Contacts of the helix formed by residues 129 - 150 (chain B) in PDB entry 2JB3
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 TYR 129 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ASN 3.4 19.5 - - - +
110B ALA* 3.4 4.0 + - - +
112B THR* 2.8 46.2 + - - -
113B PHE 4.2 5.6 - - - -
114B VAL* 3.4 28.1 - - + +
127B VAL 3.7 0.6 + - - -
128B THR* 1.3 72.0 - - - +
130B ARG* 1.3 57.0 + - - +
132B ALA* 3.3 3.8 + - - +
133B LYS* 2.8 53.8 + - + +
219B ASN* 3.0 33.2 + - + -
220B PHE* 4.0 26.9 - + - -
223B ASP* 5.8 4.0 - - - -
343B ALA 3.6 12.1 + - - -
345B ASN* 3.3 13.0 - - - +
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Residues in contact with ARG 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A PRO* 5.7 2.4 - - - +
87A GLN* 4.5 9.5 + - - +
88A SER* 6.0 2.4 - - - +
224A PHE 4.9 1.4 + - - +
225A GLY 4.6 0.2 - - - -
226A TYR* 3.2 49.0 + - - +
229A ALA* 3.8 22.5 + - + +
110B ALA* 3.1 40.9 + - + +
111B ASN* 2.9 33.9 + - - +
128B THR* 3.2 7.4 - - + +
129B TYR* 1.3 73.8 - - - +
131B ALA* 1.3 60.7 + - - +
133B LYS* 4.0 6.1 - - - +
134B ALA* 3.0 31.5 + - - +
186B ARG* 3.4 23.4 + - - +
187B ARG 3.6 16.2 - - - +
188B GLY* 3.9 9.2 - - - +
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Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL* 3.7 11.7 - - + -
128B THR* 3.2 21.6 + - - +
130B ARG* 1.3 77.5 - - - +
132B ALA* 1.3 63.7 + - - +
134B ALA* 3.8 0.7 - - - +
135B ASP* 3.1 30.0 + - - +
187B ARG* 3.7 44.6 - - - +
203B LYS* 5.2 3.6 - - + -
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Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B VAL* 4.2 7.4 - - + -
127B VAL* 3.8 2.4 - - + +
128B THR 3.0 15.8 + - - +
129B TYR* 3.7 4.3 - - - +
131B ALA* 1.3 77.2 - - - +
133B LYS* 1.3 56.8 + - - +
135B ASP* 3.5 3.8 + - - +
136B THR* 2.9 33.6 + - - -
206B PHE* 6.1 0.7 - - - -
216B ILE* 3.7 38.3 - - + +
220B PHE* 3.6 17.0 - - + -
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Residues in contact with LYS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A PHE* 4.8 15.8 - - + -
108B GLN* 4.0 21.0 - - - +
109B ASN 6.2 0.4 - - - -
110B ALA* 6.4 0.6 - - - +
129B TYR* 2.8 40.3 + - + +
130B ARG* 4.0 5.8 - - - +
132B ALA* 1.3 71.8 - - - +
134B ALA* 1.3 58.0 + - - +
137B PHE* 2.7 61.1 + - + -
220B PHE* 3.6 40.6 - - + -
223B ASP* 2.6 31.4 + - - -
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Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A PHE* 6.5 0.9 - - - -
130B ARG 3.0 18.0 + - - +
131B ALA 3.8 0.7 - - - +
132B ALA 3.4 0.2 - - - -
133B LYS* 1.3 76.5 - - - +
135B ASP* 1.3 57.0 + - - +
137B PHE* 5.2 1.1 - - - -
138B GLY* 2.9 27.4 + - - +
173B GLY 4.7 0.9 - - - +
181B TYR* 3.3 12.9 - - - +
184B SER* 4.6 3.8 - - - -
186B ARG* 4.1 16.6 - - + +
187B ARG* 3.7 32.8 - - + +
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Residues in contact with ASP 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ALA 3.1 9.5 + - - +
132B ALA* 3.9 4.0 - - - +
134B ALA* 1.3 75.6 - - - +
136B THR* 1.3 64.6 + - - +
139B TYR* 3.0 32.5 + - + -
181B TYR* 2.6 37.7 + - + -
187B ARG* 2.7 38.7 + - - -
205B PRO* 3.5 1.4 - - - +
206B PHE* 3.0 32.1 + - + +
211B VAL* 3.7 17.5 - - + -
216B ILE* 6.0 0.4 - - + -
