Contacts of the helix formed by residues 95 - 124 (chain I) in PDB entry 5JKL
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 SER 95 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I TYR* 3.8 4.1 + - - -
41I PHE* 3.6 7.4 - - - -
46I VAL* 6.3 0.7 - - - -
93I TRP 2.9 7.9 + - - +
94I GLU* 1.3 77.8 + - - +
96I GLY* 1.3 64.3 + - - +
97I LEU* 3.6 2.1 + - - +
98I ASN* 3.0 24.6 + - - +
99I ALA* 2.9 23.6 + - - +
161I PRO* 3.6 24.0 - - - +
167I GLU* 3.6 15.0 - - - -
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Residues in contact with GLY 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I PHE* 3.6 15.2 - - - -
48I LEU* 5.2 0.2 - - - -
51I PHE* 3.4 27.0 - - - -
95I SER* 1.3 72.5 - - - +
97I LEU* 1.3 62.6 + - - +
99I ALA* 3.3 1.9 + - - +
100I MET* 3.1 27.5 + - - +
155I LEU* 4.2 2.7 - - - -
167I GLU* 2.9 20.8 + - - -
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Residues in contact with LEU 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95I SER* 4.0 3.4 - - - +
96I GLY* 1.3 69.1 - - - +
98I ASN* 1.3 66.1 + - - +
100I MET* 3.2 2.1 + - - -
101I GLU* 2.9 50.0 + - - +
152I VAL* 3.9 32.5 - - + +
155I LEU* 3.9 17.0 - - + +
156I ARG* 4.0 14.6 - - + +
160I ALA* 3.6 32.8 - - + +
161I PRO* 3.8 14.1 - - + -
167I GLU* 2.8 19.5 + - - +
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Residues in contact with ASN 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90I GLU* 5.7 3.8 + - - +
92I ASP 5.5 0.2 + - - -
93I TRP* 2.9 33.8 + - - +
94I GLU* 4.0 25.7 + - - +
95I SER* 3.0 17.6 + - - +
97I LEU* 1.3 76.8 - - - +
99I ALA* 1.3 57.6 + - - +
101I GLU* 3.2 16.8 + - - +
102I GLU* 2.9 46.5 + - - +
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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
----------------------------------------------------------
37I MET* 3.5 18.3 - - - +
41I PHE* 3.6 37.2 - - + -
55I PHE* 4.0 12.8 - - + -
93I TRP* 3.9 13.4 + - + -
95I SER 2.9 8.3 + - - +
96I GLY 3.7 2.7 - - - +
97I LEU 3.2 0.2 - - - -
98I ASN* 1.3 78.3 - - - +
100I MET* 1.3 57.3 + - - +
102I GLU* 3.3 1.5 + - - -
103I ALA* 2.8 30.1 + - - +
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Residues in contact with MET 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I PHE* 3.8 22.2 - - + -
54I TYR* 3.9 22.9 - - + -
55I PHE* 3.9 14.4 - - + -
96I GLY 3.1 16.5 + - - +
97I LEU 3.7 4.5 - - - +
99I ALA* 1.3 75.9 - - - +
101I GLU* 1.4 57.0 + - - +
103I ALA* 3.3 3.4 + - - +
104I LEU* 3.0 27.7 + - - +
148I LEU* 3.6 28.7 - - + +
151I HIS* 3.9 22.4 - - + -
152I VAL* 3.9 18.5 - - + +
155I LEU* 3.9 16.8 - - + -
170I PHE* 4.4 4.0 - - + -
175I LEU* 4.1 8.7 - - + -
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Residues in contact with GLU 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97I LEU* 2.9 42.2 + - + +
98I ASN* 3.6 18.2 - - - +
100I MET* 1.4 74.4 - - - +
102I GLU* 1.3 64.7 + - + +
104I LEU* 3.3 8.8 + - + +
105I GLU* 3.1 25.1 + - - +
152I VAL* 4.1 12.6 - - + -
156I ARG* 3.0 36.4 + - - +
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Residues in contact with GLU 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I MET* 3.7 20.8 - - + +
89I ASP* 4.5 14.4 - - - +
90I GLU* 5.1 4.8 - - - +
93I TRP* 3.7 20.1 - - + -
98I ASN* 2.9 39.7 + - - +
