Contacts of the helix formed by residues 92 - 119 (chain U) 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 U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37U PHE* 3.6 19.7 - - - -
44U LEU* 3.8 8.3 - - - +
47U VAL* 4.1 16.9 - - + +
91U ASN* 1.3 72.1 - - - +
93U LEU* 1.3 57.6 + - - +
95U ALA* 3.6 1.0 + - - +
96U MET* 3.0 38.2 + - + +
151U LEU* 4.1 7.6 - - + -
156U LEU* 4.0 7.0 - - - -
163U GLU* 2.8 30.4 + - - +
166U PHE* 3.8 35.4 - - + -
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Residues in contact with LEU 93 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91U ASN* 2.9 10.9 + - - +
92U THR* 1.3 76.9 - - - +
94U GLU* 1.3 62.6 - - - +
96U MET* 3.3 1.0 + - - +
97U GLN* 2.9 53.3 + - + +
148U ILE* 3.9 29.4 - - + +
151U LEU* 3.9 23.8 - - + -
152U LYS* 4.3 16.4 - - + -
156U LEU* 3.4 17.2 - - + +
157U PRO* 3.7 34.5 - - + -
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Residues in contact with GLU 94 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86U ARG* 3.0 39.9 + - - +
89U TRP 3.4 12.1 - - - +
90U GLY* 3.7 9.0 - - - -
91U ASN* 3.1 27.0 + - - +
92U THR 3.4 0.2 - - - -
93U LEU* 1.3 79.4 - - - +
95U ALA* 1.3 58.0 + - - +
97U GLN* 3.5 13.9 + - - +
98U ALA* 3.0 26.7 + - - +
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Residues in contact with ALA 95 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33U MET* 3.8 9.6 - - - +
37U PHE* 3.7 27.6 - - + -
51U PHE* 4.1 11.4 - - + -
89U TRP* 3.7 16.5 + - + -
91U ASN 3.0 18.6 + - - +
92U THR 3.9 2.2 - - - +
94U GLU* 1.3 75.4 - - - +
96U MET* 1.3 60.7 + - - +
98U ALA* 3.4 7.3 + - - +
99U ALA* 2.9 28.1 + - - +
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Residues in contact with MET 96 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47U VAL* 4.6 3.4 - - + -
50U PHE* 4.0 17.3 - - + -
51U PHE* 3.7 30.7 - - + -
92U THR* 3.0 26.5 + - + +
93U LEU 3.3 4.2 + - - +
95U ALA* 1.3 74.1 - - - +
97U GLN* 1.3 60.2 + - - +
99U ALA* 3.3 2.6 + - - +
100U LEU* 2.8 23.9 + - - +
144U ILE* 3.4 20.3 - - + +
147U PHE* 3.9 33.7 - - + -
148U ILE* 3.7 18.1 - - + +
151U LEU* 3.8 17.0 - - + -
166U PHE* 4.3 16.6 - - + -
171U VAL* 5.3 1.6 - - + -
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Residues in contact with GLN 97 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93U LEU* 2.9 43.4 + - + +
94U GLU* 3.8 15.8 - - - +
96U MET* 1.3 72.8 - - - +
98U ALA* 1.3 66.1 + - - +
100U LEU* 3.3 3.6 + - - +
101U GLN* 3.1 25.5 + - - +
148U ILE* 4.0 20.9 - - + +
152U LYS* 4.1 21.8 + - - -
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Residues in contact with ALA 98 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29U THR* 6.1 0.2 - - - +
33U MET* 4.0 4.7 - - + -
85U GLU* 5.4 4.5 - - - +
86U ARG* 5.6 2.7 - - - +
89U TRP* 3.8 32.1 - - + -
94U GLU 3.0 15.1 + - - +
95U ALA 3.5 8.1 - - - +
97U GLN* 1.3 76.3 - - - +
99U ALA* 1.3 57.3 + - - +
101U GLN* 3.4 7.3 + - - +
102U LEU* 3.0 27.8 + - - +
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Residues in contact with ALA 99 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30U TYR* 3.9 28.0 + - + +
33U MET* 4.2 5.6 - - + +
51U PHE* 4.2 8.3 - - + -
95U ALA 2.9 17.4 + - - +
96U MET* 3.5 10.5 - - - +
97U GLN 3.2 0.2 - - - -
98U ALA* 1.3 73.9 - - - +
100U LEU* 1.3 59.7 + - - +
102U LEU* 3.2 5.8 + - - +
103U GLU* 2.9 34.2 + - - +
144U ILE* 4.1 12.8 - - + -
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Residues in contact with LEU 100 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3P GLN* 3.8 37.2 - - + +
4P VAL* 4.9 0.7 - - + -
96U MET 2.8 20.4 + - - +
97U GLN* 3.3 6.0 + - - +
99U ALA* 1.3 73.4 - - - +
101U GLN* 1.3 57.3 + - + +
103U GLU* 3.4 3.7 + - - +
104U LYS* 3.0 41.8 + - + +
141U ILE* 3.9 41.7 - - + +
144U ILE* 3.9 11.4 - - + +
145U GLY* 4.5 3.6 - - - +
148U ILE* 3.7 22.9 - - + -
