Contacts of the helix formed by residues 92 - 119 (chain I) 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 I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I PHE* 3.6 19.6 - - - -
44I LEU* 3.8 8.1 - - - +
47I VAL* 4.1 17.1 - - + +
91I ASN* 1.3 73.4 - - - +
93I LEU* 1.3 58.3 + - - +
95I ALA* 3.9 1.2 - - - +
96I MET* 3.0 38.5 + - + +
151I LEU* 4.1 7.6 - - + -
156I LEU* 4.0 7.0 - - - -
163I GLU* 2.8 29.9 + - - +
166I PHE* 3.8 35.2 - - + -
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Residues in contact with LEU 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91I ASN* 2.9 10.6 + - - +
92I THR* 1.3 75.8 - - - +
94I GLU* 1.3 61.1 - - - +
96I MET* 3.3 1.0 + - - +
97I GLN* 2.9 53.3 + - + +
148I ILE* 3.9 29.4 - - + +
151I LEU* 3.9 23.8 - - + -
152I LYS* 4.3 16.2 - - + -
156I LEU* 3.4 19.0 - - + +
157I PRO* 3.7 35.4 - - + -
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Residues in contact with GLU 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I ARG* 3.0 40.7 + - - +
89I TRP 3.4 12.1 - - - +
90I GLY* 3.7 8.4 - - - -
91I ASN* 3.1 28.5 + - - +
92I THR 3.4 0.2 - - - -
93I LEU* 1.3 78.6 - - - +
95I ALA* 1.3 57.5 + - - +
97I GLN* 3.5 13.9 + - - +
98I ALA* 3.0 26.9 + - - +
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Residues in contact with ALA 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I MET* 3.8 9.8 - - - +
37I PHE* 3.7 28.0 - - + -
51I PHE* 4.1 10.8 - - + -
89I TRP* 3.7 16.7 + - + -
91I ASN 3.0 16.9 + - - +
92I THR 3.9 2.5 - - - +
94I GLU* 1.3 76.5 - - - +
96I MET* 1.3 60.6 + - - +
98I ALA* 3.4 7.1 + - - +
99I ALA* 2.9 27.7 + - - +
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Residues in contact with MET 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I VAL* 4.6 3.4 - - + -
50I PHE* 4.0 17.3 - - + -
51I PHE* 3.7 31.4 - - + -
92I THR* 3.0 27.4 + - + +
93I LEU 3.7 3.6 - - - +
95I ALA* 1.3 73.7 - - - +
97I GLN* 1.3 61.8 + - - +
99I ALA* 3.3 2.8 + - - +
100I LEU* 2.8 23.7 + - - +
144I ILE* 3.4 20.3 - - + +
147I PHE* 3.9 32.5 - - + -
148I ILE* 3.7 18.5 - - + +
151I LEU* 3.8 16.6 - - + -
166I PHE* 4.3 16.6 - - + -
171I VAL* 5.3 1.3 - - + -
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Residues in contact with GLN 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93I LEU* 2.9 43.2 + - + +
94I GLU* 3.8 14.8 - - - +
96I MET* 1.3 73.0 - - - +
98I ALA* 1.3 66.7 + - - +
100I LEU* 3.3 3.6 + - - +
101I GLN* 3.1 25.3 + - - +
148I ILE* 4.0 20.9 - - + +
152I LYS* 4.1 21.5 + - - -
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Residues in contact with ALA 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I MET* 4.0 4.2 - - + +
85I GLU* 5.4 4.5 - - - +
86I ARG* 5.6 2.7 - - - +
89I TRP* 3.8 32.3 - - + -
94I GLU 3.0 15.7 + - - +
95I ALA 3.5 8.5 - - - +
97I GLN* 1.3 76.9 - - - +
99I ALA* 1.3 56.6 + - - +
101I GLN* 3.4 6.9 + - - +
102I LEU* 3.0 27.8 + - - +
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Residues in contact with ALA 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I TYR* 3.9 27.4 - - + +
33I MET* 4.2 5.3 - - + +
51I PHE* 4.2 8.5 - - + -
95I ALA 2.9 16.6 + - - +
96I MET* 3.5 10.3 - - - +
97I GLN 3.2 0.2 - - - -
98I ALA* 1.3 75.1 - - - +
100I LEU* 1.3 59.2 + - - +
102I LEU* 3.2 6.0 + - - +
103I GLU* 2.9 34.6 + - - +
144I ILE* 4.1 12.6 - - + -
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Residues in contact with LEU 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D GLN* 3.8 36.8 - - + +
4D VAL* 5.0 0.9 - - + -
96I MET 2.8 19.8 + - - +
97I GLN* 3.3 6.3 + - + +
99I ALA* 1.3 73.1 - - - +
101I GLN* 1.3 58.2 + - + +
103I GLU* 3.4 3.7 + - - +
104I LYS* 3.0 42.2 + - + +
141I ILE* 3.9 41.5 - - + +
144I ILE* 3.9 11.8 - - + +
145I GLY* 4.5 3.4 - - - +
148I ILE* 3.7 21.8 - - + -
