Contacts of the helix formed by residues 92 - 119 (chain T) 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 T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37T PHE* 3.6 19.9 - - - -
44T LEU* 3.8 8.1 - - - +
47T VAL* 4.1 17.6 - - + +
91T ASN* 1.3 72.6 - - - +
93T LEU* 1.3 56.5 + - - +
95T ALA* 3.9 1.4 - - - +
96T MET* 3.0 38.6 + - + +
151T LEU* 4.1 7.9 - - + -
156T LEU* 4.0 7.2 - - - -
163T GLU* 2.8 29.9 + - - +
166T PHE* 3.8 34.8 - - + -
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Residues in contact with LEU 93 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91T ASN* 2.9 10.3 + - - +
92T THR* 1.3 75.2 - - - +
94T GLU* 1.3 62.4 + - - +
96T MET* 3.3 1.0 + - - +
97T GLN* 2.9 52.4 + - - +
148T ILE* 3.9 28.7 - - + +
151T LEU* 3.9 23.8 - - + -
152T LYS* 4.3 16.2 - - + -
156T LEU* 3.4 17.8 - - + +
157T PRO* 3.7 36.1 - - + -
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Residues in contact with GLU 94 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86T ARG* 3.0 40.1 + - - +
89T TRP 3.4 12.1 - - - +
90T GLY* 3.7 8.4 - - - -
91T ASN* 3.1 28.0 + - - +
93T LEU* 1.3 79.5 - - - +
95T ALA* 1.3 57.3 + - - +
97T GLN* 3.8 15.0 - - - +
98T ALA* 3.0 26.7 + - - +
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Residues in contact with ALA 95 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33T MET* 3.8 10.1 - - - +
37T PHE* 3.7 27.8 - - + -
51T PHE* 4.1 11.4 - - + -
89T TRP* 3.7 16.1 + - + -
91T ASN 3.0 17.3 + - - +
92T THR 3.9 2.2 - - - +
94T GLU* 1.3 75.4 - - - +
96T MET* 1.3 59.5 + - - +
98T ALA* 3.4 7.8 + - - +
99T ALA* 2.9 27.5 + - - +
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Residues in contact with MET 96 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47T VAL* 4.6 4.3 - - + -
50T PHE* 4.0 17.0 - - + -
51T PHE* 3.7 31.2 - - + -
92T THR* 3.0 25.9 + - + +
93T LEU 3.3 4.0 + - - +
95T ALA* 1.3 72.6 - - - +
97T GLN* 1.3 61.3 + - - +
99T ALA* 3.3 2.4 + - - +
100T LEU* 2.8 24.3 + - - +
144T ILE* 3.4 20.6 - - + +
147T PHE* 3.9 32.1 - - + -
148T ILE* 3.7 17.9 - - + +
151T LEU* 3.8 17.0 - - + -
166T PHE* 4.3 16.6 - - + -
171T VAL* 5.3 1.6 - - + -
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Residues in contact with GLN 97 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93T LEU* 2.9 41.7 + - + +
94T GLU* 3.8 15.2 - - - +
95T ALA 3.3 0.2 - - - -
96T MET* 1.3 73.0 - - - +
98T ALA* 1.3 65.4 + - - +
100T LEU* 3.3 3.7 + - + +
101T GLN* 3.1 25.6 + - - +
148T ILE* 4.0 21.9 - - + +
152T LYS* 4.1 21.1 + - - -
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Residues in contact with ALA 98 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33T MET* 4.0 4.0 - - + -
85T GLU* 5.4 4.7 - - - +
86T ARG* 5.6 2.2 - - - +
89T TRP* 3.8 32.5 - - + -
94T GLU 3.0 15.1 + - - +
95T ALA 3.5 8.3 - - - +
97T GLN* 1.3 76.3 - - - +
99T ALA* 1.3 59.1 + - - +
101T GLN* 3.4 6.0 + - - +
102T LEU* 3.0 27.9 + - - +
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Residues in contact with ALA 99 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30T TYR* 3.9 27.6 - - + +
33T MET* 4.2 5.4 - - + +
51T PHE* 4.2 8.5 - - + -
95T ALA 2.9 17.7 + - - +
96T MET* 3.5 10.1 - - - +
97T GLN 3.2 0.2 - - - -
98T ALA* 1.3 75.0 - - - +
100T LEU* 1.3 59.5 + - - +
102T LEU* 3.2 5.9 + - - +
103T GLU* 2.9 34.7 + - - +
144T ILE* 4.1 12.6 - - + -
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Residues in contact with LEU 100 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3M GLN* 3.8 37.9 - - + +
4M VAL* 4.9 0.7 - - + -
96T MET 2.8 20.6 + - - +
97T GLN* 3.7 5.6 - - - +
99T ALA* 1.3 72.3 - - - +
101T GLN* 1.3 61.0 + - + +
103T GLU* 3.4 3.7 + - - +
104T LYS* 3.0 42.1 + - + +
141T ILE* 3.9 41.7 - - + +
144T ILE* 3.9 11.6 - - + +
145T GLY* 4.5 2.9 - - - +
148T ILE* 3.7 22.2 - - + -
