Contacts of the helix formed by residues 125 - 148 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A THR* 2.6 24.0 + - - -
124A ILE* 1.3 82.0 - - - +
126A SER* 1.3 65.9 + - - -
127A SER* 3.2 3.4 + - - -
128A GLU* 3.7 4.1 + - - +
129A ALA* 3.4 7.3 + - - +
275A HIS* 3.8 11.7 - - - -
284A CYS 4.2 0.2 - - - -
285A GLY* 3.6 13.9 - - - -
467A PO4 3.7 8.1 - - - -
316F ASN* 5.2 0.4 + - - -
318F SER 5.0 0.2 - - - -
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Residues in contact with SER 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLY* 1.3 70.7 - - - -
127A SER* 1.3 58.8 + - - +
129A ALA* 3.4 8.1 + - - +
130A CYS* 2.8 43.1 + - - -
163A GLN* 6.5 0.2 - - - -
165A CYS* 5.0 1.1 - - - -
243A ASP* 5.1 1.1 + - - -
245A ALA* 3.7 15.1 - - - +
271A SER* 4.9 1.1 - - - -
272A ALA* 3.2 7.2 + - - -
273A SER* 2.6 40.6 + - - -
276A LYS* 4.4 0.2 - - - -
285A GLY* 4.4 0.4 - - - -
467A PO4 3.0 20.3 + - - -
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Residues in contact with SER 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLY 3.2 0.4 - - - -
126A SER* 1.3 72.6 - - - +
128A GLU* 1.3 66.7 + - - +
130A CYS* 3.1 5.7 + - - +
131A MET* 3.0 32.6 + - - +
165A CYS* 4.0 20.4 - - - +
168A LYS* 4.2 4.3 + - - -
467A PO4 2.8 18.8 + - - -
315F ILE 2.5 25.7 + - - -
316F ASN* 3.8 4.1 + - - -
317F PHE* 3.7 19.4 - - - +
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Residues in contact with GLU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ASN 5.4 0.4 - - - -
123A THR* 3.3 21.3 - - + -
124A ILE 3.0 20.6 + - - +
125A GLY 3.7 4.0 + - - +
127A SER* 1.3 77.9 - - - +
129A ALA* 1.3 66.1 + - - +
131A MET* 3.0 13.8 + - - +
132A LEU* 3.0 32.6 + - + +
314A ALA* 3.7 6.5 - - - +
315A ILE* 2.8 38.1 + - + -
316A ASN* 2.8 35.5 + - - +
319A ARG* 4.9 1.5 + - - -
315F ILE* 4.3 3.6 + - + -
316F ASN* 3.8 14.7 + - - +
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Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A THR* 3.7 24.4 - - + +
125A GLY 3.4 4.8 + - - +
126A SER* 3.4 11.4 + - - +
127A SER 3.3 0.2 - - - -
128A GLU* 1.3 79.9 - - - +
130A CYS* 1.3 55.4 + - - +
132A LEU* 3.3 3.2 + - - +
133A GLY* 3.0 25.1 + - - -
271A SER* 3.7 15.4 - - - -
286A TRP 3.8 7.2 - - - +
287A VAL* 3.7 30.5 - - + +
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Residues in contact with CYS 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A SER* 2.8 29.4 + - - -
127A SER 3.1 8.3 + - - +
129A ALA* 1.3 70.3 - - - +
131A MET* 1.3 57.4 + - - +
133A GLY 3.2 1.4 + - - -
134A GLY* 2.6 34.1 + - - -
165A CYS* 2.9 37.7 - - + +
166A TRP* 3.5 36.4 - - + -
169A PHE* 5.3 0.4 - - + -
241A HIS* 4.7 0.9 - - - -
243A ASP* 4.1 7.0 - - - -
271A SER* 4.0 12.8 - - - -
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Residues in contact with MET 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A SER* 3.0 25.4 + - - +
128A GLU* 3.3 7.9 - - - +
130A CYS* 1.3 75.3 - - - +
132A LEU* 1.3 54.5 + - - +
134A GLY* 3.7 0.2 - - - -
135A MET* 2.7 40.2 + - - +
165A CYS* 4.3 6.7 - - + +
168A LYS* 4.3 22.7 - - + -
169A PHE* 4.1 21.6 - - - -
172A TYR* 4.9 3.1 - - + -
173A TRP* 3.7 29.6 - - + -
315A ILE* 3.5 29.6 - - + -
315F ILE* 3.3 36.3 - - + +
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A THR* 3.8 19.7 - - + -
123A THR* 3.9 20.0 - - + -
128A GLU* 3.0 20.4 + - + +
129A ALA 3.7 5.2 - - - +
131A MET* 1.3 71.8 - - - +
133A GLY* 1.3 57.3 - - - +
135A MET* 3.3 9.8 + - + -
