Contacts of the helix formed by residues 120 - 148 (chain B) in PDB entry 3VPM
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 LYS 120 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B SER 3.9 1.7 + - - +
119B LEU* 1.3 74.4 - - - +
121B PRO* 1.4 75.4 - - + +
122B GLU* 3.2 25.1 + - + +
123B GLU* 3.0 42.6 + - + +
124B ARG* 3.2 11.2 + - - +
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Residues in contact with PRO 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU 4.2 1.1 - - - +
120B LYS* 1.4 86.5 - - + +
122B GLU* 1.3 64.2 + - - +
124B ARG* 3.5 29.5 + - - +
125B TYR* 3.2 23.2 + - - +
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Residues in contact with GLU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LYS* 3.5 34.6 + - + +
121B PRO* 1.3 85.6 - - - +
123B GLU* 1.3 61.8 + - + +
125B TYR* 3.4 11.7 + - + +
126B PHE* 3.1 25.6 + - - +
312B LEU* 4.1 36.8 - - + +
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Residues in contact with GLU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU* 3.8 20.6 - - + +
120B LYS* 3.0 48.6 + - + +
122B GLU* 1.3 74.7 - - + +
124B ARG* 1.3 57.9 + - - +
125B TYR 3.0 4.8 + - - -
126B PHE* 3.1 2.9 + - - +
127B ILE* 2.9 35.9 + - + +
246B LEU* 5.9 1.1 - - + -
249B ARG* 2.7 44.9 + - - -
251B LEU* 5.8 0.2 - - - -
312B LEU 3.4 16.2 - - - +
313B ILE* 4.0 18.8 - - + -
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Residues in contact with ARG 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B TRP* 3.1 87.2 + - + +
117B GLU* 3.5 13.0 + - - +
119B LEU* 2.6 34.2 + - + +
120B LYS 3.2 3.2 + - - +
121B PRO* 3.5 40.5 - - - +
122B GLU 3.4 0.2 - - - -
123B GLU* 1.3 77.5 - - - +
125B TYR* 1.3 59.4 + - - +
127B ILE 4.1 0.7 - - - -
128B SER* 3.1 17.8 + - - -
184B ILE* 5.4 0.3 - - - +
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Residues in contact with TYR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B PRO 3.2 14.1 + - - +
122B GLU* 3.4 13.0 - - + +
123B GLU 3.0 0.6 - - - -
124B ARG* 1.3 76.2 - - - +
126B PHE* 1.3 67.2 + - - +
128B SER* 2.8 20.2 + - - -
129B HIS* 3.0 54.4 + + - +
308B LEU* 3.9 17.3 - - + +
312B LEU* 4.2 19.5 - - + -
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Residues in contact with PHE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B GLU 3.1 14.4 + - - +
123B GLU 3.5 7.0 - - - +
125B TYR* 1.3 77.3 - - - +
127B ILE* 1.3 67.6 + - + +
129B HIS* 3.0 5.2 + - - +
130B VAL* 2.9 44.0 + - + +
242B SER* 3.5 36.6 - - - -
243B ILE* 5.8 1.3 - - + -
246B LEU* 6.3 0.2 - - + -
303B PHE* 6.3 0.4 - + - -
304B LEU* 5.4 4.3 - - + -
308B LEU* 3.6 45.0 - - + +
309B PRO 3.8 18.4 - - - -
310B VAL* 4.0 15.7 - - + -
312B LEU* 4.2 8.7 - - + -
313B ILE* 3.7 30.1 - - + -
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B TRP* 3.6 20.6 - - + -
119B LEU* 3.8 25.6 - - + -
123B GLU* 2.9 22.9 + - + +
126B PHE* 1.3 88.7 - - + +
128B SER* 1.3 63.6 + - - +
130B VAL* 3.2 6.5 + - - +
131B LEU* 3.0 36.5 + - + +
183B TYR* 4.9 1.8 - - + -
243B ILE* 5.4 3.8 - - + -
246B LEU* 3.4 40.2 - - + -
252B MET* 3.9 4.9 - - + -
