Contacts of the helix formed by residues 127 - 151 (chain A) in PDB entry 3NA1
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 ASN 127 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A GLU 3.4 16.6 + - - -
124A ALA 3.1 20.9 + - - +
125A THR 3.0 1.2 - - - -
126A LYS* 1.3 89.2 + - - +
128A PHE* 1.3 62.5 + - - +
129A LEU 3.3 0.8 + - - -
130A PRO* 3.6 15.4 - - - +
131A LEU* 4.1 6.4 - - - +
259A TYR* 3.5 49.5 - - + +
265A ARG* 3.6 21.8 + - - +
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Residues in contact with PHE 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLU 3.4 22.0 - - - -
119A VAL* 3.9 4.0 - - - -
124A ALA 4.1 7.0 - - - -
125A THR* 2.8 42.0 + - + +
127A ASN* 1.3 81.0 - - - +
129A LEU* 1.3 64.4 + - - +
130A PRO 3.5 0.2 - - - -
131A LEU* 3.1 6.7 + - + +
132A LEU* 2.9 40.0 + - + +
174A VAL* 4.1 19.1 - - + -
259A TYR* 3.2 28.7 - + - -
262A ILE* 3.7 22.7 - - + -
428A ILE* 3.5 30.7 - - + -
431A LEU* 4.4 9.0 - - + -
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Residues in contact with LEU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A THR 4.2 3.6 - - - +
126A LYS* 3.5 20.2 - - + +
127A ASN 3.3 0.2 - - - -
128A PHE* 1.3 76.1 - - - +
130A PRO* 1.4 65.1 - - + +
132A LEU* 3.3 0.5 + - - -
133A ASP* 2.8 32.9 + - - +
328A MET* 4.7 8.1 - - + -
329A ALA* 3.7 38.6 - - + +
332A LEU* 3.8 16.4 - - + -
431A LEU* 3.7 38.8 - - + -
435A ILE* 3.9 15.2 - - + +
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Residues in contact with PRO 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LYS 4.3 3.6 - - - +
127A ASN* 3.6 16.4 - - - +
129A LEU* 1.4 97.5 - - + +
131A LEU* 1.3 60.2 + - + +
133A ASP* 4.3 5.6 - - + -
134A ALA* 3.0 31.5 + - - +
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Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ASN 4.1 9.2 - - - +
128A PHE* 3.1 7.0 + - - +
130A PRO* 1.3 81.5 - - + +
132A LEU* 1.3 62.1 + - - +
134A ALA* 4.0 1.6 - - - +
135A VAL* 3.4 12.1 + - - +
173A ASN* 2.8 61.2 + - - +
174A VAL* 4.0 20.6 - - + +
177A GLY* 4.7 9.9 - - - +
259A TYR* 3.9 36.3 - - + +
260A ARG 5.7 0.2 - - - -
261A GLY* 4.8 3.4 - - - +
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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
----------------------------------------------------------
128A PHE* 2.9 33.6 + - + +
129A LEU 4.0 2.0 - - - +
131A LEU* 1.3 76.3 - - - +
133A ASP* 1.3 64.9 + - - +
135A VAL* 3.1 8.2 + - - +
136A SER* 3.1 22.2 + - - -
166A PHE* 5.1 1.2 - - - -
170A SER* 3.8 30.6 + - - +
174A VAL* 3.9 20.2 - - + -
428A ILE* 4.2 9.9 - - + +
431A LEU* 3.7 30.5 - - + -
432A GLU* 3.7 25.4 - - + +
435A ILE* 4.1 12.6 - - + -
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Residues in contact with ASP 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU 2.8 19.5 + - - +
130A PRO* 4.0 6.3 - - + +
132A LEU* 1.3 77.8 - - - +
134A ALA* 1.3 56.0 + - - +
136A SER* 3.3 0.9 + - - -
137A ARG* 2.9 50.1 + - - +
321A ARG* 5.1 2.8 + - - -
328A MET* 3.8 30.7 - - + +
435A ILE* 3.5 12.7 - - + +
439A ASN* 3.0 27.5 + - - +
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Residues in contact with ALA 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A PRO 3.0 19.5 + - - +
131A LEU* 4.0 7.2 - - - +
133A ASP* 1.3 77.1 - - - +
135A VAL* 1.3 61.3 + - - +
137A ARG* 3.6 8.6 + - - +
138A ASP* 3.2 28.1 + - - +
173A ASN* 4.7 3.1 - - - +
179A ARG* 3.9 13.9 - - - +
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Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU 3.4 17.0 - - - +
132A LEU* 3.1 7.4 + - - +
134A ALA* 1.3 73.9 - - - +
