Contacts of the helix formed by residues 120 - 148 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A SER 5.5 0.7 - - - +
119A LEU* 1.3 74.3 - - - +
121A PRO* 1.3 77.3 - - + +
122A GLU* 3.1 28.7 - - - +
123A GLU* 2.8 48.3 + - + +
124A ARG* 3.3 4.6 + - - -
312A LEU 5.8 0.2 - - - +
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Residues in contact with PRO 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU 4.2 0.9 - - - +
120A LYS* 1.3 85.4 - - + +
122A GLU* 1.3 59.8 + - - +
123A GLU 3.2 0.2 - - - -
124A ARG* 3.3 30.5 + - - +
125A TYR* 3.2 23.6 + - - +
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Residues in contact with GLU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LYS* 3.1 34.6 - - - +
121A PRO* 1.3 79.7 - - - +
123A GLU* 1.3 63.3 + - - +
125A TYR* 3.8 12.4 - - + +
126A PHE* 3.3 21.7 + - - +
312A LEU* 3.5 47.6 - - + +
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Residues in contact with GLU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 3.4 25.3 - - + +
120A LYS* 2.8 55.3 + - + +
122A GLU* 1.3 77.6 - - + +
124A ARG* 1.3 63.6 + - - +
126A PHE* 3.5 2.3 + - - +
127A ILE* 3.1 31.6 + - - +
249A ARG* 2.8 39.0 + - - -
312A LEU 3.3 19.0 - - - +
313A ILE* 4.1 14.1 - - + +
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Residues in contact with ARG 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A TRP* 3.0 80.3 + - + +
117A GLU* 3.5 12.6 + - - +
119A LEU* 2.6 31.7 + - + -
120A LYS 3.3 0.8 + - - -
121A PRO* 3.3 36.5 + - - +
123A GLU* 1.3 75.1 - - - +
125A TYR* 1.3 56.4 + - - +
128A SER* 2.8 37.0 + - - -
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Residues in contact with TYR 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PRO 3.2 13.3 + - - +
122A GLU* 3.8 13.0 - - + +
123A GLU 3.3 0.4 - - - -
124A ARG* 1.3 76.5 - - - +
126A PHE* 1.3 59.4 + - - +
128A SER* 3.1 4.4 + - - -
129A HIS* 2.8 74.5 + + - +
202A CYS* 5.8 1.4 - - - -
307A ALA 5.2 4.9 + - - -
308A LEU* 3.8 23.0 - - + +
309A PRO* 6.3 0.2 - - + -
312A LEU* 4.2 15.5 - - + -
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Residues in contact with PHE 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLU 3.3 15.9 + - - +
123A GLU 3.6 4.5 - - - +
125A TYR* 1.3 81.1 - - - +
127A ILE* 1.3 65.1 + - + +
129A HIS* 3.3 3.1 + - - +
130A VAL* 2.8 42.7 + - + +
242A SER* 3.2 33.0 - - - -
243A ILE* 5.9 1.6 - - + -
246A LEU* 6.3 0.4 - - + -
303A PHE* 6.3 0.9 - + - -
304A LEU* 5.7 2.2 - - + -
308A LEU* 3.6 50.0 - - + +
309A PRO 3.8 11.2 - - - -
310A VAL* 3.9 19.7 - - + -
312A LEU* 4.2 5.8 - - + -
313A ILE* 3.5 37.9 - - + -
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Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A TRP* 4.0 19.3 - - + -
119A LEU* 3.7 25.4 - - + -
123A GLU 3.1 18.2 + - - +
124A ARG 4.1 0.2 - - - +
125A TYR 3.3 0.2 - - - -
126A PHE* 1.3 85.0 - - + +
128A SER* 1.3 60.8 + - - +
130A VAL* 2.9 7.8 + - - +
131A LEU* 2.8 41.0 + - + +
243A ILE* 5.1 6.1 - - + -
246A LEU* 3.6 33.4 - - + -
252A MET* 4.6 7.0 - - + -
255A LEU* 4.1 20.6 - - + -
313A ILE* 4.5 3.6 - - + -
