Contacts of the helix formed by residues 131 - 155 (chain B) in PDB entry 1EQR
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 ARG 131 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 6.4 0.4 - - - -
121B ARG* 3.6 25.1 - - - +
127B LEU 5.0 1.8 - - - +
128B ASP* 3.1 39.3 + - - +
130B ARG* 1.3 77.3 - - - +
132B PRO* 1.3 65.2 - - + +
133B GLU* 2.5 40.8 + - + +
134B MET* 2.7 39.5 + - + +
135B ALA 2.8 11.6 + - - -
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Residues in contact with PRO 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ASN* 4.7 7.9 - - - +
39B ARG* 3.9 23.1 - - + -
43B GLY* 5.3 9.0 - - - -
44B ILE* 4.0 24.2 - - + -
130B ARG 3.0 5.4 - - - +
131B ARG* 1.3 83.8 - - + +
133B GLU* 1.3 62.4 + - - +
135B ALA* 3.9 6.9 - - + +
136B GLN* 3.0 26.9 + - - +
139B LYS* 5.7 0.3 - - - -
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Residues in contact with GLU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ARG* 2.5 37.8 + - + +
132B PRO* 1.3 79.6 - - - +
134B MET* 1.3 60.4 + - - +
136B GLN* 3.9 4.6 + - - +
137B ARG* 3.2 53.1 + - - +
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Residues in contact with MET 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A PHE* 5.0 0.9 - - - -
121B ARG* 3.8 18.8 - - - -
125B ARG* 4.0 25.4 - - - +
128B ASP* 3.1 36.8 - - - +
129B LEU* 3.9 16.6 - - + -
131B ARG* 2.7 33.6 + - + +
133B GLU* 1.3 76.9 - - - +
135B ALA* 1.3 67.2 + - - +
136B GLN 3.3 0.3 + - - -
137B ARG* 3.3 36.0 + - - +
138B LEU* 3.6 12.6 + - - +
550B ASP* 4.0 24.0 - - - +
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A SER 5.6 1.1 - - - +
205A GLY 6.3 1.1 - - - -
206A PHE* 3.7 25.0 - - + +
41B ARG* 4.8 17.9 - - - +
129B LEU 3.7 9.7 + - - +
130B ARG 4.8 2.7 - - - +
131B ARG 2.8 17.1 + - - +
132B PRO* 3.9 9.0 - - + +
134B MET* 1.3 72.7 - - - +
136B GLN* 1.3 63.4 + - - +
138B LEU* 3.0 8.5 + - - +
139B LYS* 2.9 24.7 + - + +
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Residues in contact with GLN 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLU 5.2 0.2 - - - +
132B PRO 3.0 19.0 + - - +
133B GLU* 4.0 6.1 - - - +
135B ALA* 1.3 76.6 - - - +
137B ARG* 1.3 57.7 + - + +
139B LYS* 2.9 40.6 + - - +
140B THR* 2.9 44.3 + - - +
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Residues in contact with ARG 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLU* 3.2 52.6 + - - +
134B MET* 3.3 33.7 + - - +
135B ALA 3.2 1.2 + - - -
136B GLN* 1.3 76.9 - - + +
138B LEU* 1.3 59.0 + - - +
140B THR* 3.5 2.6 + - - -
141B ARG* 3.1 25.6 + - - +
539B THR* 4.2 7.1 - - - +
543B THR* 3.8 28.7 + - + +
544B GLY 5.6 0.8 + - - -
545B THR* 2.5 32.5 + - - +
550B ASP* 3.6 41.7 + - - +
551B VAL* 4.6 3.8 - - + -
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU* 5.6 0.7 - - - +
159A ASP 5.3 0.3 - - - +
160A ILE* 4.8 18.3 - - + +
206A PHE* 3.6 22.4 - - + -
129B LEU* 3.3 34.8 - - + -
134B MET 3.6 3.3 + - - +
135B ALA 3.0 8.8 + - - +
137B ARG* 1.3 78.9 - - - +
139B LYS* 1.3 62.8 + - - +
141B ARG* 3.8 10.9 - - - +
142B ALA* 3.4 19.6 + - - +
550B ASP 4.2 5.6 - - - +
551B VAL* 3.4 35.2 - - - +
552B ILE 4.1 0.9 - - - -
553B ALA* 3.7 27.8 - - + +
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Residues in contact with LYS 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU* 4.4 24.2 - - + +
206A PHE* 4.6 6.3 - - + -
41B ARG* 2.6 42.1 + - + +
42B GLU* 3.4 34.8 + - - +
43B GLY* 5.1 0.2 - - - -
135B ALA* 2.9 15.0 + - + +
