Contacts of the helix formed by residues 129 - 150 (chain A) in PDB entry 3NIE
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 THR 129 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A PHE 5.6 1.1 - - - +
128A LEU* 1.3 78.5 - - - +
130A GLU* 1.3 63.8 + - - +
131A GLN* 3.4 9.7 + - - +
132A HIS* 3.1 50.4 + - + +
133A VAL* 3.2 7.0 + - - +
254A MET* 4.8 1.3 - - - -
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Residues in contact with GLU 130 (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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129A THR* 1.3 72.0 - - - +
131A GLN* 1.3 63.9 + - - +
133A VAL* 3.4 3.7 + - + +
134A LYS* 3.0 33.7 + - - +
254A MET* 3.9 25.2 - - + -
338A SER 4.4 7.9 - - - +
339A ILE* 3.5 24.1 - - - +
340A SER 4.6 0.9 + - - -
369A TYR* 2.7 40.6 + - - +
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Residues in contact with GLN 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A THR* 3.2 9.3 + - - +
130A GLU* 1.3 78.7 - - - +
132A HIS* 1.3 56.2 + - - +
134A LYS* 3.3 9.0 + - + +
135A THR* 2.6 52.5 + - - +
372A ASP* 5.8 2.8 + - + -
373A VAL* 4.4 15.1 - - + +
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Residues in contact with HIS 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PHE 5.3 2.2 - - - -
128A LEU* 3.7 28.9 - - + +
129A THR* 3.1 46.6 + - + +
131A GLN* 1.3 79.2 + - - +
133A VAL* 1.3 67.6 + - - +
135A THR* 3.2 6.5 + - - -
136A ILE* 3.0 29.5 + - + +
168A CYS* 3.8 23.1 - - - -
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Residues in contact with VAL 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 4.2 13.7 - - + +
129A THR 3.2 11.7 + - - +
130A GLU* 3.6 8.7 - - - +
132A HIS* 1.3 78.7 - - - +
134A LYS* 1.3 59.4 + - + +
136A ILE* 3.4 2.3 + - - +
137A LEU* 3.0 26.7 + - - +
247A PHE* 3.9 28.3 - - + -
250A LEU* 3.4 42.7 - - + +
251A LEU* 4.0 8.7 - - + -
254A MET* 3.8 22.2 - - + -
369A TYR* 4.6 4.5 - - - +
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Residues in contact with LYS 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLU* 3.0 31.1 + - - +
131A GLN* 3.5 9.2 - - + +
133A VAL* 1.3 73.4 - - - +
135A THR* 1.3 68.0 + - - +
137A LEU* 3.3 2.7 + - - +
138A TYR* 3.0 26.2 + - - +
369A TYR* 2.9 67.1 + - + +
370A LEU* 4.0 14.5 - - + +
372A ASP* 3.0 31.6 + - + -
373A VAL* 3.9 20.2 - - + +
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Residues in contact with THR 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A GLN* 2.6 38.0 + - - +
132A HIS* 3.6 7.2 - - - -
134A LYS* 1.3 72.9 - - - +
136A ILE* 1.3 57.2 + - - +
138A TYR* 3.8 2.5 - - - +
139A ASN* 3.1 44.1 + - - +
167A ASP 5.0 1.8 - - - +
168A CYS* 3.8 25.6 - - + -
373A VAL* 3.8 19.4 - - + +
375A LYS* 6.1 2.2 - - - +
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Residues in contact with ILE 136 (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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118A LEU* 4.2 16.4 - - + -
121A LEU* 4.4 8.7 - - + -
128A LEU* 4.2 16.2 - - + -
132A HIS* 3.0 21.2 + - + +
133A VAL 3.8 2.2 - - - +
135A THR* 1.3 75.2 - - - +
137A LEU* 1.3 67.1 + - - +
139A ASN* 3.3 3.1 + - - +
140A LEU* 3.0 22.0 + - + +
164A LEU* 3.8 20.6 - - + -
168A CYS* 3.8 34.1 - - - +
170A VAL* 3.6 8.9 - - + +
250A LEU* 3.4 37.9 - - + -
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Residues in contact with LEU 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 VAL 3.0 17.1 + - - +
