Contacts of the helix formed by residues 133 - 157 (chain A) in PDB entry 2GYQ
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 HIS 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A GLU* 3.0 34.9 + - - -
15A LEU* 3.9 20.9 - - + -
70A LEU* 4.1 14.1 - - + +
128A ALA* 3.0 10.7 + - + +
129A GLU* 5.0 0.6 - - - +
131A LEU* 3.7 25.5 - - + +
132A GLY* 1.3 75.8 + - - +
134A ASP* 1.3 65.9 + - - +
135A ASP 3.3 2.5 - - - -
136A ILE* 3.2 30.3 + - + +
137A VAL* 3.0 24.6 + - - +
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Residues in contact with ASP 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLU* 4.9 11.0 - - - +
132A GLY* 3.2 14.6 + - - +
133A HIS* 1.3 73.1 - - - +
135A ASP* 1.3 66.5 + - - +
137A VAL* 3.3 10.1 + - - +
138A ARG* 3.1 40.8 + - - +
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Residues in contact with ASP 135 (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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69A LYS* 2.9 43.8 + - + +
133A HIS 3.3 0.4 - - - -
134A ASP* 1.3 77.2 - - - +
136A ILE* 1.3 67.7 + - + +
138A ARG* 2.9 32.0 + - - +
139A PHE* 2.9 32.7 + - + -
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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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15A LEU* 5.2 2.0 - - + -
19A LEU* 5.0 4.3 - - + -
66A VAL* 3.8 39.9 - - + +
69A LYS* 4.6 14.4 - - + -
70A LEU* 3.6 39.5 - - + -
128A ALA* 3.9 10.8 - - + -
133A HIS* 3.2 28.6 + - + +
135A ASP* 1.3 75.2 - - + +
137A VAL* 1.3 64.4 + - - +
139A PHE* 3.3 1.3 + - - +
140A LEU* 2.9 45.7 + - + +
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Residues in contact with VAL 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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125A ILE* 3.8 17.9 - - + +
128A ALA* 3.8 7.6 - - + -
129A GLU* 3.4 51.4 - - - +
133A HIS 3.0 18.8 + - - +
134A ASP* 3.5 10.1 - - - +
136A ILE* 1.3 76.0 - - - +
138A ARG* 1.3 56.1 + - + +
140A LEU* 3.8 5.1 - - - +
141A THR* 2.7 45.6 + - - +
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Residues in contact with ARG 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 ASP* 3.1 28.2 + - - +
135A ASP* 2.9 48.7 + - - +
137A VAL* 1.3 77.2 - - + +
139A PHE* 1.3 66.2 + - + +
141A THR* 3.2 6.4 + - - -
142A THR* 2.9 27.6 + - - +
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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
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62A ARG* 3.7 37.3 - - + +
65A GLN* 3.6 30.7 - - + -
66A VAL* 3.6 27.6 - - + -
69A LYS* 3.9 25.1 - - - -
135A ASP* 2.9 31.5 + - + -
136A ILE 3.8 2.0 - - - +
138A ARG* 1.3 77.4 - - + +
140A LEU* 1.3 63.9 + - - +
142A THR* 3.3 8.0 + - - -
143A ASN* 3.0 27.2 + - - +
416A ACT 5.3 3.8 - - - -
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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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15A LEU* 5.1 0.7 - - + -
19A LEU* 3.8 24.5 - - + -
63A LEU* 3.9 19.7 - - + -
66A VAL* 4.6 5.8 - - + -
121A TYR* 3.9 21.6 - - + -
124A LEU* 3.8 37.0 - - + +
125A ILE* 3.5 18.5 - - + +
128A ALA* 4.4 1.8 - - + -
136A ILE* 2.9 40.1 + - + +
139A PHE* 1.3 77.5 - - - +
141A THR* 1.3 52.6 + - - +
143A ASN* 3.3 6.7 + - - +
144A LEU* 2.8 34.7 + - - +
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Residues in contact with THR 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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125A ILE* 3.6 21.4 - - + +
137A VAL* 2.7 31.4 + - - +