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Residues in contact with THR 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PHE* 3.8 36.1 - - + -
132B ALA 2.9 20.1 + - - -
133B LYS 3.9 0.2 - - - -
135B ASP* 1.3 75.2 - - - +
137B PHE* 1.3 62.9 + - + +
139B TYR* 3.9 1.4 - - - +
140B MET* 2.9 31.1 + - + +
211B VAL* 3.5 22.7 - - + +
216B ILE* 3.5 12.5 - - - +
217B GLY* 4.4 2.8 - - - -
220B PHE* 3.6 19.2 - - + -
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Residues in contact with PHE 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A PHE* 6.3 0.2 - + - -
168A PHE* 4.6 0.9 - + - -
172A PHE* 3.5 35.9 - + - -
224A PHE* 3.6 33.9 - + + -
133B LYS* 2.7 48.5 + - + +
134B ALA* 4.6 1.3 - - - +
136B THR* 1.3 75.7 - - + +
138B GLY* 1.3 56.2 + - - +
140B MET* 3.5 21.9 - - + +
141B SER* 2.7 37.7 + - - -
172B PHE* 3.6 26.5 - + + +
173B GLY* 4.2 2.5 - - - -
220B PHE* 3.7 28.3 - + + -
224B PHE* 5.9 1.1 - + - -
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Residues in contact with GLY 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ALA 2.9 22.2 + - - -
137B PHE* 1.3 77.9 - - - +
139B TYR* 1.3 57.2 + - - +
142B GLU* 3.0 23.7 + - - +
173B GLY* 3.5 12.0 - - - -
175B LEU* 3.5 9.9 - - - +
181B TYR* 3.4 26.5 - - - -
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Residues in contact with TYR 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ASP* 3.0 29.3 + - + +
136B THR* 4.1 2.5 - - - +
138B GLY* 1.3 72.2 - - - +
140B MET* 1.3 65.7 + - - +
142B GLU* 3.2 9.3 + - - +
143B LEU* 2.9 36.8 + - + +
180B ARG* 6.2 1.1 - - - -
181B TYR* 3.6 38.4 + + - -
205B PRO* 4.6 4.7 - - - +
206B PHE 2.8 29.2 + - - -
207B ALA* 3.6 4.9 - - - -
208B MET* 3.3 63.8 + - + +
211B VAL* 3.9 13.9 - - + -
212B ILE* 6.1 4.7 - - + -
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Residues in contact with MET 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A MET* 3.2 37.2 - - + +
141A SER* 5.3 0.7 - - - -
144A LEU* 3.6 26.9 - - + +
165A LEU* 5.5 4.7 - - + -
168A PHE* 4.1 25.6 - - + -
169A LEU* 4.2 11.0 - - + -
172A PHE* 4.3 13.2 - - + -
136B THR* 2.9 19.3 + - + +
137B PHE* 3.5 30.5 - - + +
139B TYR* 1.3 75.4 - - - +
141B SER* 1.3 56.5 + - - +
143B LEU* 3.4 4.4 + - - -
144B LEU* 3.0 28.6 + - - +
172B PHE* 3.6 11.2 - - + -
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Residues in contact with SER 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A MET* 3.9 5.4 - - - +
137B PHE 2.7 21.3 + - - -
138B GLY 3.7 3.4 - - - -
140B MET* 1.3 74.5 - - - +
142B GLU* 1.3 58.5 + - - +
144B LEU* 3.4 1.0 + - - +
145B LYS* 2.8 32.7 + - - +
169B LEU* 3.3 38.1 + - - +
172B PHE* 3.6 15.4 - - - -
173B GLY* 3.5 16.8 + - - -
175B LEU* 4.1 5.3 - - - +
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Residues in contact with GLU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B GLY 3.0 14.7 + - - +
139B TYR* 3.2 14.0 + - - +
141B SER* 1.3 75.3 - - - +
143B LEU* 1.3 62.6 + - - +
145B LYS* 3.4 2.0 + - - +
146B LYS* 2.9 37.6 + - + +
175B LEU* 4.0 5.3 - - + +
179B GLY 3.5 23.7 - - - +
180B ARG* 3.6 18.6 + - + +
181B TYR* 2.8 37.6 + - - +
208B MET* 3.3 30.0 - - - +
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Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LEU* 4.0 7.0 - - + -
153A LEU* 3.7 22.7 - - + +