136B GLN* 2.9 51.2 + - - +
138B LEU* 1.3 75.1 - - - +
140B THR* 1.3 64.6 + - - +
142B ALA* 3.3 8.9 + - - +
143B LYS* 3.2 19.1 + - - +
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Residues in contact with THR 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B GLN* 2.9 28.2 + - - +
137B ARG 3.8 2.7 - - - -
139B LYS* 1.3 76.1 - - - +
141B ARG* 1.3 58.9 + - - +
143B LYS* 3.0 11.4 + - + +
144B ILE* 2.8 44.4 + - + +
259B VAL* 4.4 18.0 - - + +
542B LEU 4.5 1.8 - - - +
543B THR* 3.4 28.8 - - + +
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Residues in contact with ARG 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ASP 5.3 3.1 - - - +
160A ILE* 6.5 1.1 - - - +
161A GLU* 2.6 43.6 + - - +
137B ARG 3.1 18.2 + - - +
138B LEU* 3.9 13.2 - - - +
140B THR* 1.3 75.7 - - - +
142B ALA* 1.3 56.7 + - - +
144B ILE* 3.1 7.6 + - - +
145B THR* 2.9 36.4 + - + +
230B THR* 4.3 2.4 + - - -
535B LEU* 3.2 24.1 - - + +
536B ASP* 2.4 47.7 + - - +
539B THR* 3.6 25.2 + - + +
551B VAL* 2.8 27.7 + - - +
552B ILE* 4.0 7.0 - - - +
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Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU* 4.3 18.2 - - + -
159A ASP* 3.8 35.0 + - - +
160A ILE* 5.5 0.2 - - + -
138B LEU 3.4 10.4 + - - +
139B LYS 3.3 11.8 + - - +
140B THR 3.1 0.2 - - - -
141B ARG* 1.3 81.5 - - - +
143B LYS* 1.3 56.5 + - - +
145B THR* 3.3 9.3 + - - -
146B SER* 3.0 27.9 + - - -
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Residues in contact with LYS 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LYS 3.2 11.2 + - - +
140B THR* 3.0 13.5 + - - +
142B ALA* 1.3 73.9 - - - +
144B ILE* 1.3 60.6 + - - +
146B SER* 3.6 6.2 - - - -
147B LEU* 2.9 49.1 + - + +
258B GLU* 3.3 29.9 + - - +
259B VAL* 3.6 28.7 - - + +
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Residues in contact with ILE 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B THR* 2.8 29.9 + - + +
141B ARG* 3.4 9.4 - - - +
143B LYS* 1.3 74.9 - - - +
145B THR* 1.3 66.0 + - - +
147B LEU* 3.3 8.5 + - - +
148B VAL* 3.0 28.3 + - + +
232B ILE* 5.8 0.2 - - + -
255B LEU* 4.3 16.4 - - + -
259B VAL* 4.3 10.5 - - + -
535B LEU* 4.1 20.9 - - + -
538B LEU* 4.6 3.4 - - + +
539B THR* 4.1 19.5 - - - +
542B LEU* 3.2 45.3 - - + -
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Residues in contact with THR 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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159A ASP* 4.3 15.2 + - - +
161A GLU* 4.9 3.6 - - - +
141B ARG* 2.9 22.1 + - + +
142B ALA* 3.3 13.2 + - - -
144B ILE* 1.3 76.2 - - - +
146B SER* 1.3 65.0 + - - +
148B VAL* 3.7 7.6 - - + +
149B ARG* 3.1 50.8 + - - +
212B ILE* 4.6 7.4 - - + -
535B LEU* 3.5 35.9 - - + -
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Residues in contact with SER 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ASP* 2.4 32.5 + - - -
142B ALA 3.0 19.8 + - - -
143B LYS* 3.6 9.4 - - - -
144B ILE 3.1 0.2 - - - -
145B THR* 1.3 80.3 + - - +
147B LEU* 1.3 61.7 + - - +
149B ARG* 3.6 6.8 + - - +
150B ARG* 3.2 36.6 + - - +
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Residues in contact with LEU 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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143B LYS* 2.9 38.2 + - + +
144B ILE* 3.6 4.3 - - - +
146B SER* 1.3 76.5 - - - +
148B VAL* 1.3 65.4 + - - +
150B ARG* 4.0 7.9 - - + +
151B PHE* 3.0 25.3 + - - +
254B HIS* 3.8 22.1 + - + +
255B LEU* 3.8 19.3 - - + +
