Contacts of the helix formed by residues 120 - 148 (chain D) in PDB entry 3OLJ
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D SER 5.5 0.9 - - - +
119D LEU* 1.3 75.5 - - - +
121D PRO* 1.4 75.7 - - + +
122D GLU* 3.3 34.6 + - - +
123D GLU* 2.9 41.6 + - - +
124D ARG* 3.2 10.7 + - - +
249D ARG* 5.9 0.4 - - - +
312D LEU 5.9 0.6 + - - -
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Residues in contact with PRO 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D LEU 4.2 1.1 - - - +
120D LYS* 1.4 86.9 - - + +
122D GLU* 1.3 64.3 + - - +
124D ARG* 3.4 28.1 + - - +
125D TYR* 2.9 27.4 + - - +
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Residues in contact with GLU 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D LYS* 3.3 42.0 + - + +
121D PRO* 1.3 86.1 - - - +
123D GLU* 1.3 60.9 + - + +
125D TYR* 3.5 9.9 + - + +
126D PHE* 3.0 27.2 + - - +
312D LEU* 3.8 41.6 - - + +
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Residues in contact with GLU 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D LEU* 3.6 22.4 - - + +
120D LYS* 2.9 53.4 + - + +
122D GLU* 1.3 75.9 - - + +
124D ARG* 1.3 60.0 + - - +
126D PHE* 3.3 1.9 + - - +
127D ILE* 2.9 38.2 + - + +
246D LEU* 6.1 0.2 - - + -
249D ARG* 2.7 40.8 + - - -
312D LEU 3.2 19.5 - - - +
313D ILE* 4.1 14.7 - - + -
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Residues in contact with ARG 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D TRP* 3.0 80.3 + - + +
117D GLU* 3.4 12.2 + - - +
119D LEU* 2.7 34.8 + - + +
120D LYS 3.2 3.0 + - - -
121D PRO* 3.7 33.9 - - - +
123D GLU* 1.3 75.1 - - - +
125D TYR* 1.3 60.9 + - - +
128D SER* 2.9 31.2 + - - -
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Residues in contact with TYR 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D PRO 2.9 16.5 + - - +
122D GLU* 3.5 8.5 - - - +
123D GLU 3.2 0.2 - - - -
124D ARG* 1.3 76.6 - - - +
126D PHE* 1.3 63.7 + - - +
128D SER* 2.9 20.0 + - - -
129D HIS* 3.1 57.1 + + - +
202D CYS* 5.9 0.2 - - - -
308D LEU* 3.7 20.9 - - + +
309D PRO* 6.2 0.2 - - + -
312D LEU* 4.0 20.0 - - + -
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Residues in contact with PHE 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D GLU 3.0 18.4 + - - +
123D GLU 3.7 3.6 - - - +
125D TYR* 1.3 82.5 - - - +
127D ILE* 1.3 68.9 + - + +
129D HIS* 3.4 2.1 + - - +
130D VAL* 3.0 42.7 + - + +
242D SER* 3.4 26.9 - - - -
243D ILE* 6.1 0.9 - - + -
246D LEU* 5.9 1.3 - - + -
304D LEU* 5.3 4.0 - - + -
308D LEU* 3.6 41.5 - - + +
309D PRO 3.7 18.6 - - - -
310D VAL* 4.0 14.4 - - + -
312D LEU* 4.0 9.4 - - + -
313D ILE* 3.5 39.7 - - + -
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Residues in contact with ILE 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D TRP* 3.7 19.3 - - + -
119D LEU* 3.7 26.9 - - + -
123D GLU* 2.9 25.1 + - + +
126D PHE* 1.3 85.4 - - + +
128D SER* 1.3 65.0 + - - +
129D HIS 3.2 0.2 + - - -
130D VAL* 3.2 6.5 + - + +
131D LEU* 3.0 37.7 + - + +
183D TYR* 4.9 0.9 - - + -
243D ILE* 6.1 2.0 - - + -
246D LEU* 3.7 35.2 - - + -
252D MET* 4.6 5.6 - - - -
255D LEU* 4.0 21.1 - - + -
313D ILE* 4.6 0.9 - - + -
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Residues in contact with SER 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D TRP* 4.1 10.2 - - - -
124D ARG 2.9 14.9 + - - -
125D TYR* 2.9 22.7 + - - -
127D ILE* 1.3 76.9 - - - +
129D HIS* 1.3 65.6 + - - +
131D LEU* 3.5 12.5 + - - +
132D ALA* 3.0 28.1 + - - +
180D ILE* 4.8 0.8 - - - +
184D ILE* 4.4 11.0 - - - -
189D GLU* 5.0 3.0 + - - -
193D LEU* 3.8 27.2 - - - +
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Residues in contact with HIS 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D TYR* 3.1 60.3 + + - +
126D PHE 3.7 3.6 - - - +
127D ILE 3.1 0.6 - - - -
128D SER* 1.3 87.0 + - - +
130D VAL* 1.3 59.5 + - - +
132D ALA* 3.5 2.5 + - - +
133D PHE* 2.9 29.3 + - - +
189D GLU* 4.9 4.5 - - - -
192D PHE* 4.0 27.5 - + - -
193D LEU* 4.0 6.5 - - + +
200D MET* 3.5 31.3 - - + +
202D CYS* 4.1 11.4 - - - -
308D LEU* 3.8 21.3 - - + +
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Residues in contact with VAL 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D PHE* 3.0 51.0 + - + +