255B LEU* 4.2 18.2 - - + -
313B ILE* 4.9 0.9 - - + -
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Residues in contact with SER 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B TRP* 4.3 3.8 - - - -
124B ARG 3.1 16.2 + - - -
125B TYR* 2.8 22.2 + - - -
127B ILE* 1.3 80.1 - - - +
129B HIS* 1.3 66.2 + - - +
131B LEU* 3.6 9.9 + - - +
132B ALA 3.1 20.4 + - - -
180B ILE* 4.9 1.0 - - - +
184B ILE* 4.3 15.7 - - - -
189B GLU* 5.1 3.3 + - - -
193B LEU* 3.5 31.3 - - - +
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Residues in contact with HIS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B TYR* 3.0 64.9 + + - +
126B PHE 3.4 4.7 - - - +
128B SER* 1.3 87.2 + - - +
130B VAL* 1.3 59.6 + - - +
132B ALA* 4.4 0.2 - - - -
133B PHE* 3.0 25.5 + - - +
189B GLU* 5.1 4.0 - - - -
192B PHE* 3.9 26.3 - + - -
193B LEU* 4.1 5.1 - - + +
200B MET* 3.4 39.1 - - + +
202B CYS* 4.1 8.3 - - - -
303B PHE* 5.6 0.2 - - - -
308B LEU* 3.7 25.1 - - + +
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B PHE* 2.9 45.9 + - + +
127B ILE* 3.2 7.6 + - - +
129B HIS* 1.3 74.5 - - - +
131B LEU* 1.3 62.1 + - + +
133B PHE* 3.0 7.5 + - - +
134B PHE* 2.8 56.0 + - + +
239B SER* 3.8 24.2 - - - +
243B ILE* 4.0 19.3 - - + -
303B PHE* 5.2 2.9 - - + -
304B LEU* 6.4 0.2 - - + -
308B LEU* 4.0 11.7 - - + -
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B TRP* 6.1 0.2 - - + -
127B ILE* 3.0 26.7 + - + +
128B SER* 3.8 8.5 - - - +
130B VAL* 1.3 84.2 - - + +
132B ALA* 1.3 62.6 - - - +
134B PHE* 3.2 4.6 + - + +
135B ALA* 2.9 25.5 + - - +
176B TYR* 3.9 26.6 - - + +
179B LEU* 3.8 26.2 - - + -
180B ILE* 3.8 27.4 - - + +
183B TYR* 4.1 19.7 - - + -
243B ILE* 5.4 1.3 - - + -
255B LEU* 3.8 25.8 - - + -
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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
----------------------------------------------------------
128B SER 3.1 15.7 + - - +
129B HIS 3.8 4.3 - - - +
131B LEU* 1.3 77.8 - - - +
133B PHE* 1.3 63.0 + - - +
135B ALA* 3.4 3.2 + - - +
136B ALA* 3.0 24.9 + - - +
180B ILE* 3.8 8.9 - - - +
193B LEU* 3.3 34.8 - - + +
196B ALA* 3.9 4.2 - - + +
200B MET* 3.8 20.6 - - - -
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Residues in contact with PHE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B HIS 3.0 16.5 + - - +
130B VAL* 3.0 9.8 + - - +
132B ALA* 1.3 76.0 - - - +
134B PHE* 1.3 81.2 + + - +
136B ALA* 3.3 3.9 + - - +
137B SER* 2.6 58.6 + - - -
200B MET* 4.5 0.6 - - - +
203B VAL* 3.8 33.7 - - + -
206B LYS* 3.3 45.5 - - + -
235B PHE* 3.4 20.9 - + + -
236B PHE* 3.7 9.4 - + - -
239B SER* 3.7 18.8 - - - -
303B PHE* 4.2 13.0 - + + -
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Residues in contact with PHE 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B VAL* 2.8 37.6 + - + -
131B LEU* 3.6 5.8 - - + +
133B PHE* 1.3 88.0 - + - +
135B ALA* 1.3 65.6 + - - +
137B SER* 3.8 2.0 - - - -
138B ASP* 3.0 28.5 + - - +
176B TYR* 3.2 48.5 - + + -
236B PHE* 3.6 38.6 - + + -
239B SER* 3.2 23.1 - - - -
240B PHE* 3.7 28.5 - + - -
243B ILE* 4.9 3.4 - - + -
259B ASN* 4.6 4.9 - - - -