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Residues in contact with GLN 101 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97U GLN 3.1 12.1 + - - +
98U ALA* 3.7 9.2 - - - +
100U LEU* 1.3 76.7 - - + +
102U LEU* 1.3 60.6 + - - +
104U LYS* 3.2 10.9 + - - +
105U THR* 2.9 33.9 + - - +
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Residues in contact with LEU 102 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22U LEU* 5.4 1.6 - - + -
25U TYR* 4.1 27.8 - - + -
26U ALA* 3.9 26.9 - - + +
29U THR* 3.7 28.9 - - + -
30U TYR* 3.9 33.2 - - + +
98U ALA 3.0 18.1 + - - +
99U ALA* 3.2 6.0 + - - +
101U GLN* 1.3 75.9 - - - +
103U GLU* 1.3 60.4 + - + +
105U THR* 3.4 10.8 + - + -
106U VAL* 3.1 36.2 + - + +
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Residues in contact with GLU 103 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26U ALA* 6.2 0.6 - - - +
30U TYR* 2.8 27.5 + - - +
54U HIS* 3.6 14.7 + - - -
58U GLU* 3.4 12.9 - - - +
99U ALA 2.9 14.5 + - - +
100U LEU* 3.8 5.2 - - - +
102U LEU* 1.3 75.9 - - - +
104U LYS* 1.3 59.5 + - - +
106U VAL* 3.3 5.6 + - - +
107U ASN* 2.8 25.8 + - - +
137U GLN* 3.0 29.1 + - - +
140U ASP* 4.4 7.0 - - + -
141U ILE* 3.9 13.9 - - + -
144U ILE* 3.9 15.3 - - + -
177U MG 2.9 27.5 - - - -
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Residues in contact with LYS 104 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2P SER 5.0 0.6 + - - -
3P GLN* 2.9 30.0 + - - +
4P VAL 4.4 6.1 - - - +
5P ARG 3.5 17.2 + - - -
6P GLN* 3.1 44.8 + - + +
100U LEU* 3.0 28.6 + - + +
101U GLN* 3.2 10.3 + - - +
103U GLU* 1.3 75.5 - - - +
105U THR* 1.3 57.2 + - - +
107U ASN* 4.1 0.2 - - - -
108U GLN* 2.9 25.8 + - - +
141U ILE* 4.2 10.5 - - + -
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Residues in contact with THR 105 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22U LEU* 4.6 19.5 - - + -
25U TYR* 6.5 0.4 - - + -
101U GLN* 2.9 20.1 + - - +
102U LEU* 3.5 12.1 - - + +
104U LYS* 1.3 77.1 - - - +
106U VAL* 1.3 63.4 + - - +
108U GLN* 3.4 6.6 + - - +
109U ALA* 3.1 22.0 + - - +
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Residues in contact with VAL 106 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19U MET* 5.1 2.0 - - - -
22U LEU* 3.9 29.6 - - + +
23U GLU* 4.0 9.9 - - - +
26U ALA* 4.2 24.9 - - + -
58U GLU* 4.9 0.9 - - - +
102U LEU* 3.1 19.9 + - + +
103U GLU* 3.7 9.9 - - - +
105U THR* 1.3 71.7 - - - +
107U ASN* 1.3 65.5 + - - +
109U ALA* 3.2 2.8 + - - +
110U LEU* 3.0 31.3 + - + +
137U GLN* 3.9 11.9 - - - +
176U MG 3.8 22.2 - - - -
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Residues in contact with ASN 107 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6P GLN* 3.1 40.3 + - - +
103U GLU 2.8 21.3 + - - +
104U LYS 3.6 0.2 - - - +
106U VAL* 1.3 73.6 - - - +
108U GLN* 1.3 58.1 - - - +
110U LEU* 3.1 10.3 + - - +
111U LEU* 2.9 41.7 + - - +
134U LEU* 4.8 8.3 - - - +
137U GLN* 3.6 23.1 - - - +
138U VAL* 5.0 10.1 - - - +
141U ILE* 3.9 16.2 - - + +
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Residues in contact with GLN 108 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6P GLN* 3.6 22.3 + - - +
7P ASN* 5.9 1.9 - - - +
104U LYS 2.9 17.7 + - - +
105U THR* 3.6 7.0 - - - +
107U ASN* 1.3 79.1 - - - +
109U ALA* 1.3 56.7 + - - +
111U LEU* 3.4 16.2 + - - +
112U ASP* 2.9 64.0 + - - +
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Residues in contact with ALA 109 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19U MET* 3.1 20.4 - - + +
22U LEU* 3.7 22.0 - - + -
105U THR 3.1 14.1 + - - +
106U VAL 3.4 9.0 - - - +
108U GLN* 1.3 76.9 - - - +
110U LEU* 1.3 58.4 + - - +
112U ASP* 3.4 9.8 + - - +
113U LEU* 2.9 22.3 + - - +
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Residues in contact with LEU 110 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19U MET* 3.7 24.7 - - + -