136A ALA* 2.8 36.7 + - - +
287A VAL* 4.0 2.0 - - + -
289A TRP* 3.8 12.8 - - + -
313A PHE* 3.4 68.4 - - + +
314A ALA* 4.2 12.6 - - + -
315A ILE* 4.4 6.7 - - + +
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Residues in contact with GLY 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ALA 3.0 13.7 + - - -
130A CYS 3.5 3.4 - - - -
132A LEU* 1.3 76.4 - - - +
134A GLY* 1.3 54.8 + - - +
136A ALA* 3.6 2.9 - - - +
137A MET* 3.0 35.6 + - - +
166A TRP* 4.9 0.4 - - - -
241A HIS* 3.9 24.0 - - - -
269A SER* 4.3 7.2 + - - -
287A VAL* 4.9 0.2 - - - -
289A TRP* 4.1 9.6 - - - -
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Residues in contact with GLY 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A CYS 2.6 19.9 + - - -
133A GLY* 1.3 68.9 - - - +
135A MET* 1.3 67.7 + - - +
137A MET* 3.1 18.3 + - - +
138A LYS* 2.9 19.8 + - - +
166A TRP* 4.2 3.7 - - - -
169A PHE* 3.4 30.7 - - - -
203A ILE* 4.2 0.2 - - - +
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Residues in contact with MET 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A MET 2.7 23.8 + - - +
132A LEU* 3.8 14.1 - - + +
134A GLY* 1.3 74.1 - - - +
136A ALA* 1.3 62.7 + - - +
138A LYS* 3.3 5.2 + - - -
139A TRP* 3.0 36.3 + - + +
169A PHE* 3.5 3.3 - - + -
173A TRP* 3.3 48.2 - - + +
299A LEU* 4.0 5.4 - - + -
313A PHE* 3.5 31.0 - - + -
315A ILE* 4.6 5.4 - - + -
172F TYR* 3.5 43.3 - - + +
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Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LEU 2.8 21.2 + - - +
133A GLY 3.6 3.4 - - - +
135A MET* 1.3 72.2 - - - +
137A MET* 1.3 53.1 + - - +
139A TRP* 3.1 2.6 + - - +
140A ARG* 2.8 49.6 + - - +
289A TRP* 3.6 26.5 - - + +
295A LEU* 4.4 2.7 - - + -
296A PRO* 4.1 13.1 - - + +
299A LEU* 3.8 15.0 - - + +
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Residues in contact with MET 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLY 3.0 11.3 + - - +
134A GLY* 3.4 23.6 - - - +
136A ALA* 1.3 74.4 - - - +
138A LYS* 1.3 64.0 + - - +
140A ARG* 3.2 29.5 + - - +
141A TRP* 2.9 25.5 + - - +
157A LEU* 3.5 25.8 - - + -
166A TRP* 4.2 4.7 - - + -
203A ILE* 3.8 17.2 - - + +
204A GLY* 3.6 29.6 - - - -
205A VAL 4.5 1.6 - - - -
206A VAL* 3.9 14.6 - - + -
239A ASP* 5.0 0.7 - - + +
240A MET 4.8 1.1 - - - -
241A HIS* 4.1 25.8 - - + +
269A SER* 5.3 0.4 - - - +
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Residues in contact with LYS 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLY 2.9 13.0 + - - +
135A MET* 3.6 9.6 - - - +
137A MET* 1.3 77.0 - - - +
139A TRP* 1.3 72.8 + - + +
141A TRP* 3.3 8.5 + - + +
142A ARG* 2.8 56.7 + - + +
152A THR 6.0 0.9 - - - -
155A PRO* 4.3 12.1 - - + -
169A PHE* 4.8 2.2 - - + -
173A TRP* 3.0 40.1 + - + +
174A ASP* 4.8 2.6 + - - +
175A VAL* 4.2 16.6 - - + -
203A ILE* 3.7 25.1 - - + +
174F ASP* 3.8 9.1 + - - -
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Residues in contact with TRP 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A MET* 3.0 44.5 + - + +
138A LYS* 1.3 91.8 - - + +
140A ARG* 1.3 66.4 + - - +
142A ARG* 3.2 38.5 - - + +
143A LYS* 3.1 31.6 + - + +
173A TRP* 4.9 1.1 - + - -
296A PRO* 3.6 23.1 - - + -
298A GLU* 4.1 29.3 - - + +
299A LEU* 3.7 26.3 - - + +
171F ARG* 3.3 32.2 - - + +
172F TYR* 3.5 20.6 - - - -
174F ASP* 3.8 5.6 - - - -
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Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ALA* 2.8 35.1 + - - +