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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
----------------------------------------------------------
80A PHE 5.0 2.8 - - - +
81A VAL* 5.9 1.2 - - - -
82A ILE* 5.9 1.1 - - + -
131B LEU 2.9 16.7 + - - +
132B ALA* 3.8 7.2 - - - +
134B PHE* 1.3 76.8 - - - +
136B ALA* 1.3 62.2 + - - +
139B GLY* 3.7 6.6 + - - -
173B SER* 3.4 22.8 + - - +
176B TYR* 3.9 21.8 - - + -
177B SER* 4.4 13.9 - - - +
180B ILE* 4.8 5.8 - - + -
193B LEU 6.0 0.4 - - - +
194B PHE* 5.8 5.8 - - + -
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PHE 5.3 0.4 - - - +
81A VAL* 6.0 5.2 - - + -
132B ALA 3.0 16.8 + - - +
133B PHE* 3.7 5.6 - - + +
135B ALA* 1.3 77.6 - - - +
137B SER* 1.3 61.9 + - - +
139B GLY* 3.2 12.3 + - - -
140B ILE* 3.4 14.4 + - + +
194B PHE 5.4 5.4 - - - +
196B ALA* 4.4 14.1 - - + +
197B ILE* 3.8 33.0 - - + +
203B VAL* 5.4 3.8 - - + -
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Residues in contact with SER 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B PHE* 2.6 47.1 + - - -
134B PHE 3.8 1.1 - - - -
136B ALA* 1.3 72.8 - - - +
138B ASP* 1.3 61.4 + - - +
140B ILE* 2.8 17.8 + - - +
141B VAL* 2.8 32.4 + - - +
231B VAL* 5.3 5.2 - - - -
236B PHE* 3.5 26.0 - - - -
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Residues in contact with ASP 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B PHE* 3.0 17.5 + - - +
135B ALA 3.8 0.4 - - - +
137B SER* 1.3 76.1 - - - +
139B GLY* 1.3 52.5 + - - +
141B VAL* 3.2 7.8 + - - +
142B ASN* 2.7 36.5 + - - +
169B GLU* 3.4 27.4 - - + +
172B HIS* 3.1 29.8 + - - +
173B SER* 3.1 25.3 + - - +
176B TYR* 3.7 13.0 - - - -
236B PHE* 4.0 17.2 - - - -
262B ILE* 5.9 0.3 - - - +
266B GLU* 5.1 0.7 - - - +
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Residues in contact with GLY 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PHE* 3.4 41.3 - - - +
135B ALA 3.7 3.4 + - - -
136B ALA 3.2 9.1 + - - -
137B SER 3.1 0.8 - - - -
138B ASP* 1.3 79.0 - - - +
140B ILE* 1.3 58.7 - - - +
142B ASN* 3.4 6.6 - - - +
143B GLU* 2.9 24.6 + - - +
173B SER* 4.2 2.6 + - - -
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Residues in contact with ILE 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ALA 3.4 14.5 + - - +
137B SER* 2.8 15.3 + - - +
139B GLY* 1.3 74.5 - - - +
141B VAL* 1.3 66.6 + - + +
143B GLU* 3.2 9.5 + - - +
144B ASN* 3.2 17.7 + - - +
197B ILE* 4.1 15.7 - - + -
207B ALA* 3.7 39.5 - - + +
210B ALA* 3.6 27.1 - - + -
211B LEU* 4.2 20.0 - - + +
214B ILE* 3.6 19.0 - - + +
228B PHE* 4.2 4.0 - - + -
231B VAL* 6.2 0.4 - - + -
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Residues in contact with VAL 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B SER 2.8 24.0 + - - +
138B ASP* 3.5 10.1 - - - +
140B ILE* 1.3 69.8 - - + +
142B ASN* 1.3 64.6 + - - +
144B ASN* 3.1 5.7 + - - +
145B LEU* 3.0 30.8 + - + +
165B GLN* 4.0 6.3 - - - +
169B GLU* 3.7 15.3 - - - +
228B PHE* 4.2 15.5 - - + -
231B VAL* 3.9 26.9 - - + -
232B GLU* 3.7 37.7 - - + +
236B PHE* 4.5 6.1 - - + -