258B GLU* 3.6 26.7 - - + +
259B VAL* 3.6 30.5 - - + -
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Residues in contact with VAL 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ILE* 3.0 25.9 + - + +
145B THR* 3.7 8.1 - - - +
147B LEU* 1.3 75.0 - - - +
149B ARG* 1.3 54.5 + - - +
151B PHE* 3.1 2.8 + - - +
152B MET* 2.7 54.6 + - + +
210B TYR* 4.8 1.6 - - + -
212B ILE* 3.8 23.1 - - + -
232B ILE* 4.0 31.4 - - + -
251B LEU* 4.2 15.3 - - + -
255B LEU* 4.0 20.4 - - + -
535B LEU* 5.8 0.4 - - + -
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Residues in contact with ARG 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ARG* 2.9 66.1 - - + +
159A ASP* 4.0 7.8 + - - -
145B THR* 3.1 38.4 + - - +
146B SER* 3.8 6.7 - - - +
148B VAL* 1.3 79.5 - - - +
150B ARG* 1.3 58.1 + - + +
152B MET 3.2 0.5 + - - -
153B ASP* 2.8 40.7 + - - +
159B ASP* 4.2 6.6 + - - -
210B TYR* 3.5 23.1 + - + +
212B ILE* 3.1 50.4 + - + +
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Residues in contact with ARG 150 (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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150A ARG* 3.7 43.1 - - + +
153A ASP* 5.1 5.7 + - - +
154A ASP* 5.0 9.3 + - - -
146B SER* 3.2 27.3 + - - +
147B LEU* 4.1 8.7 - - + +
149B ARG* 1.3 78.7 - - + +
151B PHE* 1.3 62.0 + - - +
153B ASP* 4.0 5.5 - - - +
154B ASP* 3.0 36.5 + - - +
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Residues in contact with PHE 151 (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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147B LEU 3.0 20.0 + - - +
148B VAL 3.5 2.5 - - - +
150B ARG* 1.3 79.7 - - - +
152B MET* 1.3 75.7 + - - +
154B ASP* 3.3 4.1 + - - +
155B HIS* 3.0 66.4 + + + -
247B VAL* 3.9 15.0 - - + -
250B ALA* 3.8 21.3 - - + -
251B LEU* 3.4 43.5 - - + -
254B HIS* 4.0 29.4 + + + +
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Residues in contact with MET 152 (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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148B VAL* 2.7 38.9 + - + +
151B PHE* 1.3 92.5 - - - +
153B ASP* 1.3 66.9 + - - +
155B HIS 3.2 7.6 + - - -
156B GLY 3.3 0.2 + - - -
157B PHE* 2.9 76.1 + - + -
210B TYR* 3.6 37.7 - - + -
232B ILE* 5.4 2.7 - - + -
234B VAL* 4.2 7.4 - - + -
248B MET* 3.9 17.3 - - + +
251B LEU* 4.3 9.0 - - - -
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Residues in contact with ASP 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A SER* 3.6 29.4 + - - +
149B ARG* 2.8 26.5 + - - +
150B ARG* 4.1 6.0 - - - +
152B MET* 1.3 72.0 - - - +
154B ASP* 1.3 63.8 + - - +
156B GLY* 3.3 12.6 + - - -
157B PHE 3.8 9.3 + - - +
159B ASP* 5.0 2.3 - - - +
210B TYR* 2.4 35.8 + - - -
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Residues in contact with ASP 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B ARG* 3.0 31.4 + - - +
151B PHE* 3.7 6.1 - - - +
152B MET 3.2 0.2 - - - -
153B ASP* 1.3 75.7 - - - +
155B HIS* 1.3 64.9 + - + +
156B GLY 3.1 8.6 + - - -
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Residues in contact with HIS 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B PHE* 3.0 62.1 + + + +
152B MET 3.2 1.3 + - - +
154B ASP* 1.3 81.9 - - + +
156B GLY* 1.3 56.0 + - - +
157B PHE* 3.3 21.8 - - + -
208B ARG* 2.7 35.1 + - - +
247B VAL* 4.4 11.7 - - + -
250B ALA* 5.2 3.8 - - + +
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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