138A ARG* 3.6 6.7 - - - -
140A LEU* 1.3 74.9 - - - +
142A THR* 1.3 60.1 + - - +
144A LEU* 3.2 5.3 + - + +
145A ASN* 2.9 46.9 + - - +
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Residues in contact with THR 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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62A ARG* 3.4 37.2 - - - +
138A ARG* 2.9 14.7 + - - +
139A PHE* 3.3 9.1 + - - -
141A THR* 1.3 76.1 - - - +
143A ASN* 1.3 62.6 + - - +
145A ASN* 3.3 8.6 + - - +
146A GLU* 3.1 25.3 + - + +
416A ACT 3.8 15.8 + - + +
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Residues in contact with ASN 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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59A GLN* 3.3 34.6 + - + +
62A ARG* 3.0 39.6 + - - +
63A LEU* 3.8 8.7 - - - +
121A TYR* 3.0 40.9 + - + -
139A PHE 3.0 14.3 + - - +
140A LEU* 3.6 8.0 - - - +
142A THR* 1.3 73.7 - - - +
144A LEU* 1.3 64.8 + - - +
146A GLU* 3.1 6.2 + - - +
147A GLU* 3.1 25.9 + - - +
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Residues in contact with LEU 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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118A ILE* 3.8 40.6 - - + +
121A TYR* 3.9 15.8 - - + -
122A GLY* 4.6 8.1 - - - -
125A ILE* 3.7 20.9 - - + -
140A LEU 2.8 21.2 + - - +
141A THR* 3.5 7.9 - - + +
143A ASN* 1.3 71.5 - - - +
145A ASN* 1.3 63.7 + - - +
147A GLU* 3.0 8.3 + - + +
148A LYS* 2.9 59.4 + - + +
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Residues in contact with ASN 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 THR* 2.9 36.3 + - - +
142A THR* 3.8 7.6 - - - +
143A ASN 3.2 0.4 - - - -
144A LEU* 1.3 81.8 - - - +
146A GLU* 1.3 57.9 + - + +
148A LYS* 3.4 20.0 + - - +
149A ALA* 2.9 29.6 + - - +
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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
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52A HIS* 4.1 1.8 - - - -
55A GLU* 3.8 33.4 - - - +
58A LYS* 4.9 4.5 - - - +
59A GLN* 3.0 29.5 + - - +
62A ARG* 2.9 45.2 + - - -
142A THR* 3.1 14.4 + - + +
143A ASN 3.1 4.2 + - - +
145A ASN* 1.3 73.9 - - - +
147A GLU* 1.3 62.0 + - - +
149A ALA* 3.4 5.9 + - - +
150A ALA* 2.9 29.5 + - - +
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Residues in contact with GLU 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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26A GLU* 3.1 4.7 - - - +
52A HIS* 3.1 5.4 + - - -
59A GLN* 2.9 14.3 + - - +
114A GLU* 2.6 20.2 - - - +
117A GLU* 2.7 20.0 - - + +
118A ILE* 3.8 18.6 - - + -
121A TYR* 3.6 12.5 - - + -
143A ASN 3.1 12.5 + - - +
144A LEU* 3.0 7.2 + - - +
146A GLU* 1.3 75.1 - - - +
148A LYS* 1.3 57.9 + - - +
150A ALA 3.3 0.3 + - - -
151A ASN* 2.9 28.9 + - - +
401A FE 2.1 28.9 - - - -
407A ZN 2.0 33.1 - - - -
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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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118A ILE* 4.1 29.2 - - + -
144A LEU* 2.9 45.3 + - - +
145A ASN* 3.8 20.3 + - - +
147A GLU* 1.3 76.1 - - - +
149A ALA* 1.3 62.8 + - - +
151A ASN* 3.3 4.2 + - - +
152A THR* 3.0 28.5 + - - +
414B ACT 4.8 10.5 - - - +
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Residues in contact with ALA 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 ASN 2.9 18.5 + - - +
146A GLU* 3.8 6.5 - - - +
148A LYS* 1.3 78.2 - - - +
150A ALA* 1.3 57.0 + - - +
152A THR* 3.3 7.3 + - - -
153A LYS* 2.9 50.7 + - - +