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Residues in contact with GLN 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97I GLN 3.1 13.1 + - - +
98I ALA* 3.7 9.2 - - - +
100I LEU* 1.3 76.5 - - + +
102I LEU* 1.3 60.3 + - - +
104I LYS* 3.2 11.8 + - - +
105I THR* 2.9 34.4 + - - +
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Residues in contact with LEU 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I LEU* 5.4 1.6 - - + -
25I TYR* 4.1 27.6 - - + -
26I ALA* 3.9 25.6 - - + +
29I THR* 3.7 28.7 - - + -
30I TYR* 3.9 33.4 - - + +
98I ALA 3.0 18.1 + - - +
99I ALA* 3.5 5.4 - - - +
101I GLN* 1.3 77.1 - - - +
103I GLU* 1.3 59.8 + - - +
105I THR* 3.4 10.2 + - + -
106I VAL* 3.1 35.8 + - + +
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Residues in contact with GLU 103 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I ALA* 6.2 0.6 - - - +
30I TYR* 2.8 28.2 + - - +
54I HIS* 3.6 14.2 + - - -
58I GLU* 3.4 12.1 - - - +
99I ALA 2.9 14.3 + - - +
100I LEU* 3.8 5.4 - - - +
102I LEU* 1.3 77.0 - - - +
104I LYS* 1.3 59.8 + - - +
106I VAL* 3.3 5.7 + - - +
107I ASN* 2.8 25.6 + - - +
137I GLN* 3.0 28.6 + - - +
140I ASP* 4.4 6.5 - - + -
141I ILE* 3.9 14.6 - - + -
144I ILE* 3.9 13.9 - - + -
177I MG 2.9 27.0 - - - -
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Residues in contact with LYS 104 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D SER 5.0 0.4 + - - -
3D GLN* 2.9 30.1 + - - +
4D VAL 4.5 5.2 - - - +
5D ARG 3.6 16.6 + - - -
6D GLN* 3.2 43.3 + - + +
100I LEU* 3.0 30.3 + - + +
101I GLN* 3.2 9.8 + - - +
103I GLU* 1.3 75.1 - - - +
105I THR* 1.3 55.9 + - - +
107I ASN* 4.1 0.2 - - - -
108I GLN* 2.9 26.2 + - - +
141I ILE* 4.2 11.4 - - + -
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Residues in contact with THR 105 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I LEU* 4.6 18.8 - - + -
25I TYR* 6.5 0.4 - - + -
101I GLN* 2.9 19.9 + - - +
102I LEU* 3.5 13.2 - - + +
103I GLU 3.2 0.2 - - - -
104I LYS* 1.3 77.4 - - - +
106I VAL* 1.3 62.0 + - - +
108I GLN* 3.4 6.4 + - - +
109I ALA* 3.1 21.7 + - - +
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Residues in contact with VAL 106 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I MET* 4.6 1.7 - - - +
22I LEU* 3.9 30.1 - - + +
23I GLU* 4.0 9.9 - - - +
26I ALA* 4.2 24.0 - - + -
58I GLU* 4.9 0.7 - - - +
102I LEU* 3.1 20.5 + - + +
103I GLU* 3.7 9.9 - - - +
105I THR* 1.3 72.1 - - - +
107I ASN* 1.3 66.0 + - - +
109I ALA* 3.2 2.9 + - - +
110I LEU* 3.0 31.5 + - + +
137I GLN* 3.9 11.7 - - - +
176I MG 3.8 22.0 - - - -
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Residues in contact with ASN 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D GLN* 3.0 40.5 + - - +
103I GLU 2.8 21.4 + - - +
104I LYS 3.6 0.4 - - - +
106I VAL* 1.3 72.1 - - - +
108I GLN* 1.3 57.8 - - - +
110I LEU* 3.1 9.4 + - - +
111I LEU* 2.9 42.5 + - - +
134I LEU* 4.8 8.7 - - - +
137I GLN* 3.6 23.6 - - - +
138I VAL* 5.0 9.8 - - - +
141I ILE* 3.9 16.0 - - + +
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Residues in contact with GLN 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D GLN* 3.6 19.2 + - - +
7D ASN* 6.0 1.5 - - - +
104I LYS 2.9 18.2 + - - +
105I THR* 3.6 7.0 - - - +
107I ASN* 1.3 79.1 - - - +
109I ALA* 1.3 57.1 + - - +
111I LEU* 3.4 16.1 + - - +
112I ASP* 2.9 63.6 + - - +
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Residues in contact with ALA 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I MET* 3.1 20.6 - - + +
22I LEU* 3.7 22.4 - - + -
105I THR 3.1 14.7 + - - +
106I VAL 3.2 8.5 + - - +
108I GLN* 1.3 77.5 - - - +
110I LEU* 1.3 57.4 + - - +
112I ASP* 3.4 9.8 + - - +
113I LEU* 2.9 22.7 + - - +
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Residues in contact with LEU 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I MET* 3.7 24.7 - - + -
23I GLU* 4.9 1.8 - - - +