134A LYS* 3.9 4.7 - - - +
136A ILE* 1.3 79.3 - - - +
138A TYR* 1.3 58.0 + - - +
140A LEU* 3.3 12.0 + - + +
141A LEU* 3.0 36.9 + - + +
243A THR* 3.6 32.1 - - + +
247A PHE* 3.6 54.1 - - + +
250A LEU* 4.4 9.6 - - + -
346A LEU* 4.1 16.4 - - + -
350A MET* 4.2 6.3 - - + -
369A TYR* 5.6 0.2 - - + -
370A LEU* 4.6 6.7 - - + -
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Residues in contact with TYR 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 LYS 3.0 17.5 + - - +
135A THR* 3.8 3.4 - - - +
137A LEU* 1.3 77.7 - - - +
139A ASN* 1.3 62.5 + - - +
141A LEU* 3.0 9.5 + - - +
142A LEU* 2.9 50.6 + - + +
365A LEU* 3.2 43.7 - - + -
370A LEU* 4.0 22.2 - - + +
373A VAL* 4.1 20.6 - - + -
374A ARG* 3.4 7.6 - - + +
375A LYS* 3.0 41.8 + - + -
379A GLU* 2.8 29.8 + - - +
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Residues in contact with ASN 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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88A TYR* 3.5 31.1 + - + -
135A THR* 3.1 26.0 + - - +
136A ILE 3.6 4.9 - - - +
138A TYR* 1.3 83.4 - - - +
140A LEU* 1.3 61.3 + - - +
142A LEU* 3.5 4.2 + - - +
143A GLY* 3.3 15.4 + - - -
167A ASP 5.3 0.2 + - - -
168A CYS 2.8 27.3 + - - -
169A SER* 3.2 14.9 - - - +
170A VAL* 3.9 20.2 - - + +
375A LYS* 5.4 5.9 + - - -
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Residues in contact with LEU 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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118A LEU* 5.0 3.1 - - + -
136A ILE* 3.0 13.9 + - + +
137A LEU* 3.4 14.4 - - + +
139A ASN* 1.3 75.9 - - - +
141A LEU* 1.3 58.2 + - - +
143A GLY* 3.1 5.1 + - - -
144A GLU* 3.0 38.9 + - + +
157A LEU* 4.5 6.1 - - + -
162A CYS* 3.8 24.0 - - - -
170A VAL* 4.1 14.5 - - + +
172A ILE* 4.2 19.2 - - + +
243A THR* 3.9 21.5 - - + +
246A ILE* 4.0 35.0 - - + -
250A LEU* 5.7 0.9 - - + -
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Residues in contact with LEU 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 LEU* 3.0 29.9 + - + +
138A TYR* 3.0 6.3 + - - +
140A LEU* 1.3 73.1 - - - +
142A LEU* 1.3 59.6 + - - +
144A GLU* 3.2 6.0 + - - +
145A LYS* 2.9 14.6 + - - +
240A ILE* 4.0 16.4 - - + -
243A THR* 4.0 10.3 - - + -
346A LEU* 5.5 0.2 - - + -
350A MET* 3.7 24.5 - - + -
361A ILE* 2.9 33.1 - - + +
364A ALA* 3.9 26.0 - - + +
365A LEU* 3.9 10.3 - - + +
370A LEU* 3.8 27.8 - - + -
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Residues in contact with LEU 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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88A TYR* 3.2 44.0 - - + +
138A TYR* 2.9 40.4 + - + +
139A ASN* 3.8 10.1 - - - +
140A LEU 3.3 0.2 - - - -
141A LEU* 1.3 74.4 - - - +
143A GLY* 1.3 62.7 + - - +
145A LYS* 3.4 8.4 + - + +
146A PHE* 3.2 20.6 + - - +
365A LEU* 3.3 25.8 - - + -
378A LEU* 4.2 18.6 - - + +
379A GLU* 4.0 27.8 - - + +
381A PHE* 4.9 4.9 - - + -
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Residues in contact with GLY 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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88A TYR* 3.8 22.5 - - - +
89A ILE* 4.2 2.4 - - - +
139A ASN 3.3 6.9 + - - -
140A LEU 3.1 7.6 + - - -
142A LEU* 1.3 76.9 - - - +
144A GLU* 1.3 65.9 + - - +
146A PHE* 3.2 7.2 + - - +
147A ILE* 3.1 23.0 + - - +
172A ILE* 3.7 17.4 - - - +
