Contacts of the helix formed by residues 125 - 148 (chain E) in PDB entry 3FZ7
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 GLY 125 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D SER 5.1 0.2 - - - -
123E THR* 2.6 25.6 + - - -
124E ILE* 1.3 82.0 - - - +
126E SER* 1.3 65.8 + - - -
127E SER* 3.1 3.3 + - - -
128E GLU* 3.6 3.4 + - - +
129E ALA 3.2 8.8 + - - -
275E HIS* 3.8 10.3 - - - -
284E CYS 4.2 0.2 - - - -
285E GLY* 3.8 12.8 - - - -
467E PO4 3.6 9.9 - - - -
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Residues in contact with SER 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E GLY* 1.3 73.1 - - - -
127E SER* 1.3 52.6 + - - +
129E ALA* 3.1 8.4 + - - +
130E CYS* 2.7 47.0 + - - -
163E GLN* 5.9 0.2 - - - -
165E CYS* 5.4 1.6 - - - -
243E ASP* 4.8 1.9 + - - -
245E ALA* 3.6 16.6 - - - +
271E SER* 4.8 1.2 - - - -
272E ALA* 3.4 8.0 + - - -
273E SER* 2.6 34.8 + - - -
285E GLY* 4.5 0.6 - - - -
467E PO4 3.1 21.3 + - - -
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Residues in contact with SER 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315D ILE 2.9 23.4 + - - -
316D ASN* 3.9 3.7 + - - -
317D PHE* 3.8 20.1 - - - +
126E SER* 1.3 76.6 - - - +
128E GLU* 1.3 70.1 + - - +
130E CYS* 3.1 9.0 + - - +
131E MET* 3.1 21.4 + - - +
165E CYS* 3.7 25.4 - - - +
168E LYS* 4.5 4.2 - - - -
467E PO4 2.9 18.2 + - - -
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Residues in contact with GLU 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315D ILE* 4.4 5.6 + - + -
316D ASN* 3.7 15.1 + - - +
122E ASN 5.2 0.7 - - - -
123E THR* 3.3 21.0 - - + -
124E ILE 2.9 21.4 + - - +
125E GLY* 3.6 4.3 + - - +
126E SER 3.4 0.2 - - - -
127E SER* 1.3 77.2 - - - +
129E ALA* 1.3 64.6 + - - +
131E MET* 3.0 21.8 + - - +
132E LEU* 3.1 16.4 + - + +
314E ALA* 3.7 9.4 - - - +
315E ILE* 2.8 39.4 + - + +
316E ASN* 2.7 32.8 + - - +
319E ARG* 4.6 3.3 + - - -
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Residues in contact with ALA 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E THR* 3.7 15.2 - - + +
125E GLY 3.2 13.0 + - - +
126E SER* 3.1 11.1 + - - +
128E GLU* 1.3 78.4 - - - +
130E CYS* 1.3 57.2 + - - +
132E LEU* 3.3 2.9 + - - +
133E GLY* 3.0 25.5 + - - -
241E HIS* 4.6 0.2 - - - -
271E SER* 3.7 23.1 - - - -
286E TRP 3.7 13.7 - - - +
287E VAL* 3.8 17.0 - - + +
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Residues in contact with CYS 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E SER* 2.7 23.8 + - - -
127E SER 3.1 4.9 + - - +
129E ALA* 1.3 69.0 - - - +
131E MET* 1.3 59.1 + - - +
133E GLY 3.3 0.2 + - - -
134E GLY* 2.7 33.8 + - - -
165E CYS* 2.8 40.6 - - + +
166E TRP* 3.5 38.4 - - + -
169E PHE* 5.2 0.4 - - - -
241E HIS* 4.9 0.9 - - - -
243E ASP* 4.2 7.0 - - - -
271E SER* 4.0 13.0 - - - -
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Residues in contact with MET 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315D ILE* 3.6 31.0 - - + +
127E SER* 3.1 21.7 + - - +
128E GLU* 3.0 4.6 + - - +
130E CYS* 1.3 76.1 - - - +
132E LEU* 1.3 54.3 + - - +
134E GLY 3.0 0.2 + - - -
135E MET* 2.7 39.6 + - - +
165E CYS* 4.3 5.8 - - + +
168E LYS* 4.1 24.7 - - + -
169E PHE* 4.0 23.9 - - - -
172E TYR* 4.9 2.5 - - + -
173E TRP* 3.5 30.5 - - + -
315E ILE* 3.5 31.4 - - + -
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Residues in contact with LEU 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E THR* 3.7 20.0 - - + -
123E THR* 4.0 11.9 - - + -
128E GLU* 3.1 15.5 + - + +
129E ALA 3.6 5.8 - - - +
