Contacts of the helix formed by residues 108 - 129 (chain F) in PDB entry 4HHM
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 ASP 108 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334E ARG* 2.6 55.9 + - - +
337E GLN* 3.6 8.8 + - - +
365E ALA 5.5 1.6 - - - +
368E ARG* 4.1 8.8 + - - +
370E MET* 3.8 8.8 - - - +
100F LYS* 5.9 0.3 + - - -
106F ALA* 3.3 1.6 - - + +
107F ASN* 1.3 75.2 - - - +
109F ARG* 1.3 65.5 + - - +
110F ASP* 3.0 19.4 - - - +
111F VAL* 3.2 26.0 + - + +
112F ARG* 3.3 14.7 + - - +
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Residues in contact with ARG 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337E GLN* 2.8 24.3 - - + +
340E GLU* 4.1 19.0 + - - +
341E PRO 2.9 21.4 + - - +
342E THR* 3.0 23.5 + - - +
343E ALA* 4.4 0.8 - - - +
344E ALA* 4.4 5.1 - - - +
345E ASP* 3.9 13.5 + - - -
108F ASP* 1.3 71.7 - - - +
110F ASP* 1.3 63.2 + - - +
112F ARG* 3.0 33.6 + - - +
113F ARG* 3.0 57.5 + - - +
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Residues in contact with ASP 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337E GLN* 4.5 2.5 + - - +
355E THR 6.0 0.4 - - - +
356E ALA* 5.5 2.3 - - - -
360E PHE* 3.1 34.2 - - + -
365E ALA* 3.8 12.6 - - - +
108F ASP* 3.0 29.2 - - - +
109F ARG* 1.3 75.8 + - - +
111F VAL* 1.3 61.1 + - - -
113F ARG* 3.4 11.0 + - - +
114F TYR* 3.1 22.0 + - - +
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Residues in contact with VAL 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360E PHE* 4.3 6.5 - - + -
365E ALA* 4.7 6.1 - - + +
98F VAL* 3.5 39.3 - - + +
99F PHE* 3.8 21.3 - - + -
102F GLY 4.0 9.4 - - - +
103F ALA 4.2 0.9 - - - +
106F ALA* 3.9 9.2 - - + -
108F ASP* 3.2 22.1 + - + +
110F ASP* 1.3 90.3 + - - +
112F ARG* 1.3 60.9 + - - +
114F TYR* 3.2 2.7 + - + +
115F ALA* 2.9 27.9 + - - +
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Residues in contact with ARG 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337E GLN 2.9 14.8 + - - -
338E LEU* 4.0 3.0 - - - +
340E GLU 2.8 29.3 + - - -
341E PRO 4.2 0.6 + - - -
342E THR* 2.9 29.9 + - + +
103F ALA 3.3 19.7 - - - +
104F PHE* 3.1 25.0 - - - +
106F ALA 2.8 45.5 + - - +
107F ASN 2.8 21.0 + - - -
108F ASP 3.5 2.9 - - - +
109F ARG* 3.0 35.5 + - - +
111F VAL* 1.3 77.0 - - - +
113F ARG* 1.3 60.7 + - - +
115F ALA* 3.4 3.6 + - - +
116F LEU* 3.3 27.3 + - + +
157F ARG* 3.2 18.0 - - - +
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Residues in contact with ARG 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342E THR* 2.8 35.5 + - + +
343E ALA* 3.7 12.7 - - - +
345E ASP* 4.0 12.1 + - - -
349E ALA 4.3 1.2 + - - -
350E LEU* 3.6 36.8 - - + +
353E ASP* 2.6 40.0 + - - +
355E THR* 5.3 0.6 + - - -
356E ALA* 4.1 11.8 - - + +
109F ARG* 3.0 54.5 + - + +
110F ASP* 3.7 10.8 - - - +
111F VAL 3.2 0.2 - - - -
112F ARG* 1.3 75.0 - - - +
114F TYR* 1.3 63.1 + - - +
116F LEU* 3.5 4.2 + - - +
117F ARG* 3.2 26.5 + - - +
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Residues in contact with TYR 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356E ALA* 3.5 19.2 + - - +
357E TYR* 3.6 34.0 - + - -
360E PHE* 3.5 39.0 - + + -
362E VAL* 4.0 16.9 - - + +
61F PHE* 3.3 28.0 - + - -
98F VAL* 4.4 6.3 - - + -
99F PHE* 3.6 38.4 - + - -
110F ASP 3.1 9.4 + - - +
111F VAL 3.2 6.3 + - - +
113F ARG* 1.3 75.4 - - - +
115F ALA* 1.3 59.5 + - - +
117F ARG* 3.1 1.4 + - - -
118F LYS* 2.8 46.0 + - + +