136A SER* 1.3 60.9 + - - +
138A ASP 3.2 1.9 + - - -
139A PHE* 3.0 23.6 + - - +
166A PHE* 3.7 12.1 - - + -
169A GLU* 3.5 37.5 - - + +
170A SER* 3.5 22.7 - - - +
173A ASN* 3.7 14.8 - - + +
179A ARG* 3.9 20.0 - - - +
183A LEU* 3.4 12.0 - - + +
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Residues in contact with SER 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LEU* 3.1 12.8 + - - +
133A ASP 3.7 4.0 - - - -
135A VAL* 1.3 72.1 - - - +
137A ARG* 1.3 66.3 + - - +
139A PHE* 3.1 5.2 + - - +
140A VAL* 3.0 25.8 + - - +
166A PHE* 3.5 21.2 - - - -
432A GLU 4.5 1.0 + - - -
435A ILE* 4.0 3.8 - - - +
436A PHE* 3.3 30.8 + - - -
439A ASN* 3.5 26.2 - - - +
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Residues in contact with ARG 137 (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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133A ASP* 2.9 40.1 + - - +
134A ALA* 3.9 7.4 - - - +
136A SER* 1.3 75.2 - - - +
138A ASP* 1.3 64.1 + - - +
140A VAL* 3.4 8.4 + - - +
141A SER* 3.1 24.6 + - - -
321A ARG* 4.9 13.3 - - - +
439A ASN* 3.5 25.1 + - - +
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Residues in contact with ASP 138 (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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134A ALA 3.2 13.2 + - - +
135A VAL 3.2 9.4 + - - +
137A ARG* 1.3 75.9 - - - +
139A PHE* 1.3 62.7 + - - +
141A SER* 3.2 11.8 + - - -
142A VAL* 3.0 25.5 + - - +
179A ARG* 2.5 39.8 + - - +
183A LEU* 3.9 11.9 - - + -
184A GLU* 5.8 0.4 - - - +
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Residues in contact with PHE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A VAL 3.0 12.8 + - - +
136A SER* 3.1 9.4 + - - +
138A ASP* 1.3 75.2 - - - +
140A VAL* 1.3 63.7 + - - +
142A VAL* 3.1 20.5 + - + +
143A LEU* 3.2 37.3 + - + +
159A ILE* 4.1 13.5 - - + -
162A ASP* 3.7 37.7 - - + -
163A LEU* 4.0 17.5 - - + -
166A PHE* 3.8 27.6 - + + -
183A LEU* 3.6 18.1 - - + +
436A PHE* 3.6 26.7 - + + -
440A MET* 4.0 12.1 - - + -
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Residues in contact with VAL 140 (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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136A SER 3.0 15.6 + - - +
137A ARG* 3.6 10.3 - - - +
139A PHE* 1.3 76.1 - - - +
141A SER* 1.3 57.6 + - - +
143A LEU 3.1 2.6 + - - -
144A HIS* 3.0 40.7 + - + +
439A ASN* 3.7 36.8 - - + +
440A MET* 4.3 9.0 - - + +
443A ASN* 3.4 30.1 - - + +
444A PHE* 3.6 18.7 - - + -
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Residues in contact with SER 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 ARG 3.1 15.9 + - - -
138A ASP* 3.4 15.7 + - - -
140A VAL* 1.3 73.9 - - - +
142A VAL* 1.3 66.7 + - - +
144A HIS* 3.5 8.6 + - - +
145A ARG* 3.1 32.7 + - - +
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Residues in contact with VAL 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 ASP 3.0 20.3 + - - +
139A PHE* 3.1 18.3 + - + +
141A SER* 1.3 75.9 - - - +
143A LEU* 1.3 61.8 + - + +
145A ARG* 3.3 27.2 - - - +
146A ARG* 3.0 58.5 + - + +
162A ASP* 5.2 3.1 - - + +
183A LEU* 3.3 39.3 - - + +
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Residues in contact with LEU 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 PHE* 3.2 26.4 + - + +
140A VAL 3.1 2.5 + - - +
142A VAL* 1.3 79.4 - - + +
144A HIS* 1.3 59.4 + - - +
146A ARG* 3.0 12.0 + - - +
147A ILE* 2.9 36.0 + - + +
155A TYR* 4.2 28.6 - - + +
159A ILE* 4.5 8.3 - - + -
162A ASP* 6.4 0.4 - - + -
440A MET* 3.5 35.9 - - + -
444A PHE* 3.5 28.5 - - + -
472A PHE* 4.3 20.4 - - + -