101I GLU* 1.3 78.8 - - + +
103I ALA* 1.3 56.3 + - - +
105I GLU* 3.4 10.9 + - - +
106I LEU* 3.0 27.4 + - - +
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Residues in contact with ALA 103 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I TYR* 3.8 28.9 - - + +
37I MET* 3.8 8.5 - - + +
55I PHE* 4.3 5.2 - - + -
99I ALA 2.8 17.3 + - - +
100I MET 3.6 5.2 - - - +
102I GLU* 1.3 74.3 - - - +
104I LEU* 1.3 61.4 + - - +
106I LEU* 3.3 7.6 + - - +
107I GLU* 2.9 34.8 + - - +
148I LEU* 3.7 16.6 - - + -
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Residues in contact with LEU 104 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G GLN* 3.8 42.6 - - + +
8G VAL* 5.1 0.9 - - + -
100I MET 3.0 13.8 + - - +
101I GLU* 3.5 11.7 - - + +
103I ALA* 1.3 75.7 - - - +
105I GLU* 1.3 59.6 + - + +
107I GLU* 3.3 2.3 + - - +
108I LYS* 3.0 43.4 + - + +
145I ILE* 3.8 43.5 - - + +
148I LEU* 3.8 15.4 - - + +
149I GLY* 4.4 7.0 - - - +
152I VAL* 4.5 7.9 - - + -
156I ARG* 6.3 0.2 - - - +
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Residues in contact with GLU 105 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101I GLU 3.1 11.8 + - - +
102I GLU* 3.6 14.8 - - - +
103I ALA 3.3 0.2 - - - -
104I LEU* 1.3 81.5 - - + +
106I LEU* 1.3 56.2 + - - +
108I LYS* 3.4 17.3 + - - +
109I ASN* 2.9 53.5 + - - +
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Residues in contact with LEU 106 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I LEU* 5.5 1.6 - - + -
29I TYR* 4.0 31.2 - - + -
30I ALA* 4.1 12.1 - - + -
33I VAL* 3.9 30.5 - - + -
34I TYR* 4.1 31.4 - - + +
102I GLU 3.0 14.5 + - - +
103I ALA* 3.3 8.0 + - - +
105I GLU* 1.3 76.4 - - - +
107I GLU* 1.3 59.4 + - + +
109I ASN* 3.1 10.7 + - + +
110I VAL* 2.8 48.2 + - + +
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Residues in contact with GLU 107 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I ALA* 6.2 0.4 - - - -
34I TYR* 2.5 37.4 + - - +
58I GLN* 5.4 1.4 - - - +
62I GLU* 3.4 14.8 - - - +
103I ALA 2.9 19.2 + - - +
104I LEU 3.3 3.3 + - - +
106I LEU* 1.3 80.0 - - + +
108I LYS* 1.3 57.0 + - - +
110I VAL* 4.4 5.5 - - - +
111I ASN* 2.9 25.3 + - - +
141I GLN* 2.7 45.6 + - - +
144I ALA* 3.9 17.3 - - + +
145I ILE* 3.9 17.4 - - + +
148I LEU* 3.6 14.8 - - + -
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Residues in contact with LYS 108 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G SER 4.6 0.6 + - - -
7G GLN* 2.8 30.5 + - - +
8G VAL 3.7 9.4 - - - -
9G ARG 3.0 27.6 + - - -
10G GLN* 2.8 49.4 + - - +
104I LEU* 3.0 30.0 + - + +
105I GLU* 3.8 18.2 - - - +
107I GLU* 1.3 72.8 - - - +
109I ASN* 1.3 60.3 + - - +
111I ASN* 3.4 0.3 + - - +
112I GLN* 2.9 14.9 + - - +
145I ILE* 4.0 16.2 - - + -
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Residues in contact with ASN 109 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I LEU* 4.7 4.7 - - + +
105I GLU* 2.9 37.6 + - - +
106I LEU* 3.5 11.7 - - + +
108I LYS* 1.3 76.7 - - - +
110I VAL* 1.3 65.9 + - + +
112I GLN* 3.3 7.9 + - - +
113I SER* 3.2 20.8 + - - -
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Residues in contact with VAL 110 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I GLN* 3.9 7.9 - - - +
26I LEU* 4.0 25.4 - - + +