131E MET* 1.3 74.7 - - - +
133E GLY* 1.3 57.9 + - - +
135E MET* 3.5 9.6 + - + -
136E ALA* 3.0 26.2 + - - +
287E VAL* 4.0 8.1 - - + -
289E TRP* 3.7 17.4 - - + -
313E PHE* 3.4 61.9 - - + +
314E ALA* 4.3 2.2 - - - -
315E ILE* 4.2 22.4 - - + +
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Residues in contact with GLY 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E ALA 3.0 14.1 + - - -
130E CYS 3.6 2.9 - - - -
132E LEU* 1.3 76.2 - - - +
134E GLY* 1.3 56.7 + - - +
136E ALA* 3.4 2.2 + - - +
137E MET* 2.9 38.1 + - - +
166E TRP* 5.0 0.2 - - - -
241E HIS* 3.9 23.6 + - - -
269E SER* 4.4 4.3 + - - -
287E VAL* 4.8 0.4 - - - -
289E TRP* 4.1 10.7 - - - -
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Residues in contact with GLY 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E CYS 2.7 20.5 + - - -
133E GLY* 1.3 70.6 - - - +
135E MET* 1.3 60.9 + - - +
137E MET* 3.3 17.5 + - - +
138E LYS* 2.9 23.9 + - - +
166E TRP* 4.2 2.7 - - - -
169E PHE* 3.3 33.7 - - - -
203E ILE* 4.0 0.5 - - - +
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Residues in contact with MET 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D TYR* 3.4 48.5 - - + +
131E MET 2.7 20.5 + - - +
132E LEU* 3.8 17.3 - - + +
134E GLY* 1.3 69.8 - - - +
136E ALA* 1.3 59.9 + - - +
138E LYS* 2.9 9.2 + - - +
139E TRP* 2.9 38.9 + - + +
169E PHE* 3.6 1.5 - - - -
173E TRP* 3.4 44.0 - - + +
299E LEU* 4.0 7.4 - - + -
313E PHE* 3.8 28.3 - - + -
315E ILE* 4.1 7.6 - - + -
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Residues in contact with ALA 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E LEU 3.0 16.5 + - - +
133E GLY 3.8 2.5 - - - +
135E MET* 1.3 73.4 - - - +
137E MET* 1.3 67.0 + - - +
138E LYS 3.2 0.3 + - - -
139E TRP* 3.2 1.9 + - - +
140E ARG* 3.0 36.7 + - - +
289E TRP* 3.5 30.7 - - + +
295E LEU* 4.3 2.0 - - + -
296E PRO* 3.9 15.0 - - + +
299E LEU* 3.7 13.8 - - + +
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Residues in contact with MET 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E GLY 2.9 22.4 + - - +
134E GLY* 3.7 15.0 - - - +
136E ALA* 1.3 75.5 - - - +
138E LYS* 1.3 64.2 + - - +
140E ARG* 3.3 28.8 + - - +
141E TRP* 3.1 25.8 + - - +
157E LEU* 3.5 26.7 - - + -
166E TRP* 4.1 4.9 - - + -
203E ILE* 3.6 19.9 - - + +
204E GLY* 3.7 26.7 - - - -
206E VAL* 4.0 6.5 - - + -
239E ASP* 5.7 0.4 - - + +
240E MET 4.8 1.1 - - - -
241E HIS* 3.9 33.9 - - + +
269E SER* 5.3 1.1 - - - +
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Residues in contact with LYS 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D TYR 5.7 0.2 + - - -
174D ASP* 4.1 8.1 + - - -
134E GLY 2.9 14.6 + - - +
135E MET* 2.9 11.4 + - - +
137E MET* 1.3 78.8 - - - +
139E TRP* 1.3 73.9 + - + +
141E TRP* 3.5 8.7 + - + +
142E ARG* 2.9 55.1 + - + +
152E THR 5.8 0.9 - - - -
155E PRO* 4.2 19.4 - - + +
169E PHE* 4.9 1.1 - - + -
173E TRP* 2.9 43.4 + - + +
174E ASP* 5.0 3.2 + - - +
175E VAL* 4.4 10.1 - - + -
203E ILE* 4.2 14.8 - - + -
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Residues in contact with TRP 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D ARG* 3.3 34.5 - - + +
172D TYR* 3.8 18.6 - - - -
174D ASP* 3.8 5.2 - - - -
135E MET* 2.9 35.2 + - + +
138E LYS* 1.3 93.1 - - + +
140E ARG* 1.3 65.9 + - - +
142E ARG* 3.2 39.2 - - + +
143E LYS* 2.9 32.1 + - + +
173E TRP* 5.0 0.4 - + - -
296E PRO* 3.6 23.6 - - + -
298E GLU* 3.7 33.4 + - + +
299E LEU* 3.6 29.4 - - + +