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Residues in contact with ALA 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F LEU* 3.9 13.3 - - + +
99F PHE* 4.0 5.4 - - + -
103F ALA* 3.6 33.7 - - + -
104F PHE* 3.9 12.3 - - + -
111F VAL 2.9 16.7 + - - +
112F ARG 3.6 6.1 - - - +
114F TYR* 1.3 77.7 - - - +
116F LEU* 1.3 56.3 + - - +
118F LYS* 3.5 3.0 + - - +
119F THR* 2.9 34.0 + - - -
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Residues in contact with LEU 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342E THR* 3.6 31.0 - - + -
350E LEU* 4.0 17.9 - - + -
104F PHE* 3.6 17.3 - - + -
112F ARG* 3.3 10.2 + - + +
113F ARG* 3.8 6.3 - - - +
114F TYR 3.2 0.6 - - - -
115F ALA* 1.3 75.0 - - - +
117F ARG* 1.3 55.8 + - - +
119F THR* 3.3 2.5 + - - -
120F ILE* 2.8 44.2 + - + +
161F ALA* 3.5 41.3 - - + +
164F LEU* 3.8 22.9 - - + -
165F LEU* 4.3 10.8 - - + -
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Residues in contact with ARG 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350E LEU* 3.1 34.1 + - + +
351E LEU* 3.2 34.9 + - - +
353E ASP 2.9 29.1 + - - -
356E ALA* 3.4 28.3 - - + +
357E TYR* 3.7 34.8 - - + +
358E GLU* 3.9 16.0 + - - -
113F ARG 3.2 9.1 + - - +
114F TYR 3.1 4.6 + - - +
116F LEU* 1.3 75.3 - - - +
118F LYS* 1.3 65.3 + - - +
120F ILE* 3.5 5.5 + - - +
121F ARG* 3.1 24.3 + - - +
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Residues in contact with LYS 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357E TYR* 4.0 17.4 - - + +
55F ASP* 2.6 32.3 + - - +
56F ASP* 2.7 24.7 + - - -
61F PHE* 4.7 11.1 - - - -
91F THR* 4.1 2.5 - - + +
92F ASN 3.3 15.9 + - - -
93F LEU* 3.7 21.8 - - + -
96F HIS* 6.3 1.3 - - - -
99F PHE* 4.1 16.6 - - + -
114F TYR* 2.8 37.3 + - + +
115F ALA* 3.5 5.2 - - - +
117F ARG* 1.3 79.4 - - - +
119F THR* 1.3 64.4 + - - +
121F ARG* 3.4 10.3 + - - +
122F ASN* 3.4 11.6 + - - +
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Residues in contact with THR 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F THR* 3.5 26.9 + - - +
93F LEU* 3.5 17.8 - - - +
104F PHE* 3.9 7.5 - - + -
115F ALA 2.9 22.9 + - - -
116F LEU* 3.6 7.0 - - - -
118F LYS* 1.3 76.3 - - - +
120F ILE* 1.3 63.7 + - - +
122F ASN* 2.9 14.7 + - - +
123F ILE* 3.0 20.2 + - + +
134F TYR* 4.0 9.2 - - + -
165F LEU* 4.0 27.4 - - + -
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Residues in contact with ILE 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347E LEU* 4.2 24.2 - - + -
350E LEU* 4.6 10.5 - - + -
351E LEU* 4.1 19.3 - - + -
116F LEU* 2.8 30.0 + - + +
117F ARG* 3.9 9.2 - - - +
118F LYS 3.4 0.2 - - - -
119F THR* 1.3 72.0 - - - +
121F ARG* 1.3 64.4 + - - +
123F ILE* 3.1 18.7 + - + +
124F ASP* 3.3 14.1 + - - +
164F LEU* 5.5 1.3 - - + +
165F LEU* 3.9 21.1 - - + -
168F TYR* 3.4 41.5 - - + +
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Residues in contact with ARG 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357E TYR* 2.8 43.7 + - + +
63F ALA 5.4 5.3 + - - -
65F ASP* 2.9 27.7 + - - +
68F ARG* 3.2 52.3 + - - +
117F ARG 3.1 17.9 + - - +
118F LYS 3.7 5.6 - - - +
119F THR 3.2 0.2 - - - -
120F ILE* 1.3 76.9 - - - +
122F ASN* 1.3 60.6 + - - +
124F ASP* 3.5 20.2 + - + +
125F LEU* 3.5 11.1 + - - +
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Residues in contact with ASN 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F PHE* 4.1 10.3 - - - -
55F ASP* 3.1 35.9 - - + +
68F ARG* 5.2 4.5 + - - +