137A MET* 3.4 33.9 - - - +
139A TRP* 1.3 72.6 - - - +
141A TRP* 1.3 62.4 + - - +
143A LYS* 3.4 7.5 + - - +
144A ARG* 3.2 27.4 + - - +
203A ILE 5.2 0.8 + - - -
239A ASP* 4.1 23.9 + - - +
240A MET 4.8 2.2 + - - -
268A LYS* 3.6 32.2 - - - +
269A SER* 4.6 4.9 + - - -
289A TRP* 4.3 5.5 - - - -
293A GLU 4.2 6.3 - - - +
294A ALA* 2.8 44.0 + - - +
296A PRO* 3.9 16.4 - - + -
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Residues in contact with TRP 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A MET 2.9 17.6 + - - +
138A LYS* 3.6 8.7 - - + +
140A ARG* 1.3 78.0 - - - +
142A ARG* 1.3 87.0 + - + +
144A ARG* 3.2 15.7 + - + +
145A MET* 3.1 40.5 + - + +
152A THR* 3.6 40.4 - - - -
154A LYS 4.4 0.2 - - - -
155A PRO* 3.8 22.7 - - + -
200A GLU 3.1 19.3 + - - -
201A ASN* 3.6 38.2 - - - -
202A THR 3.3 19.1 - - - -
203A ILE* 3.4 26.7 - - + +
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Residues in contact with ARG 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LYS* 2.8 46.8 + - + +
139A TRP* 3.2 42.0 - - + +
140A ARG 3.4 0.2 - - - -
141A TRP* 1.3 90.4 - - + +
143A LYS* 1.3 67.4 + - + +
145A MET* 3.3 1.4 + - - +
146A GLU* 2.9 43.4 + - - +
152A THR* 4.0 26.7 + - - +
174F ASP* 2.8 43.2 + - - -
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Residues in contact with LYS 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A TRP* 3.1 23.3 + - + +
140A ARG* 3.8 7.6 - - - +
141A TRP 3.4 0.2 - - - -
142A ARG* 1.3 77.5 - - + +
144A ARG* 1.3 62.4 + - - +
146A GLU* 3.5 13.4 + - - +
147A ALA* 3.0 26.3 + - - +
296A PRO* 3.9 20.4 - - + +
297A GLN 4.7 1.2 - - - +
298A GLU* 2.8 43.8 + - - -
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Residues in contact with ARG 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 3.2 19.9 + - - +
141A TRP* 3.6 18.1 - - + +
143A LYS* 1.3 78.6 - - - +
145A MET* 1.3 65.2 + - + +
147A ALA* 3.5 5.9 + - - +
148A ALA* 3.0 23.8 + - - +
237A ASP* 2.2 57.0 + - - +
238A ILE* 4.7 0.4 - - - +
239A ASP* 3.4 24.5 + - - +
268A LYS* 4.7 4.8 - - - +
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Residues in contact with MET 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A TRP* 3.1 35.4 + - + +
142A ARG 3.9 0.2 - - - +
143A LYS 3.3 0.2 - - - -
144A ARG* 1.3 75.6 - - + +
146A GLU* 1.3 53.8 + - - +
148A ALA* 2.8 5.5 + - - -
149A GLY 2.7 31.9 + - - -
150A LYS* 3.0 45.6 + - + +
151A PRO* 3.7 11.9 - - + +
152A THR* 3.7 19.5 - - + -
200A GLU* 3.4 38.4 - - + +
201A ASN* 3.8 11.0 - - - +
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Residues in contact with GLU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ARG* 2.9 38.6 + - - +
143A LYS* 3.9 15.0 + - - +
145A MET* 1.3 76.2 - - - +
147A ALA* 1.3 62.7 + - - +
149A GLY* 3.2 12.7 + - - +
150A LYS 4.8 4.0 - - - +
152A THR* 4.2 14.1 + - + +
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Residues in contact with ALA 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LYS 3.0 18.3 + - - +
144A ARG* 3.7 7.0 - - + +
146A GLU* 1.3 76.5 - - - +
148A ALA* 1.3 57.9 + - - +
149A GLY 3.3 2.6 + - - -
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Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ARG 3.0 15.7 + - - +
145A MET* 2.8 9.7 + - - +
147A ALA* 1.3 75.1 - - + +
149A GLY* 1.3 58.6 + - - +
150A LYS* 3.3 30.4 + - + -
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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