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Residues in contact with SER 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A TRP* 4.5 4.4 - - - -
124A ARG 2.8 22.9 + - - -
125A TYR* 3.1 11.4 + - - -
127A ILE* 1.3 76.5 - - - +
129A HIS* 1.3 65.9 + - - +
131A LEU* 3.7 15.1 - - - +
132A ALA* 2.9 27.9 + - - +
180A ILE* 4.9 0.8 - - - +
184A ILE* 4.1 19.1 - - - +
189A GLU* 4.8 2.3 + - - -
193A LEU* 3.7 23.9 - - - +
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Residues in contact with HIS 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A TYR* 2.8 70.6 + + - +
127A ILE 3.0 0.2 - - - -
128A SER* 1.3 85.5 + - - +
130A VAL* 1.3 64.8 + - - +
132A ALA* 4.5 0.4 - - - -
133A PHE* 3.0 23.9 + - - +
189A GLU* 4.5 5.6 - - - -
192A PHE* 3.8 22.8 - + - -
193A LEU* 4.0 15.4 - - + +
200A MET* 3.3 34.1 - - + +
202A CYS* 4.4 6.5 - - - -
308A LEU* 3.6 24.0 - - + +
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Residues in contact with VAL 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A PHE* 2.8 45.7 + - + +
127A ILE* 3.4 9.6 - - - +
129A HIS* 1.3 71.9 - - - +
131A LEU* 1.3 69.1 + - + +
133A PHE* 3.3 7.7 + - - +
134A PHE* 3.0 47.8 + - + -
239A SER* 3.7 25.1 - - - +
242A SER* 4.8 0.7 - - - +
243A ILE* 4.0 19.1 - - + -
303A PHE* 5.3 3.4 - - + -
304A LEU* 6.4 0.4 - - + -
308A LEU* 4.2 9.4 - - + -
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Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ILE* 2.8 31.1 + - + +
128A SER* 3.7 13.7 - - - +
130A VAL* 1.3 76.5 - - + +
132A ALA* 1.3 62.6 + - - +
134A PHE* 3.2 7.5 + - + +
135A ALA* 3.1 23.0 + - - +
176A TYR* 3.7 28.8 - - + +
179A LEU* 3.8 35.0 - - + -
180A ILE* 3.8 24.1 - - + +
183A TYR* 4.0 22.7 - - + -
243A ILE* 5.8 1.3 - - + -
255A LEU* 4.0 12.6 - - + -
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Residues in contact with ALA 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A SER 2.9 18.4 + - - +
129A HIS 3.9 1.1 - - - +
130A VAL 3.3 0.4 - - - -
131A LEU* 1.3 75.7 - - - +
133A PHE* 1.3 63.2 + - - +
135A ALA* 3.4 3.5 + - - +
136A ALA* 3.0 24.6 + - - +
180A ILE* 4.1 7.1 - - - +
193A LEU* 3.3 43.2 - - + +
196A ALA* 3.8 5.6 - - + +
200A MET* 3.8 16.2 - - - -
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Residues in contact with PHE 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A HIS 3.0 17.9 + - - +
130A VAL 3.5 6.3 - - - +
132A ALA* 1.3 76.5 - - - +
134A PHE* 1.3 64.9 + + - +
136A ALA* 3.4 4.1 + - + +
137A SER* 2.9 46.4 + - - -
203A VAL* 3.8 33.5 - - + +
206A LYS* 3.1 47.3 - - + -
207A ALA 5.9 0.4 - - - -
235A PHE* 3.1 22.7 - + + -
236A PHE* 3.8 17.7 - + - -
239A SER* 3.7 20.6 - - - -
303A PHE* 4.2 12.8 - + + -
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Residues in contact with PHE 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A VAL* 3.0 28.1 + - + -
131A LEU* 3.2 7.6 + - + +
133A PHE* 1.3 77.5 - + - +
135A ALA* 1.3 67.0 + - - +
137A SER* 3.3 2.3 + - - +
138A ASP* 3.0 29.6 + - - +
176A TYR* 3.3 48.7 - + + -
236A PHE* 3.5 46.2 - + + -
239A SER* 3.3 34.1 - - - -
240A PHE* 3.7 27.4 - + - -
243A ILE* 4.9 2.5 - - + -
259A ASN* 4.6 5.2 - - - -