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Residues in contact with GLU 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 LEU* 3.0 30.2 + - + +
141A LEU* 3.2 14.7 + - - +
143A GLY* 1.3 75.2 - - - +
145A LYS* 1.3 64.0 + - - +
147A ILE* 3.0 14.4 + - + +
148A HIS* 2.9 22.4 + - - +
157A LEU* 3.7 19.5 - - + +
172A ILE* 4.5 2.9 - - + -
236A ASN* 4.8 1.7 + - - -
239A ASP* 3.2 26.8 - - + +
240A ILE* 3.7 8.3 + - - +
243A THR* 2.3 41.6 + - - +
361A ILE* 4.1 8.5 - - + -
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Residues in contact with LYS 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 LEU 2.9 10.3 + - - +
142A LEU* 3.5 11.0 - - + +
143A GLY 3.2 0.2 - - - -
144A GLU* 1.3 74.6 - - - +
146A PHE* 1.3 56.9 + - - +
148A HIS* 3.0 8.1 + - + +
149A GLU* 2.8 45.3 + - - +
361A ILE* 3.7 27.7 - - + +
362A ASP* 4.3 12.3 - - - +
365A LEU* 3.5 26.2 - - + -
379A GLU* 3.6 26.0 - - + +
381A PHE* 3.9 14.6 - - + -
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Residues in contact with PHE 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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84A LEU* 3.5 30.7 - - + -
85A LYS* 3.4 30.5 - - + -
86A SER* 3.6 31.2 - - - +
88A TYR* 5.7 0.4 - - + -
89A ILE* 4.2 8.7 - - + -
142A LEU 3.2 8.7 + - - +
143A GLY* 3.2 11.1 + - - +
145A LYS* 1.3 78.2 - - - +
147A ILE* 1.3 56.6 + - - +
149A GLU 3.9 0.5 - - - -
150A SER* 2.6 39.9 + - - -
381A PHE* 3.6 30.4 - + + -
383A THR* 3.5 28.9 - - - -
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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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84A LEU* 5.2 4.0 - - + -
89A ILE* 4.1 6.7 - - + -
143A GLY 3.1 11.1 + - - +
144A GLU* 3.0 15.3 + - + +
146A PHE* 1.3 75.4 - - - +
148A HIS* 1.3 64.4 + - - +
150A SER* 3.4 5.2 + - - -
151A GLY 3.3 3.3 + - - -
152A ILE* 3.0 62.7 + - + +
153A ILE* 4.4 0.2 - - - -
154A HIS* 4.1 18.2 - - + +
157A LEU* 5.4 1.3 - - + -
172A ILE* 3.6 33.9 - - + -
175A PHE* 3.7 29.8 - - + -
236A ASN* 4.5 0.9 - - - +
239A ASP* 4.4 6.5 - - - +
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Residues in contact with HIS 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 GLU 2.9 11.0 + - - +
145A LYS* 3.3 11.2 - - + +
147A ILE* 1.3 77.5 - - - +
149A GLU* 1.3 68.5 + - - +
151A GLY* 2.6 26.7 + - - -
152A ILE 4.0 0.2 - - - -
181A ILE* 3.6 11.5 - - + +
236A ASN* 3.2 42.7 + - + +
361A ILE* 4.2 22.4 - - + -
362A ASP* 5.6 2.5 - - - -
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Residues in contact with GLU 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 LYS* 2.8 35.6 + - + +
146A PHE 4.2 1.6 - - - +
147A ILE 3.4 0.2 - - - -
148A HIS* 1.3 86.0 + - - +
150A SER* 1.3 57.8 + - - +
151A GLY 3.3 0.8 + - - -
361A ILE* 6.1 0.2 - - - +
362A ASP* 5.2 6.8 - - - +
381A PHE* 3.8 30.7 - - + +
383A THR* 4.1 20.8 - - - +
384A GLU 4.3 0.6 - - - +
385A LYS* 4.0 12.3 - - - +
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Residues in contact with SER 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 3.8 18.7 - - - +
146A PHE* 2.6 33.2 + - - -
147A ILE 3.8 4.7 - - - -
148A HIS 3.0 0.8 - - - -
149A GLU* 1.3 77.1 - - - +
151A GLY* 1.3 62.6 + - - +
152A ILE* 3.4 20.6 + - - +
383A THR* 4.8 1.9 - - - -
384A GLU 3.8 17.4 + - - -
385A LYS* 3.5 6.4 - - - +
386A ILE* 3.4 22.7 + - - +
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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