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Residues in contact with GLN 101 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97T GLN 3.1 12.5 + - - +
98T ALA* 3.7 8.5 - - - +
100T LEU* 1.3 77.2 - - + +
102T LEU* 1.3 61.1 + - - +
104T LYS* 3.2 10.3 + - - +
105T THR* 2.9 34.8 + - - +
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Residues in contact with LEU 102 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22T LEU* 5.4 1.6 - - + -
25T TYR* 4.1 26.9 - - + -
26T ALA* 3.9 25.6 - - + +
29T THR* 3.7 28.7 - - + -
30T TYR* 3.9 33.0 - - + +
98T ALA 3.0 18.9 + - - +
99T ALA* 3.2 5.6 + - - +
101T GLN* 1.3 75.8 - - - +
103T GLU* 1.3 59.7 + - + +
105T THR* 3.4 10.6 + - + -
106T VAL* 3.1 35.6 + - + +
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Residues in contact with GLU 103 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26T ALA* 6.5 0.4 - - - -
30T TYR* 2.8 29.3 + - - +
54T HIS* 3.6 14.7 + - - -
58T GLU* 3.4 12.0 - - - +
99T ALA 2.9 14.3 + - - +
100T LEU* 3.8 5.2 - - - +
102T LEU* 1.3 75.7 - - - +
104T LYS* 1.3 60.5 + - - +
106T VAL* 3.3 6.1 + - - +
107T ASN* 2.8 25.6 + - - +
137T GLN* 3.0 28.8 + - - +
140T ASP* 4.4 6.7 - - + -
141T ILE* 3.9 15.5 - - + -
144T ILE* 3.9 13.9 - - + -
177T MG 2.9 26.6 - - - -
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Residues in contact with LYS 104 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2M SER 4.9 0.6 + - - -
3M GLN* 2.9 30.4 + - - +
4M VAL 4.4 5.6 - - - +
5M ARG 3.5 16.6 + - - -
6M GLN* 3.1 42.6 + - + +
100T LEU* 3.0 29.2 + - + +
101T GLN* 3.7 10.1 - - - +
103T GLU* 1.3 75.4 - - - +
105T THR* 1.3 56.9 + - - +
107T ASN* 4.1 0.4 - - - -
108T GLN* 2.9 26.0 + - - +
141T ILE* 4.2 10.5 - - + -
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Residues in contact with THR 105 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22T LEU* 4.6 19.5 - - + -
25T TYR* 6.5 0.4 - - + -
101T GLN* 2.9 21.1 + - - +
102T LEU* 3.5 12.1 - - + +
104T LYS* 1.3 76.6 - - - +
106T VAL* 1.3 63.0 + - + +
108T GLN* 3.4 6.3 + - - +
109T ALA* 3.1 22.7 + - - +
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Residues in contact with VAL 106 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19T MET* 5.1 2.0 - - - -
22T LEU* 3.9 29.2 - - + +
23T GLU* 4.0 10.1 - - - +
26T ALA* 4.2 23.8 - - + -
58T GLU* 4.9 1.1 - - - +
102T LEU* 3.1 19.3 + - + +
103T GLU* 3.7 9.4 - - - +
105T THR* 1.3 72.2 - - - +
107T ASN* 1.3 66.1 + - - +
109T ALA* 3.2 3.5 + - - +
110T LEU* 3.0 30.9 + - + +
137T GLN* 3.9 11.9 - - - +
176T MG 3.8 22.0 - - - -
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Residues in contact with ASN 107 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M GLN* 3.0 40.2 + - - +
103T GLU 2.8 21.4 + - - +
104T LYS 3.6 0.4 - - - +
105T THR 3.3 0.2 - - - -
106T VAL* 1.3 72.8 - - - +
108T GLN* 1.3 57.1 + - - +
110T LEU* 3.1 9.9 + - - +
111T LEU* 2.9 42.3 + - - +
134T LEU* 4.8 8.5 - - - +
137T GLN* 3.6 23.5 - - - +
138T VAL* 5.0 9.7 - - - +
141T ILE* 3.9 16.6 - - + +
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Residues in contact with GLN 108 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M GLN* 3.6 21.0 + - - +
7M ASN* 5.9 2.0 - - - +
104T LYS 2.9 17.9 + - - +
105T THR* 3.6 7.2 - - - +
107T ASN* 1.3 78.3 - - - +
109T ALA* 1.3 57.8 + - - +
111T LEU* 3.4 16.1 + - - +
112T ASP* 2.9 63.6 + - - +
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Residues in contact with ALA 109 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19T MET* 3.1 20.7 - - + +
22T LEU* 3.7 22.4 - - + -
105T THR 3.1 13.4 + - - +
106T VAL 3.4 8.5 - - - +
108T GLN* 1.3 77.3 - - - +
110T LEU* 1.3 58.9 + - - +
112T ASP* 3.4 9.3 + - - +
113T LEU* 2.9 22.5 + - - +
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Residues in contact with LEU 110 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19T MET* 3.7 24.2 - - + -
23T GLU* 4.9 1.8 - - - +
65T PHE* 4.0 21.3 - - + -