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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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52A HIS* 3.5 32.8 - - + +
55A GLU* 4.9 1.8 + - - +
114A GLU* 3.6 10.5 - - - +
146A GLU 2.9 17.7 + - - +
149A ALA* 1.3 73.1 - - - +
151A ASN* 1.3 64.9 + - - +
153A LYS* 3.3 10.5 + - - +
154A LEU* 3.0 30.1 + - + +
409A ZN 3.7 7.4 - - - -
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Residues in contact with ASN 151 (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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111A GLN* 3.7 10.7 - - - +
114A GLU* 3.9 13.6 - - + +
115A HIS* 3.6 17.0 + - - -
118A ILE* 4.4 9.2 - - + +
147A GLU 2.9 17.0 + - - +
148A LYS* 3.6 6.0 + - - +
150A ALA* 1.3 75.6 - - - +
152A THR* 1.3 59.6 + - - +
154A LEU* 3.2 6.2 + - - +
155A ASN* 2.9 39.7 + - - -
417A ACT 2.5 45.3 + - - +
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Residues in contact with THR 152 (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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148A LYS 3.0 18.8 + - - -
149A ALA* 3.6 8.2 - - - +
151A ASN* 1.3 78.8 + - - +
153A LYS* 1.3 63.5 + - + +
155A ASN* 3.1 11.5 + - + +
156A THR* 3.1 34.9 + - + +
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Residues in contact with LYS 153 (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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55A GLU* 4.5 15.2 + - - -
149A ALA* 2.9 37.2 + - - +
150A ALA* 3.6 8.2 - - - +
152A THR* 1.3 78.1 - - + +
154A LEU* 1.3 57.9 + - + +
156A THR* 3.3 8.8 + - - -
157A VAL* 2.9 36.6 + - + +
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Residues in contact with LEU 154 (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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45A LEU* 4.3 23.3 - - + -
49A LEU* 4.6 9.2 - - + -
52A HIS* 6.5 0.2 - - + -
107A VAL* 3.7 16.5 - - + +
110A ALA* 3.8 34.3 - - + -
111A GLN* 3.7 31.8 + - + +
114A GLU* 4.0 16.2 - - + +
150A ALA* 3.0 20.3 + - + +
151A ASN* 3.4 6.7 - - - +
153A LYS* 1.3 77.1 - - + +
155A ASN* 1.3 61.4 + - - +
157A VAL* 3.2 24.9 - - + +
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Residues in contact with ASN 155 (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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111A GLN* 2.4 40.1 - - - +
151A ASN* 2.9 27.3 + - - +
152A THR* 3.1 13.8 + - + +
154A LEU* 1.3 75.0 - - - +
156A THR* 1.3 64.2 + - + +
157A VAL 5.2 0.7 - - - +
417A ACT 2.7 21.9 - - - +
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Residues in contact with THR 156 (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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152A THR* 3.1 27.4 + - + +
153A LYS* 3.3 11.3 + - - +
154A LEU 3.1 0.2 - - - -
155A ASN* 1.3 86.4 - - + +
157A VAL* 1.3 65.4 + - - +
158A ALA* 3.0 8.1 + - - +
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Residues in contact with VAL 157 (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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44A ASP* 4.9 23.8 - - + +
45A LEU* 5.1 5.6 - - + +
107A VAL* 4.0 24.0 - - + -
153A LYS* 2.9 27.1 + - + +
154A LEU* 3.2 27.0 - - + +
155A ASN 5.2 1.0 - - - +
156A THR* 1.3 70.4 - - - +
158A ALA* 1.3 60.1 + - - +
159A LEU* 3.1 24.1 + - + +
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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
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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