65I PHE* 4.0 21.3 - - + -
106I VAL* 3.0 24.9 + - + +
107I ASN* 3.1 7.4 + - - +
109I ALA* 1.3 76.3 - - - +
111I LEU* 1.3 59.6 + - - +
113I LEU* 3.4 3.0 + - - +
114I HIS* 2.9 26.7 + - - +
129I LEU* 4.2 14.3 - - + +
133I TYR* 3.9 31.0 - - + -
134I LEU* 3.9 14.6 - - + +
137I GLN* 3.7 31.2 - - + +
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Residues in contact with LEU 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D GLN* 4.5 4.0 - - + -
7D ASN* 3.8 33.0 - - + +
123D PRO* 3.8 34.5 - - + +
124D HIS* 5.4 3.6 - - + +
107I ASN* 2.9 42.9 + - - +
108I GLN* 3.7 20.0 - - - +
110I LEU* 1.3 74.4 - - - +
112I ASP* 1.3 59.3 + - - +
114I HIS* 3.2 5.8 + - - +
115I LYS* 3.0 27.2 + - - +
134I LEU* 4.6 15.9 - - + -
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Residues in contact with ASP 112 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108I GLN* 2.9 48.8 + - - +
109I ALA* 3.4 9.8 - - - +
111I LEU* 1.3 76.3 - - - +
113I LEU* 1.3 60.8 + - - +
115I LYS* 3.3 8.2 + - - +
116I LEU* 3.0 26.2 + - - +
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Residues in contact with LEU 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I CYS 4.3 8.5 - - - +
15I ALA* 3.5 32.5 - - + +
16I VAL* 4.3 17.7 - - + -
19I MET* 3.7 35.2 - - + -
65I PHE* 4.5 2.0 - - + -
109I ALA 2.9 17.2 + - - +
110I LEU* 3.7 5.4 - - + +
111I LEU 3.3 0.2 - - - -
112I ASP* 1.3 76.2 - - - +
114I HIS* 1.3 58.3 + - - +
116I LEU* 3.4 9.7 + - + +
117I ALA* 3.0 25.8 + - - +
125I LEU* 4.4 9.9 - - + -
129I LEU* 3.9 25.4 - - + -
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Residues in contact with HIS 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D VAL* 6.1 1.4 - - - +
123D PRO* 3.5 36.3 - - + +
110I LEU 2.9 15.2 + - - +
111I LEU* 3.3 13.0 - - - +
112I ASP 3.1 0.2 - - - -
113I LEU* 1.3 74.7 - - - +
115I LYS* 1.3 61.9 + - - +
117I ALA* 3.3 3.9 + - - +
118I THR* 2.9 43.5 + - - -
126I CYS* 3.6 31.1 + - - +
129I LEU* 3.8 18.1 - - + +
130I GLU* 2.9 25.4 + - - -
134I LEU* 4.2 6.7 - - + -
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Residues in contact with LYS 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D VAL* 4.4 23.6 - - + -
111I LEU 3.0 13.4 + - - +
112I ASP* 3.3 11.9 + - - +
114I HIS* 1.3 73.8 + - - +
116I LEU* 1.3 60.6 + - - +
118I THR* 3.2 9.4 + - + +
119I ASP* 2.9 30.0 + - - +
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Residues in contact with LEU 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I ASP* 3.6 40.8 - - + +
12I CYS* 4.0 11.2 - - - -
15I ALA* 3.7 19.7 - - + -
18I ARG* 5.4 2.2 - - - +
112I ASP 3.0 13.8 + - - +
113I LEU* 3.6 11.0 - - + +
115I LYS* 1.3 77.5 - - - +
117I ALA* 1.3 55.9 + - - +
119I ASP* 3.3 5.8 + - + +
120I LYS* 2.9 49.6 + - + +
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Residues in contact with ALA 117 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I CYS* 4.3 10.7 - - - -
113I LEU 3.0 14.5 + - - +
114I HIS* 3.5 10.1 - - - +
116I LEU* 1.3 73.5 - - - +
118I THR* 1.3 64.8 + - - +
120I LYS 3.5 0.7 + - - +
121I VAL 3.1 3.6 + - - -
122I ASP* 2.9 35.3 + - + +
125I LEU* 3.9 27.4 - - + -
126I CYS* 3.6 17.7 - - - +
129I LEU* 5.1 0.2 - - + -
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Residues in contact with THR 118 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D VAL* 6.4 2.5 - - + -
114I HIS* 2.9 30.9 + - - -
115I LYS* 3.2 11.4 + - + +
117I ALA* 1.3 76.1 - - - +
119I ASP* 1.3 63.8 + - - +
121I VAL* 3.1 17.7 + - - +
126I CYS* 3.5 14.8 - - - -
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Residues in contact with ASP 119 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115I LYS 2.9 17.1 + - - +
116I LEU* 3.3 9.6 + - + +
118I THR* 1.3 78.8 - - - +
120I LYS* 1.3 72.8 + - + +
121I 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