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Residues in contact with HIS 144 (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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140A VAL* 3.0 36.9 + - + +
141A SER* 3.9 7.9 - - - +
142A VAL 3.4 0.2 - - - -
143A LEU* 1.3 74.1 - - - +
145A ARG* 1.3 62.3 + - - +
147A ILE* 3.4 12.2 + - - +
148A LYS* 3.1 23.6 + - - +
443A ASN* 3.0 32.7 + - - -
444A PHE* 3.5 20.8 - + - -
474A PRO* 4.5 13.8 - - + +
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Residues in contact with ARG 145 (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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141A SER* 3.1 19.3 + - - +
142A VAL* 3.3 37.0 + - - +
144A HIS* 1.3 75.9 - - - +
146A ARG* 1.3 64.5 + - + +
148A LYS* 3.4 7.8 + - - +
149A LYS* 3.1 24.8 + - + +
183A LEU 3.5 23.4 + - - -
184A GLU* 4.4 1.2 - - - +
185A GLU* 3.8 43.7 + - - +
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Residues in contact with ARG 146 (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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142A VAL* 3.0 38.5 + - + +
143A LEU* 3.0 10.9 + - - +
145A ARG* 1.3 79.2 - - + +
147A ILE* 1.3 58.4 + - - +
149A LYS* 3.8 9.8 - - + +
150A ALA* 3.0 28.6 + - - +
155A TYR* 3.1 58.6 + - + -
159A ILE* 4.3 3.4 - - - +
162A ASP* 2.7 44.8 + - - -
165A ARG* 4.8 1.6 - - - +
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Residues in contact with ILE 147 (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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143A LEU* 2.9 17.2 + - + +
144A HIS* 3.6 12.3 - - - +
145A ARG 3.2 0.2 - - - -
146A ARG* 1.3 73.7 - - - +
148A LYS* 1.3 65.8 + - - +
150A ALA* 3.2 13.0 + - - +
151A GLY* 3.3 10.2 + - - -
152A SER 4.3 2.1 + - - -
153A GLY* 3.8 10.0 + - - -
154A ASN 3.7 29.8 - - - +
155A TYR* 3.6 17.3 - - + -
444A PHE* 3.5 36.6 - - + -
472A PHE* 4.1 9.4 - - + +
474A PRO* 4.0 25.8 - - + -
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Residues in contact with LYS 148 (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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144A HIS 3.1 13.0 + - - +
145A ARG* 3.8 9.4 - - - +
147A ILE* 1.3 76.8 - - - +
149A LYS* 1.3 63.6 + - - +
151A GLY* 3.2 13.9 + - - -
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Residues in contact with LYS 149 (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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145A ARG* 3.1 18.2 + - + +
146A ARG* 3.8 10.5 - - + +
147A ILE 3.3 0.2 - - - -
148A LYS* 1.3 77.2 - - - +
150A ALA* 1.3 63.1 + - - +
151A GLY* 3.3 1.2 + - - -
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Residues in contact with ALA 150 (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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146A ARG 3.0 14.3 + - - +
147A ILE 3.2 4.2 + - - +
149A LYS* 1.3 75.8 - - - +
151A GLY* 1.3 58.6 + - - +
152A SER* 3.1 12.8 + - - +
154A ASN 3.4 26.0 - - - +
155A TYR* 4.9 7.2 - - + -
158B ASP* 4.6 4.5 - - - +
467B PRO* 3.4 17.5 - - - +
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Residues in contact with GLY 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ILE 3.3 3.4 + - - -
148A LYS* 3.2 16.4 + - - -
149A LYS 4.3 1.3 - - - -
150A ALA* 1.3 76.3 - - - +
152A SER* 1.3 57.5 + - - +
153A GLY 3.5 3.1 - - - -
466B LYS* 5.0 2.6 - - - +
467B PRO* 3.3 21.3 - - - +
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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
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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