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Residues in contact with ALA 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU 3.1 14.8 + - - +
132A ALA* 4.0 5.2 - - - +
134A PHE* 1.3 76.3 - - - +
136A ALA* 1.3 64.8 + - - +
138A ASP* 3.7 5.9 + - - +
139A GLY* 3.5 12.8 + - - -
173A SER* 4.2 8.8 + - - +
176A TYR* 4.0 19.9 - - + -
177A SER* 4.4 13.9 - - - +
180A ILE* 5.0 5.8 - - + -
193A LEU 5.9 1.1 - - - +
194A PHE* 5.5 7.2 - - + -
80B PHE 4.9 4.0 - - - +
81B VAL* 5.9 2.1 - - + -
82B ILE* 5.0 7.7 - - + +
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Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ALA 3.0 18.1 + - - +
133A PHE* 3.6 6.5 - - + +
135A ALA* 1.3 76.5 - - - +
137A SER* 1.3 64.1 + - - +
139A GLY* 3.1 13.3 + - - -
140A ILE* 3.4 15.7 + - + +
194A PHE 5.9 3.8 - - - +
196A ALA* 4.6 10.5 - - + +
197A ILE* 3.8 31.0 - - + +
203A VAL* 5.1 6.1 - - + -
81B VAL* 6.2 4.0 - - - -
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Residues in contact with SER 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A PHE* 2.9 43.8 + - - -
134A PHE 3.9 1.3 - - - -
136A ALA* 1.3 70.1 - - - +
138A ASP* 1.3 67.2 + - - +
140A ILE* 2.8 25.2 + - - +
141A VAL* 2.9 17.0 + - - +
206A LYS* 5.5 0.9 - - - +
207A ALA* 5.8 2.3 + - - +
231A VAL* 5.3 6.2 - - - +
235A PHE* 5.8 0.7 - - - +
236A PHE* 3.3 28.7 - - - -
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Residues in contact with ASP 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A PHE* 3.0 20.0 + - - +
135A ALA 3.8 2.0 - - - +
137A SER* 1.3 73.2 - - - +
139A GLY* 1.3 53.3 + - - +
141A VAL* 3.2 9.2 + - - +
142A ASN* 2.7 37.8 + - - +
169A GLU* 3.7 23.4 - - + +
172A HIS* 3.1 15.4 + - - +
173A SER* 3.1 39.8 + - - +
176A TYR* 3.6 14.0 - - - -
236A PHE* 4.1 16.3 - - - -
262A ILE* 5.9 0.7 - - - +
266A GLU* 5.3 0.7 - - - +
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Residues in contact with GLY 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ALA 3.5 4.4 + - - -
136A ALA 3.1 10.5 + - - -
138A ASP* 1.3 78.0 - - - +
140A ILE* 1.3 56.7 + - - +
142A ASN* 3.3 7.4 - - - +
143A GLU* 2.8 28.4 + - - +
173A SER* 4.3 2.3 + - - -
80B PHE* 3.5 39.1 + - - +
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Residues in contact with ILE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ALA 3.4 12.3 + - - +
137A SER* 2.8 18.3 + - - +
139A GLY* 1.3 69.4 - - - +
141A VAL* 1.3 68.3 + - + +
143A GLU* 3.1 8.8 + - - +
144A ASN* 3.0 21.7 + - - +
197A ILE* 4.3 14.1 - - + -
207A ALA* 3.7 41.1 - - + +
210A ALA* 3.6 26.7 - - + -
211A LEU* 4.0 22.4 - - + +
214A ILE* 3.7 18.9 - - + +
228A PHE* 4.3 3.4 - - + -
231A VAL* 6.3 0.4 - - + -
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Residues in contact with VAL 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A SER 2.9 18.2 + - - +
138A ASP* 3.4 9.0 - - - +
140A ILE* 1.3 73.6 - - - +
142A ASN* 1.3 64.0 + - - +
144A ASN* 3.1 5.4 + - - +
145A LEU* 3.0 35.9 + - + +
165A GLN* 3.9 0.2 - - - +
169A GLU* 3.7 27.8 - - - +
228A PHE* 4.1 13.7 - - + -
231A VAL* 3.9 26.9 - - + -
232A GLU* 3.9 26.2 - - + +
236A PHE* 4.4 7.9 - - + -