27I GLU* 3.6 26.9 - - - +
30I ALA* 4.6 11.4 - - + -
62I GLU* 5.9 0.4 - - - +
106I LEU* 2.8 41.1 + - + +
107I GLU* 4.4 3.6 - - - +
109I ASN* 1.3 70.1 - - + +
111I ASN* 1.3 64.6 + - - +
113I SER* 3.1 4.2 + - - -
114I LEU* 2.9 27.0 + - + +
141I GLN* 3.8 21.5 - - - +
201I FE 4.5 2.9 - - - -
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Residues in contact with ASN 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G GLN* 3.0 35.0 + - - +
107I GLU 2.9 18.5 + - - +
108I LYS 3.6 0.4 - - - +
109I ASN 3.3 0.2 - - - -
110I VAL* 1.3 77.3 - - - +
112I GLN* 1.3 64.1 + - - +
114I LEU* 3.1 2.7 + - - +
115I LEU* 2.8 39.0 + - - +
138I LEU* 4.2 16.6 - - - +
141I GLN* 3.4 30.7 - - + +
142I VAL* 5.0 10.4 - - - +
145I ILE* 3.9 12.0 - - + +
----------------------------------------------------------
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Residues in contact with GLN 112 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G GLN* 3.8 18.5 + - - +
11G ASN* 6.0 0.7 - - - +
108I LYS 2.9 16.6 + - - +
109I ASN* 3.3 8.7 + - - +
111I ASN* 1.3 74.1 - - - +
113I SER* 1.3 58.6 + - - +
115I LEU* 3.2 15.3 + - - +
116I GLU* 2.9 68.0 + - - +
----------------------------------------------------------
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Residues in contact with SER 113 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I ARG* 5.9 0.5 - - - +
23I GLN* 2.5 23.0 + - - -
26I LEU* 3.5 28.9 - - - +
109I ASN 3.2 5.6 + - - -
110I VAL 3.1 5.0 + - - -
112I GLN* 1.3 81.0 - - - +
114I LEU* 1.3 56.4 + - - +
116I GLU* 3.3 14.0 + - - +
117I LEU* 2.9 27.2 + - - +
----------------------------------------------------------
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Residues in contact with LEU 114 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I GLN* 3.5 29.6 - - + +
27I GLU* 4.3 2.9 - - - +
69I LEU* 5.7 1.3 - - + -
110I VAL* 2.9 27.9 + - + +
111I ASN 3.1 6.0 + - - +
113I SER* 1.3 76.4 - - - +
115I LEU* 1.3 56.6 + - - +
117I LEU* 3.3 15.9 + - + +
118I HIS* 2.9 28.1 + - - +
133I ILE* 4.1 10.2 - - + +
137I TYR* 3.9 37.9 - - + +
138I LEU* 3.9 15.0 - - + -
141I GLN* 3.6 30.3 - - + +
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Residues in contact with LEU 115 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G GLN* 4.6 3.4 - - + +
11G ASN* 4.0 33.2 - - + +
126G ASP* 6.1 0.2 - - - +
127G PRO* 3.7 32.5 - - + +
128G HIS* 5.2 4.9 - - + +
111I ASN* 2.8 40.3 + - - +
112I GLN* 3.6 19.3 - - - +
114I LEU* 1.3 72.3 - - - +
116I GLU* 1.3 61.6 + - + +
118I HIS* 3.3 5.6 + - - +
119I LYS* 2.9 28.8 + - - +
138I LEU* 4.1 17.0 - - + -
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Residues in contact with GLU 116 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112I GLN* 2.9 52.3 + - - +
113I SER* 3.7 11.0 - - - +
115I LEU* 1.3 76.8 - - + +
117I LEU* 1.3 57.5 + - - +
119I LYS* 3.2 10.5 + - + +
120I LEU* 2.9 28.4 + - - +
----------------------------------------------------------
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Residues in contact with LEU 117 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I SER 4.8 0.7 - - - +
19I ALA* 3.5 37.2 - - + +
20I ILE* 3.9 27.8 - - + +
23I GLN* 4.3 17.3 - - + +
69I LEU* 5.2 1.8 - - + -
113I SER 2.9 13.0 + - - +