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Residues in contact with ASN 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PHE* 3.7 16.5 - - + -
159A ARG* 5.3 0.2 + - - -
138B ASP 2.7 20.5 + - - +
139B GLY* 3.4 9.6 - - - +
141B VAL* 1.3 72.6 - - - +
143B GLU* 1.3 63.1 + - - +
145B LEU* 3.1 10.0 + - - +
146B VAL* 2.9 36.2 + - - +
166B ILE* 3.4 30.1 + - - +
169B GLU* 3.8 11.0 - - + +
170B ASN* 3.0 28.8 + - - +
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Residues in contact with GLU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 4.9 4.4 + - - -
80A PHE* 3.3 41.4 - - + -
139B GLY 2.9 17.7 + - - +
140B ILE* 3.2 11.1 + - - +
142B ASN* 1.3 71.8 + - - +
144B ASN* 1.3 56.8 + - - +
146B VAL* 3.9 1.0 - - - +
147B GLU* 2.9 54.4 + - - +
211B LEU* 3.7 21.9 - - - +
214B ILE* 3.6 22.8 - - + +
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Residues in contact with ASN 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ILE 3.2 3.9 + - - +
141B VAL* 3.1 9.6 + - - +
143B GLU* 1.3 75.7 - - - +
145B LEU* 1.3 62.2 + - - +
148B ARG* 2.9 43.0 + - - +
149B PHE* 3.1 52.6 + - - -
213B TRP 4.7 1.0 - - - +
214B ILE* 3.6 16.6 - - + +
224B ARG* 5.3 1.0 + - - +
228B PHE* 3.4 43.2 - - + -
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Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B VAL* 3.0 19.8 + - + +
142B ASN* 3.6 3.8 - - - +
144B ASN* 1.3 79.1 - - - +
146B VAL* 1.3 54.8 + - - +
149B PHE* 3.8 17.9 + - + -
150B SER* 2.8 39.6 + - - +
162B TYR* 3.6 34.3 - - + +
165B GLN* 3.5 41.5 - - + +
166B ILE* 3.5 27.1 - - + -
169B GLU* 4.0 15.5 - - + -
232B GLU* 5.9 0.4 - - - +
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PHE* 4.9 0.9 - - + -
150A SER* 4.5 9.9 - - - +
151A GLN* 3.2 36.2 + - - +
159A ARG* 4.1 24.2 - - - +
142B ASN* 2.9 35.2 + - - +
143B GLU* 4.1 3.6 - - - +
145B LEU* 1.3 79.5 - - - +
147B GLU* 1.3 63.3 + - + +
150B SER* 3.6 4.7 + - - -
151B GLN* 3.4 13.5 + - - +
166B ILE* 3.7 27.4 - - + -
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Residues in contact with GLU 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 3.2 35.2 + - - -
80A PHE* 4.0 3.7 - - - -
151A GLN* 3.9 16.2 - - - +
159A ARG* 4.9 1.9 + - - +
143B GLU* 2.9 44.7 + - - +
144B ASN* 5.2 0.2 - - - -
146B VAL* 1.3 80.8 - - + +
148B ARG* 1.3 70.1 + - + +
151B GLN* 3.5 13.8 - - - +
214B ILE* 4.1 8.1 - - + +
----------------------------------------------------------
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Residues in contact with ARG 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ASN* 2.9 28.7 + - - +
146B VAL 3.5 1.0 - - - -
147B GLU* 1.3 91.8 - - + +
149B PHE* 1.3 67.8 + - + +
150B SER 3.3 1.3 - - - -
151B GLN* 2.9 14.5 + - - +
152B GLU* 2.9 28.0 + - - +
213B TRP 3.5 4.4 + - - -
214B ILE* 3.0 32.6 + - + +
216B ASP 3.0 27.3 + - - -
217B LYS* 5.1 8.9 + - - +
219B ALA 4.7 2.2 + - - -
224B ARG* 3.1 41.1 - - - +
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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
------------------------------------------------------------
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