23U GLU* 4.9 1.6 - - - +
65U PHE* 4.0 20.6 - - + -
106U VAL* 3.0 25.3 + - + +
107U ASN* 3.1 7.2 + - - +
109U ALA* 1.3 76.1 - - - +
111U LEU* 1.3 59.8 + - - +
113U LEU* 3.4 3.2 + - - +
114U HIS* 2.9 26.9 + - - +
129U LEU* 4.2 14.5 - - + +
133U TYR* 3.9 32.3 - - + -
134U LEU* 3.9 14.9 - - + +
137U GLN* 3.7 30.3 - - + +
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Residues in contact with LEU 111 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6P GLN* 4.5 4.5 - - + -
7P ASN* 3.8 32.3 - - + +
123P PRO* 3.7 35.8 - - + +
124P HIS* 5.3 4.0 - - + +
107U ASN* 2.9 43.2 + - - +
108U GLN* 3.7 20.0 - - - +
110U LEU* 1.3 74.6 - - - +
112U ASP* 1.3 59.9 + - - +
114U HIS* 3.2 6.4 + - - +
115U LYS* 3.0 27.4 + - - +
134U LEU* 4.6 15.9 - - + -
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Residues in contact with ASP 112 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108U GLN* 2.9 48.3 + - - +
109U ALA* 3.4 9.7 - - - +
111U LEU* 1.3 76.9 - - - +
113U LEU* 1.3 60.9 + - - +
115U LYS* 3.3 8.5 + - - +
116U LEU* 3.0 26.3 + - - +
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Residues in contact with LEU 113 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12U CYS 4.3 9.0 - - - +
15U ALA* 3.5 31.6 - - + +
16U VAL* 4.3 17.5 - - + -
19U MET* 3.7 35.7 - - + -
65U PHE* 4.5 2.2 - - + -
109U ALA 2.9 16.5 + - - +
110U LEU* 3.7 4.9 - - + +
111U LEU 3.3 0.2 - - - -
112U ASP* 1.3 74.8 - - - +
114U HIS* 1.3 58.9 + - - +
116U LEU* 3.4 10.2 + - + +
117U ALA* 3.0 26.0 + - - +
125U LEU* 4.4 10.3 - - + -
129U LEU* 3.9 25.6 - - + -
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Residues in contact with HIS 114 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121P VAL* 6.1 1.4 - - - +
123P PRO* 3.5 37.5 - - + +
110U LEU 2.9 14.3 + - - +
111U LEU* 3.3 12.8 - - - +
112U ASP 3.1 0.2 - - - -
113U LEU* 1.3 74.8 - - - +
115U LYS* 1.3 62.1 + - - +
117U ALA* 3.3 4.6 + - - +
118U THR* 2.9 42.8 + - - -
126U CYS* 3.6 30.7 + - - +
129U LEU* 3.8 18.1 - - + +
130U GLU* 2.9 25.8 + - - -
134U LEU* 4.2 7.2 - - + -
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Residues in contact with LYS 115 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121P VAL* 4.4 23.1 - - + -
111U LEU 3.0 12.6 + - - +
112U ASP* 3.3 11.4 + - - +
114U HIS* 1.3 74.9 + - - +
116U LEU* 1.3 62.3 + - - +
118U THR* 3.2 9.3 + - + -
119U ASP* 2.9 29.5 + - - +
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Residues in contact with LEU 116 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11U ASP* 3.6 40.8 - - + +
12U CYS* 4.0 11.7 - - - -
15U ALA* 3.7 19.7 - - + -
18U ARG* 5.4 2.5 - - - +
112U ASP 3.0 13.8 + - - +
113U LEU* 3.6 11.2 - - + +
115U LYS* 1.3 77.1 - - - +
117U ALA* 1.3 56.2 + - - +
119U ASP* 3.3 5.8 + - + +
120U LYS* 2.9 50.0 + - + +
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Residues in contact with ALA 117 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12U CYS* 4.3 10.9 - - - -
113U LEU 3.0 14.5 + - - +
114U HIS* 3.5 10.1 - - - +
116U LEU* 1.3 73.1 - - - +
118U THR* 1.3 64.5 + - - +
120U LYS 3.5 0.9 + - - +
121U VAL 3.1 3.6 + - - -
122U ASP* 2.9 34.7 + - + +
125U LEU* 3.9 27.6 - - + -
126U CYS* 3.6 18.4 - - - +
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Residues in contact with THR 118 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121P VAL* 6.4 1.8 - - + -
114U HIS* 2.9 31.4 + - - -
115U LYS* 3.5 10.3 - - + +
117U ALA* 1.3 76.5 - - - +
119U ASP* 1.3 64.6 + - - +
121U VAL* 3.1 17.7 + - - +
126U CYS* 3.5 16.0 - - - -
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Residues in contact with ASP 119 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115U LYS 2.9 17.5 + - - +
116U LEU* 3.6 8.7 - - + +
118U THR* 1.3 78.6 - - - +
120U LYS* 1.3 73.3 + - + +
121U 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