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Residues in contact with ARG 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E ALA* 3.0 28.9 + - - +
137E MET* 3.4 34.4 - - - +
139E TRP* 1.3 77.8 - - - +
141E TRP* 1.3 65.2 + - - +
143E LYS* 3.5 7.3 + - - +
144E ARG* 3.5 24.9 + - - +
203E ILE 5.1 1.2 + - - -
239E ASP* 4.3 22.3 + - - +
240E MET 5.0 1.4 + - - -
268E LYS* 3.6 31.4 - - - +
269E SER* 4.7 4.4 + - - -
289E TRP* 4.3 4.9 - - - +
293E GLU 4.0 7.4 - - - +
294E ALA* 2.8 46.4 + - - +
296E PRO* 3.9 16.4 - - + -
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Residues in contact with TRP 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E MET 3.1 17.4 + - - +
138E LYS* 3.6 9.4 - - + +
140E ARG* 1.3 78.3 - - - +
142E ARG* 1.3 85.7 + - + +
144E ARG* 3.4 17.6 + - - +
145E MET* 3.2 42.1 + - + +
152E THR* 3.6 40.8 - - + -
155E PRO* 3.6 24.2 - - + -
200E GLU 2.9 22.3 + - - -
201E ASN* 3.5 36.7 - - - -
202E THR 3.6 17.9 - - - -
203E ILE* 3.6 24.2 - - + +
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Residues in contact with ARG 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D ASP* 2.8 43.8 + - - -
138E LYS* 2.9 44.4 + - + +
139E TRP* 3.2 45.0 + - + +
141E TRP* 1.3 94.0 - - + +
143E LYS* 1.3 56.8 + - - +
145E MET* 3.2 3.6 + - - +
146E GLU* 2.9 55.4 + - - +
152E THR* 4.0 23.9 + - - +
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Residues in contact with LYS 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E TRP* 2.9 22.0 + - + +
140E ARG* 3.8 6.5 - - - +
142E ARG* 1.3 75.3 - - - +
144E ARG* 1.3 58.7 + - + +
146E GLU* 3.5 13.5 + - - +
147E ALA* 3.0 27.0 + - - +
296E PRO* 4.0 24.7 - - - +
297E GLN 4.6 1.0 - - - +
298E GLU* 2.8 43.3 + - - +
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Residues in contact with ARG 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E ARG 3.5 12.7 + - - +
141E TRP* 3.4 20.4 + - - +
142E ARG 3.2 0.8 - - - -
143E LYS* 1.3 78.2 - - + +
145E MET* 1.3 74.9 + - - +
146E GLU 3.2 0.2 - - - -
147E ALA* 3.3 9.4 + - - +
148E ALA* 3.2 20.8 + - - +
236E ILE* 5.6 3.8 - - - +
237E ASP* 3.8 31.8 + - - +
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Residues in contact with MET 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141E TRP* 3.2 36.6 + - + +
144E ARG* 1.3 86.6 - - + +
146E GLU* 1.3 54.6 + - - +
148E ALA* 3.4 3.7 + - - +
149E GLY 3.3 4.3 + - - -
150E LYS* 2.8 70.6 + - + +
151E PRO* 3.9 9.0 - - + +
152E THR* 3.7 17.9 - - + -
200E GLU* 3.6 39.5 - - + +
201E ASN* 3.8 16.8 - - - +
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Residues in contact with GLU 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E ARG* 2.9 40.9 + - - +
143E LYS* 3.6 15.4 + - - +
144E ARG 3.2 0.2 - - - -
145E MET* 1.3 76.2 - - - +
147E ALA* 1.3 65.1 + - - +
148E ALA 3.2 0.2 - - - -
149E GLY* 3.2 12.2 + - - +
150E LYS 4.6 4.0 - - - +
152E THR* 4.3 12.2 + - + +
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Residues in contact with ALA 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E LYS 3.0 15.1 + - - +
144E ARG* 3.4 14.1 - - - +
146E GLU* 1.3 78.5 - - - +
148E ALA* 1.3 55.6 + - + +
149E GLY 3.3 3.6 + - - -
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Residues in contact with ALA 148 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144E ARG 3.2 12.0 + - - +
145E MET* 3.4 6.0 + - - +
146E GLU 3.2 0.8 - - - -
147E ALA* 1.3 76.3 - - - +
149E GLY* 1.3 62.5 + - - +
150E LYS* 3.1 34.4 + - + +
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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