156A VAL* 3.8 28.3 - - + -
157A LEU* 4.3 16.4 - - + -
165A LEU* 4.2 26.7 - - + -
139B TYR* 2.9 28.3 + - + +
140B MET* 3.8 7.4 - - - +
142B GLU* 1.3 78.1 - - + +
144B LEU* 1.3 64.0 + - - +
146B LYS* 3.3 8.9 + - + +
147B ALA* 3.0 24.4 + - - +
208B MET* 5.2 15.0 - - + -
212B ILE* 4.8 8.3 - - + -
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Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A MET* 3.6 44.6 - - + +
143A LEU* 4.2 3.1 - - + -
144A LEU* 3.8 33.3 - - + +
147A ALA* 5.3 0.2 - - + -
140B MET 3.0 16.5 + - - +
141B SER 4.0 0.7 - - - +
143B LEU* 1.3 76.0 - - - +
145B LYS* 1.3 54.6 + - - +
147B ALA* 3.4 4.2 + - + +
148B THR* 2.7 39.9 + - - +
153B LEU* 3.8 27.4 - - + -
165B LEU* 4.3 11.2 - - + -
169B LEU* 3.8 22.9 - - + -
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Residues in contact with LYS 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B SER 2.8 20.0 + - - +
142B GLU* 3.7 4.5 - - - +
144B LEU* 1.3 77.4 - - - +
146B LYS* 1.3 55.3 + - - +
148B THR* 3.3 4.1 + - - -
149B ASP* 2.8 60.4 + - - +
166B SER* 4.3 28.9 + - - +
169B LEU* 3.7 13.8 - - + +
170B SER* 3.7 17.7 - - - +
175B LEU* 3.7 23.1 - - + -
177B ASP 5.8 2.0 + - - -
178B ASP 5.4 1.6 + - - -
179B GLY* 4.1 21.4 - - - +
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Residues in contact with LYS 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ALA 5.5 0.7 - - - +
153A LEU* 4.2 16.8 - - + -
155A GLN* 6.3 0.6 - - - +
156A VAL* 4.4 27.1 - - + +
142B GLU* 2.9 27.9 + - + +
143B LEU* 3.3 8.9 + - + +
145B LYS* 1.3 74.8 - - - +
147B ALA* 1.3 57.4 + - - +
149B ASP* 3.1 8.4 + - - +
150B GLN* 2.8 63.1 + - + +
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Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ALA* 3.6 31.4 - - + -
152A ALA* 4.4 1.8 - - + -
153A LEU* 4.3 9.8 - - + +
143B LEU 3.0 17.1 + - - +
144B LEU* 3.7 8.5 - - + +
146B LYS* 1.3 76.8 - - - +
148B THR* 1.3 63.2 + - - +
150B GLN* 3.4 11.5 + - - +
151B GLY 3.3 4.0 + - - -
152B ALA* 3.1 34.1 + - + +
153B LEU* 5.0 2.2 - - + -
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Residues in contact with THR 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU* 2.7 23.7 + - - +
145B LYS* 3.4 8.4 - - - -
147B ALA* 1.3 76.2 - - - +
149B ASP* 1.3 63.9 + - - +
151B GLY* 3.1 12.5 + - - -
153B LEU* 3.9 17.5 + - + +
154B ASP* 4.4 0.3 - - - +
157B LEU* 5.0 2.2 - - + -
162B LYS* 3.6 51.7 - - + +
165B LEU* 3.7 23.0 - - + +
166B SER* 4.1 15.5 - - - +
169B LEU* 5.4 0.4 - - - -
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Residues in contact with ASP 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LYS* 2.8 53.8 + - - +
146B LYS* 3.6 5.9 - - - +
148B THR* 1.3 75.4 - - - +
150B GLN* 1.3 61.8 + - + +
151B GLY* 3.2 1.5 + - - -
162B LYS* 5.3 4.2 + - - +
166B SER* 4.1 11.1 + - - -
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Residues in contact with GLN 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ALA* 3.4 25.7 + - - +
146B LYS* 2.8 55.1 + - + +
147B ALA* 3.8 11.0 - - - +
148B THR 3.3 0.4 - - - -
149B ASP* 1.3 76.7 - - + +
151B GLY* 1.3 59.7 + - - +
152B ALA* 3.6 3.2 + - + +
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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