106T VAL* 3.0 25.1 + - + +
107T ASN* 3.1 6.9 + - - +
109T ALA* 1.3 74.8 - - - +
111T LEU* 1.3 61.1 + - - +
113T LEU* 3.4 3.2 + - - +
114T HIS* 2.9 26.7 + - - +
129T LEU* 4.2 14.6 - - + +
133T TYR* 3.9 32.1 - - + -
134T LEU* 3.9 15.2 - - + +
137T GLN* 3.7 31.0 - - + +
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Residues in contact with LEU 111 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M GLN* 4.5 4.3 - - + +
7M ASN* 3.8 32.3 - - + +
123M PRO* 3.8 34.5 - - + +
124M HIS* 5.4 4.3 - - + +
107T ASN* 2.9 42.5 + - - +
108T GLN* 3.7 20.2 - - - +
110T LEU* 1.3 73.9 - - - +
112T ASP* 1.3 59.4 + - - +
114T HIS* 3.2 6.6 + - - +
115T LYS* 3.0 27.2 + - - +
134T LEU* 4.6 15.9 - - + -
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Residues in contact with ASP 112 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108T GLN* 2.9 47.2 + - - +
109T ALA* 3.4 10.0 - - - +
110T LEU 3.2 0.2 - - - -
111T LEU* 1.3 76.2 - - - +
113T LEU* 1.3 61.2 + - - +
115T LYS* 3.3 8.5 + - - +
116T LEU* 3.0 26.7 + - - +
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Residues in contact with LEU 113 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12T CYS* 4.3 9.6 - - - +
15T ALA* 3.5 31.6 - - + +
16T VAL* 4.3 17.0 - - + -
19T MET* 3.7 34.5 - - + -
65T PHE* 4.5 2.2 - - + -
109T ALA 2.9 17.2 + - - +
110T LEU* 3.7 4.9 - - + +
111T LEU 3.3 0.2 - - - -
112T ASP* 1.3 76.0 - - - +
114T HIS* 1.3 57.7 + - - +
116T LEU* 3.4 10.0 + - + +
117T ALA* 3.0 26.3 + - - +
125T LEU* 4.4 9.6 - - + -
129T LEU* 3.9 26.5 - - + -
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Residues in contact with HIS 114 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121M VAL* 6.1 1.4 - - - +
123M PRO* 3.5 36.4 - - + +
110T LEU 2.9 15.8 + - - +
111T LEU* 3.3 13.0 - - - +
112T ASP 3.1 0.2 - - - -
113T LEU* 1.3 74.8 - - - +
115T LYS* 1.3 60.6 + - - +
117T ALA* 3.3 4.5 + - - +
118T THR* 2.9 43.5 + - - -
126T CYS* 3.6 32.4 + - + +
129T LEU* 3.8 16.8 - - + +
130T GLU* 2.9 24.1 + - - -
134T LEU* 4.2 7.6 - - + -
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Residues in contact with LYS 115 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121M VAL* 4.3 23.8 - - + -
111T LEU 3.0 12.3 + - - +
112T ASP* 3.3 11.6 + - - +
114T HIS* 1.3 75.5 + - - +
116T LEU* 1.3 61.0 + - - +
118T THR* 3.2 10.1 + - + +
119T ASP* 2.9 29.0 + - + +
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Residues in contact with LEU 116 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11T ASP* 3.6 39.7 - - + +
12T CYS* 4.0 12.1 - - - -
15T ALA* 3.7 19.7 - - + -
18T ARG* 5.4 2.2 - - - +
112T ASP 3.0 13.8 + - - +
113T LEU* 3.6 11.2 - - + +
115T LYS* 1.3 76.6 - - - +
117T ALA* 1.3 57.1 + - - +
119T ASP* 3.3 5.8 + - + +
120T LYS* 2.9 50.1 + - + +
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Residues in contact with ALA 117 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12T CYS* 4.3 10.7 - - - -
113T LEU 3.0 14.1 + - - +
114T HIS* 3.5 10.3 - - - +
116T LEU* 1.3 73.6 - - - +
118T THR* 1.3 62.8 + - - +
120T LYS 3.5 0.5 + - - -
121T VAL 3.1 3.5 + - - -
122T ASP* 2.9 35.3 + - + +
125T LEU* 3.9 28.9 - - + -
126T CYS* 3.6 17.9 - - - +
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Residues in contact with THR 118 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121M VAL* 6.4 2.5 - - + -
114T HIS* 2.9 29.9 + - - -
115T LYS* 3.2 11.2 + - + +
117T ALA* 1.3 77.8 - - - +
119T ASP* 1.3 61.8 + - - +
121T VAL* 3.1 18.3 + - - +
126T CYS* 3.5 16.5 - - - -
----------------------------------------------------------
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Residues in contact with ASP 119 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115T LYS* 2.9 16.3 + - + +
116T LEU* 3.6 9.2 - - + +
118T THR* 1.3 79.0 - - - +
120T LYS* 1.3 72.9 + - + +
121T 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