.9 14.8 - - + -
144S ILE* 3.9 13.7 - - + -
177S MG 2.9 28.4 - - - -
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Residues in contact with LYS 104 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2R SER 4.9 0.4 + - - -
3R GLN* 2.9 30.4 + - - +
4R VAL 4.4 5.8 - - - +
5R ARG 3.5 17.0 + - - -
6R GLN* 3.1 44.4 + - + +
100S LEU* 3.0 28.6 + - + +
101S GLN* 3.2 9.6 + - - +
103S GLU* 1.3 75.1 - - - +
105S THR* 1.3 56.0 + - - +
107S ASN* 4.1 0.2 - - - -
108S GLN* 2.9 26.0 + - - +
141S ILE* 4.2 12.1 - - + -
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Residues in contact with THR 105 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22S LEU* 4.6 19.7 - - + -
25S TYR* 6.5 0.4 - - + -
101S GLN* 2.9 21.3 + - - +
102S LEU* 3.5 12.5 - - + +
103S GLU 3.2 0.2 - - - -
104S LYS* 1.3 76.6 - - - +
106S VAL* 1.3 63.2 + - - +
108S GLN* 3.4 6.6 + - - +
109S ALA* 3.1 22.0 + - - +
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Residues in contact with VAL 106 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19S MET* 5.1 2.0 - - - -
22S LEU* 3.9 29.6 - - + +
23S GLU* 4.0 9.6 - - - +
26S ALA* 4.2 24.2 - - + -
58S GLU* 4.9 0.7 - - - +
102S LEU* 3.1 20.7 + - + +
103S GLU* 3.7 9.6 - - - +
105S THR* 1.3 71.9 - - - +
107S ASN* 1.3 67.1 + - - +
109S ALA* 3.2 3.5 + - - +
110S LEU* 3.0 31.6 + - + +
137S GLN* 3.9 11.4 - - - +
176S MG 3.8 22.7 - - - -
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Residues in contact with ASN 107 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6R GLN* 3.1 38.4 + - - +
103S GLU 2.8 21.3 + - - +
104S LYS 3.6 0.7 - - - +
106S VAL* 1.3 71.7 - - - +
108S GLN* 1.3 57.9 + - - +
110S LEU* 3.1 9.6 + - - +
111S LEU* 2.9 42.3 + - - +
134S LEU* 4.8 9.4 - - - +
137S GLN* 3.6 22.1 - - - +
138S VAL* 5.0 9.8 - - - +
141S ILE* 3.9 16.8 - - + +
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Residues in contact with GLN 108 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6R GLN* 3.6 21.0 + - - +
7R ASN* 5.8 2.4 - - - +
104S LYS 2.9 17.9 + - - +
105S THR* 3.6 7.2 - - - +
107S ASN* 1.3 78.7 - - - +
109S ALA* 1.3 58.2 + - - +
111S LEU* 4.2 16.4 - - - +
112S ASP* 2.9 63.3 + - - +
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Residues in contact with ALA 109 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19S MET* 3.1 20.0 - - + +
22S LEU* 3.7 22.2 - - + -
105S THR 3.1 13.7 + - - +
106S VAL 3.4 9.2 - - - +
108S GLN* 1.3 77.9 - - - +
110S LEU* 1.3 58.5 + - - +
112S ASP* 3.4 10.1 + - - +
113S LEU* 2.9 22.3 + - - +
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Residues in contact with LEU 110 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19S MET* 3.7 24.7 - - + -
23S GLU* 4.9 1.3 - - - +
65S PHE* 4.0 20.9 - - + -
106S VAL* 3.0 24.9 + - + +
107S ASN* 3.1 6.5 + - - +
109S ALA* 1.3 75.2 - - - +
111S LEU* 1.3 60.7 + - - +
113S LEU* 3.4 3.3 + - - +
114S HIS* 2.9 26.9 + - - +
129S LEU* 4.2 14.3 - - + +
133S TYR* 3.9 33.0 - - + -
134S LEU* 3.9 16.3 - - + +
137S GLN* 3.7 31.0 - - + +
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Residues in contact with LEU 111 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6R GLN* 4.5 4.5 - - + -
7R ASN* 3.8 32.5 - - + +
123R PRO* 3.7 35.4 - - + +
124R HIS* 5.3 3.6 - - + +
107S ASN* 2.9 45.0 + - - +
108S GLN* 3.7 18.8 - - - +
110S LEU* 1.3 74.4 - - - +
112S ASP* 1.3 59.4 + - - +