114I LEU* 3.4 24.9 - - + +
116I GLU* 1.3 77.8 - - - +
118I HIS* 1.3 61.3 + - - +
120I LEU* 3.3 10.3 + - + +
121I ALA* 3.0 22.2 + - - +
129I LEU* 5.1 6.7 - - + -
133I ILE* 3.7 23.8 - - + -
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Residues in contact with HIS 118 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127G PRO* 3.4 32.2 - - + +
114I LEU 2.9 17.4 + - - +
115I LEU* 3.3 8.3 + - - +
117I LEU* 1.3 75.7 - - - +
119I LYS* 1.3 58.9 + - - +
121I ALA* 3.2 2.2 + - - +
122I THR* 2.8 52.2 + - - -
130I CYS* 3.6 29.2 - - - +
133I ILE* 4.0 20.2 - - + +
134I GLU* 2.7 36.5 + - + -
138I LEU* 4.4 1.8 - - + -
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Residues in contact with LYS 119 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G ASN* 6.1 7.4 - - + +
115I LEU 2.9 16.5 + - - +
116I GLU* 3.2 10.3 + - + +
118I HIS* 1.3 76.6 + - - +
120I LEU* 1.3 62.0 + - - +
122I THR* 3.3 6.8 + - + -
123I ASP* 3.0 56.3 + - - +
----------------------------------------------------------
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Residues in contact with LEU 120 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I ASP* 3.6 44.2 - - + +
16I SER* 4.0 10.8 - - - +
19I ALA* 3.8 19.3 - - + -
22I ARG* 5.2 3.6 - - - +
116I GLU 2.9 13.4 + - - +
117I LEU* 3.6 10.5 - - + +
118I HIS 3.2 0.2 - - - -
119I LYS* 1.3 76.7 - - - +
121I ALA* 1.3 55.8 + - - +
123I ASP* 3.1 9.3 + - + +
124I LYS* 2.9 54.9 + - + +
----------------------------------------------------------
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Residues in contact with ALA 121 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I SER* 4.8 3.6 + - - -
117I LEU 3.0 16.3 + - - +
118I HIS* 3.2 4.7 + - - +
120I LEU* 1.3 77.8 - - - +
122I THR* 1.3 60.9 + - - +
124I LYS* 3.5 1.5 + - - +
125I ASN 3.1 3.6 + - - -
126I ASP* 2.9 36.9 + - - +
129I LEU* 3.7 33.2 - - + -
130I CYS* 3.6 20.4 - - - +
133I ILE* 4.6 1.1 - - + -
----------------------------------------------------------
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Residues in contact with THR 122 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G ASN* 5.9 2.5 - - - +
118I HIS* 2.8 40.4 + - - -
119I LYS* 3.5 8.5 - - + +
121I ALA* 1.3 76.7 - - - +
123I ASP* 1.3 66.2 + - - +
125I ASN* 3.0 25.6 + - - +
130I CYS* 3.5 8.1 - - - -
----------------------------------------------------------
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Residues in contact with ASP 123 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119I LYS* 3.0 52.4 + - - +
120I LEU* 3.1 10.8 + - + +
122I THR* 1.3 82.6 - - - +
124I LYS* 1.3 68.7 + - + +
125I ASN* 3.5 11.3 + - - -
----------------------------------------------------------
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Residues in contact with LYS 124 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I ASN* 4.4 7.4 - - - +
13I HIS* 3.6 50.8 + - + -
15I ASP* 3.6 22.5 + - - -
16I SER* 4.3 8.1 - - - +
120I LEU* 2.9 36.3 + - + +
121I ALA* 4.2 2.9 - - - +
123I ASP* 1.3 82.8 - - + +
125I ASN* 1.3 73.7 + - - +
126I ASP* 3.3 6.8 + - + +
----------------------------------------------------------
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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