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Residues in contact with ASN 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ASP 2.7 20.6 + - - +
139A GLY* 3.3 10.5 - - - +
141A VAL* 1.3 73.7 - - - +
143A GLU* 1.3 63.3 + - - +
144A ASN 3.2 0.2 + - - -
145A LEU* 3.2 8.8 + - - +
146A VAL* 3.0 39.0 + - - +
166A ILE* 3.8 12.3 + - - +
169A GLU* 3.4 26.0 - - + +
170A ASN* 2.7 32.0 + - - +
173A SER* 5.2 2.0 + - - -
80B PHE* 4.5 9.4 - - + -
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Residues in contact with GLU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLY 2.8 18.4 + - - +
140A ILE* 3.1 10.1 + - - +
142A ASN* 1.3 71.7 - - - +
144A ASN* 1.3 57.2 + - - +
146A VAL* 4.7 0.2 - - - -
147A GLU* 2.8 63.5 + - - +
211A LEU* 3.6 22.6 - - - +
214A ILE* 3.8 18.3 - - + +
79B ARG* 4.5 6.1 + - - -
80B PHE* 3.5 40.3 - - + -
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Residues in contact with ASN 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ILE 3.0 7.6 + - - +
141A VAL 3.1 8.2 + - - +
143A GLU* 1.3 78.6 - - - +
145A LEU* 1.3 58.1 + - - +
148A ARG* 2.8 46.8 + - - +
149A PHE* 3.2 40.5 + - - -
213A TRP 4.8 1.2 - - - +
214A ILE* 3.6 17.3 - - + +
224A ARG* 5.1 0.9 + - - +
228A PHE* 3.3 53.1 - - + -
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Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A VAL* 3.0 24.2 + - + +
142A ASN* 3.8 3.4 - - - +
144A ASN* 1.3 77.9 - - - +
146A VAL* 1.3 56.8 + - - +
149A PHE* 3.6 25.6 + - + +
150A SER* 2.6 38.5 + - - +
162A TYR* 3.5 34.3 - - + +
165A GLN* 3.4 42.0 - - + +
166A ILE* 3.6 22.2 - - + -
169A GLU* 4.2 7.9 - - + -
232A GLU* 5.8 0.4 - - - +
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Residues in contact with VAL 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ASN* 3.0 35.5 + - - +
143A GLU* 3.9 4.0 - - - +
145A LEU* 1.3 76.8 - - - +
147A GLU* 1.3 64.7 + - + +
150A SER* 4.0 3.8 - - - -
151A GLN* 2.9 28.6 + - - -
166A ILE* 3.7 24.7 - - + -
80B PHE* 5.2 0.9 - - + -
150B SER* 4.4 13.7 - - - +
151B GLN* 3.1 24.6 + - - +
159B ARG* 4.2 23.8 - - - +
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Residues in contact with GLU 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A GLU* 2.8 54.3 + - + +
146A VAL* 1.3 80.2 - - + +
148A ARG* 1.3 69.3 + - + +
151A GLN* 3.4 15.5 - - - +
214A ILE* 3.9 10.6 - - + +
79B ARG* 3.4 25.5 + - - -
80B PHE* 3.9 4.4 - - + -
151B GLN* 4.1 16.1 - - - +
159B ARG* 5.0 2.9 + - - +
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Residues in contact with ARG 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ASN* 2.8 29.4 + - - +
146A VAL 3.4 1.8 - - - -
147A GLU* 1.3 93.1 - - + +
149A PHE* 1.3 66.8 + - - +
150A SER 3.3 1.1 - - - -
151A GLN* 3.1 4.5 + - - +
152A GLU* 2.9 34.4 + - - +
213A TRP 3.5 4.8 + - - -
214A ILE* 3.2 32.5 + - + +
216A ASP 3.2 26.8 + - - -
217A LYS* 5.0 9.5 + - - +
219A ALA 5.0 1.8 + - - -
224A ARG* 3.2 46.4 - - - +
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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).
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