114S HIS* 3.2 6.9 + - - +
115S LYS* 3.0 27.4 + - - +
134S LEU* 4.6 16.4 - - + -
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Residues in contact with ASP 112 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108S GLN* 2.9 48.9 + - - +
109S ALA* 3.4 9.9 - - - +
111S LEU* 1.3 76.5 - - - +
113S LEU* 1.3 60.5 + - - +
115S LYS* 3.3 8.2 + - - +
116S LEU* 3.0 26.3 + - - +
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Residues in contact with LEU 113 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12S CYS* 4.3 9.0 - - - +
15S ALA* 3.5 31.2 - - + +
16S VAL* 4.3 17.0 - - + -
19S MET* 3.7 35.2 - - + -
65S PHE* 4.5 2.2 - - + -
109S ALA 2.9 15.9 + - - +
110S LEU* 3.7 4.9 - - + +
111S LEU 3.3 0.2 - - - -
112S ASP* 1.3 74.8 - - - +
114S HIS* 1.3 59.4 + - - +
116S LEU* 3.4 9.9 + - + +
117S ALA* 3.0 26.0 + - - +
125S LEU* 4.4 10.3 - - + -
129S LEU* 3.9 25.6 - - + -
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Residues in contact with HIS 114 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121R VAL* 6.1 1.4 - - - +
123R PRO* 3.5 35.4 - - + +
110S LEU 2.9 14.5 + - - +
111S LEU* 3.3 13.0 - - - +
112S ASP 3.1 0.2 - - - -
113S LEU* 1.3 75.7 - - - +
115S LYS* 1.3 60.2 + - - +
117S ALA* 3.3 4.4 + - - +
118S THR* 2.9 43.6 + - - -
126S CYS* 3.6 31.7 + - - +
129S LEU* 3.8 18.3 - - + +
130S GLU* 2.9 24.7 + - - -
134S LEU* 4.2 7.4 - - + -
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Residues in contact with LYS 115 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121R VAL* 4.3 24.0 - - + -
111S LEU 3.0 12.9 + - - +
112S ASP* 3.5 11.7 - - - +
114S HIS* 1.3 75.5 + - - +
116S LEU* 1.3 60.8 + - - +
118S THR* 3.2 8.9 + - + -
119S ASP* 2.9 29.7 + - - +
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Residues in contact with LEU 116 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11S ASP* 3.6 40.8 - - + +
12S CYS* 4.0 11.4 - - - -
15S ALA* 3.7 19.7 - - + -
18S ARG* 5.4 2.2 - - - +
112S ASP 3.0 14.4 + - - +
113S LEU* 3.6 11.0 - - + +
114S HIS 3.3 0.2 - - - -
115S LYS* 1.3 76.8 - - - +
117S ALA* 1.3 57.4 + - - +
119S ASP* 3.3 5.0 + - + +
120S LYS* 2.9 49.6 + - + +
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Residues in contact with ALA 117 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12S CYS* 4.3 10.7 - - - -
113S LEU 3.0 14.1 + - - +
114S HIS* 3.3 10.3 + - - +
116S LEU* 1.3 73.3 - - - +
118S THR* 1.3 63.6 + - - +
120S LYS 3.5 0.9 + - - +
121S VAL 3.1 4.0 + - - -
122S ASP* 2.9 34.8 + - + +
125S LEU* 3.9 27.6 - - + -
126S CYS* 3.6 18.6 - - - +
129S LEU* 5.1 0.2 - - + -
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Residues in contact with THR 118 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121R VAL* 6.4 2.0 - - + -
114S HIS* 2.9 30.7 + - - -
115S LYS* 3.2 10.5 + - + +
117S ALA* 1.3 76.4 - - - +
119S ASP* 1.3 63.3 + - - +
121S VAL* 3.1 18.0 + - - +
126S CYS* 3.5 15.5 - - - -
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Residues in contact with ASP 119 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115S LYS 2.9 16.7 + - - +
116S LEU* 3.6 9.2 - - + +
118S THR* 1.3 77.8 - - - +
120S LYS* 1.3 72.7 + - + +
121S VAL* 3.4 9.0 + - - +
----------------------------------------------------------
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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