89F ALA* 4.3 1.6 - - - +
90F THR 2.9 30.7 + - - +
91F THR* 4.8 0.7 - - + +
118F LYS 3.4 7.5 + - - +
119F THR 2.9 5.7 + - - +
121F ARG* 1.3 75.8 - - - +
123F ILE* 1.3 59.4 + - - +
124F ASP 3.2 0.7 - - - -
125F LEU* 3.7 23.0 - - - +
126F ALA* 2.9 28.2 + - - +
134F TYR* 3.0 21.3 + - - +
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Residues in contact with ILE 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119F THR* 3.0 21.2 + - + +
120F ILE* 3.1 12.5 + - - +
122F ASN* 1.3 79.3 - - - +
124F ASP* 1.3 57.9 + - - +
126F ALA* 3.4 2.4 + - - +
127F VAL* 3.1 29.8 + - + +
134F TYR* 4.0 24.2 - - + -
165F LEU* 4.0 19.3 - - + -
168F TYR* 4.2 13.2 - - + -
169F VAL* 4.3 8.7 - - + -
174F TYR* 4.1 23.1 - - + -
176F ILE* 4.7 9.0 - - + -
178F PHE* 3.6 32.1 - - + -
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Residues in contact with ASP 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F ILE* 3.3 10.8 + - - +
121F ARG* 3.7 12.7 - - + +
123F ILE* 1.3 76.9 - - - +
125F LEU* 1.3 60.1 + - - +
127F VAL* 3.4 3.3 + - - +
128F GLU* 3.0 28.0 + - - +
168F TYR* 2.5 31.3 + - - -
172F GLN* 5.8 0.2 - - - -
174F TYR* 2.6 32.6 + - - +
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Residues in contact with LEU 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F PHE* 4.5 2.7 - - + -
58F LEU* 4.3 7.9 - - + -
59F ILE* 3.9 19.1 - - + -
68F ARG* 3.7 24.9 - - - +
72F VAL* 4.0 22.9 - - + -
121F ARG 3.5 9.0 + - - +
122F ASN* 3.4 23.3 + - - +
123F ILE 3.4 0.4 - - - -
124F ASP* 1.3 76.2 - - - +
126F ALA* 1.3 65.3 + - - +
128F GLU* 3.3 22.4 + - - +
129F LEU* 3.0 42.1 + - + +
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Residues in contact with ALA 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F PHE* 4.9 3.1 - - - -
89F ALA* 3.6 28.5 - - + -
122F ASN 2.9 18.0 + - - +
123F ILE 3.5 5.8 - - - +
125F LEU* 1.3 77.1 - - - +
127F VAL* 1.3 61.6 + - - +
129F LEU* 3.1 10.4 + - - -
131F ALA* 2.9 36.6 + - + +
134F TYR* 3.9 13.9 - - + -
176F ILE* 4.5 4.3 - - + -
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Residues in contact with VAL 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F ILE 3.1 17.8 + - - +
124F ASP 3.7 4.7 - - - +
125F LEU 3.3 0.2 - - - -
126F ALA* 1.3 75.2 - - - +
128F GLU* 1.3 59.8 + - - +
130F GLY* 2.9 18.9 + - - -
131F ALA 4.2 7.9 - - - +
174F TYR* 3.6 53.6 - - + -
175F ASP 5.7 1.8 - - - +
176F ILE* 4.5 17.3 - - + -
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Residues in contact with GLU 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F VAL* 6.2 0.3 - - - +
76F ARG* 3.1 36.0 + - - +
124F ASP 3.0 16.6 + - - +
125F LEU* 3.5 27.2 - - + +
127F VAL* 1.3 78.1 - - - +
129F LEU* 1.3 58.0 + - + +
130F GLY 3.3 1.1 + - - -
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Residues in contact with LEU 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F PHE* 3.5 35.7 - - + -
58F LEU* 4.3 10.5 - - + -
72F VAL* 6.5 0.4 - - + -
75F PHE* 4.7 4.5 - - + -
76F ARG* 3.4 36.3 - - + +
79F LEU* 3.9 23.1 - - + +
86F VAL* 4.0 27.7 + - + +
125F LEU* 3.0 32.8 + - + +
126F ALA 3.1 5.6 + - - +
127F VAL 3.1 0.2 - - - -
128F GLU* 1.3 77.0 - - + +
130F GLY* 1.3 60.1 + - - +
131F ALA 3.3 0.8 + - - -
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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) + - + + + + + -
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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