127D ILE* 3.2 5.6 + - + +
129D HIS* 1.3 74.6 - - - +
131D LEU* 1.3 60.6 + - + +
133D PHE* 3.3 8.0 + - - +
134D PHE* 2.9 52.8 + - + -
239D SER* 3.9 24.0 - - - +
243D ILE* 4.1 18.4 - - + -
303D PHE* 5.1 2.2 - - + -
308D LEU* 3.9 11.7 - - + -
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Residues in contact with LEU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D ILE* 3.0 28.3 + - + +
128D SER* 3.6 11.4 - - - +
130D VAL* 1.3 73.5 - - + +
132D ALA* 1.3 65.8 + - - +
134D PHE* 3.2 3.9 + - + +
135D ALA* 3.0 24.8 + - - +
176D TYR* 3.7 31.7 - - + +
179D LEU* 4.0 24.2 - - + -
180D ILE* 3.9 24.2 - - + +
183D TYR* 4.1 21.5 - - + -
243D ILE* 5.0 5.4 - - + -
255D LEU* 3.7 24.5 - - + -
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Residues in contact with ALA 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D SER 3.0 17.8 + - - +
129D HIS 3.7 1.6 - - - +
131D LEU* 1.3 75.3 - - - +
133D PHE* 1.3 62.8 + - - +
135D ALA* 4.0 3.0 - - - +
136D ALA* 3.1 24.9 + - - +
180D ILE* 4.0 8.2 - - - +
193D LEU* 3.3 34.3 - - + +
196D ALA* 3.9 4.9 - - + +
200D MET* 3.7 24.9 - - - -
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Residues in contact with PHE 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D HIS 2.9 18.6 + - - +
130D VAL* 3.5 7.9 - - - +
131D LEU 3.2 0.4 - - - -
132D ALA* 1.3 77.5 - - - +
134D PHE* 1.3 66.0 + + - +
136D ALA* 3.8 1.5 - - - +
137D SER* 2.9 55.5 + - - -
203D VAL* 3.6 35.8 - - + +
206D LYS* 3.1 54.5 - - + -
207D ALA* 5.7 0.9 - - + -
235D PHE* 3.6 16.4 - + + -
236D PHE* 4.0 18.2 - + - -
239D SER* 3.9 18.2 - - - -
303D PHE* 4.3 11.2 - + + -
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Residues in contact with PHE 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D VAL* 2.9 31.5 + - + +
131D LEU* 3.6 4.5 - - - +
133D PHE* 1.3 80.5 - + - +
135D ALA* 1.3 63.1 + - - +
137D SER* 3.8 1.6 - - - -
138D ASP* 3.0 31.5 + - - +
176D TYR* 3.3 45.1 - + + -
236D PHE* 3.7 44.4 - + + -
239D SER* 3.3 32.1 - - - -
240D PHE* 3.6 28.7 - + - -
243D ILE* 4.1 14.6 - - + -
259D ASN* 4.7 0.2 - - - -
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Residues in contact with ALA 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PHE 5.1 3.1 - - - +
81A VAL* 5.9 1.7 - - - -
82A ILE 6.0 0.3 + - - -
131D LEU 3.0 16.8 + - - +
132D ALA* 4.0 5.8 - - - +
134D PHE* 1.3 76.4 - - - +
136D ALA* 1.3 63.0 + - - +
138D ASP* 3.6 14.5 - - - +
139D GLY* 3.6 4.3 + - - -
173D SER* 3.7 11.3 + - - +
176D TYR* 3.9 22.4 - - + -
177D SER* 4.2 15.0 - - - +
180D ILE* 4.9 5.8 - - + -
193D LEU 6.0 0.2 - - - +
194D PHE* 5.9 4.3 - - + -
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Residues in contact with ALA 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PHE 6.1 0.2 - - - -
81A VAL* 5.9 6.1 - - + +
132D ALA 3.1 18.6 + - - +
133D PHE* 3.8 4.3 - - - +
135D ALA* 1.3 75.8 - - - +
137D SER* 1.3 64.3 + - - +
139D GLY* 3.1 13.2 + - - -
140D ILE* 3.4 13.2 + - - +
194D PHE 5.4 5.8 - - - +
196D ALA* 4.3 12.6 - - + +
197D ILE* 3.8 33.3 - - + +
203D VAL* 5.1 4.3 - - + -
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Residues in contact with SER 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D PHE* 2.9 47.9 + - - -
134D PHE 3.8 1.8 - - - -
136D ALA* 1.3 73.2 - - - +
138D ASP* 1.3 66.6 + - - +
140D ILE* 3.0 25.7 + - - +
141D VAL* 3.0 17.4 + - - +
207D ALA* 6.1 0.9 - - - -
231D VAL* 5.3 5.1 - - - +
236D PHE* 3.4 27.1 - - - -
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Residues in contact with ASP 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D PHE* 3.0 20.8 + - - +
135D ALA 3.6 1.8 - - - +
137D SER* 1.3 75.8 - - - +
139D GLY* 1.3 55.8 + - - +
141D VAL* 3.3 5.7 + - - +
142D ASN* 2.8 32.4 + - - +
169D GLU* 3.3 28.5 - - - +
172D HIS* 3.3 25.3 + - - +
173D SER* 3.1 28.2 + - - +
176D TYR* 3.6 12.1 - - - -
236D PHE* 4.1 17.0 - - - -
262D ILE* 6.0 0.5 - - - +
266D GLU* 5.2 0.2 - - - -
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Residues in contact with GLY 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PHE* 3.4 38.7 - - - +
135D ALA 3.6 4.2 + - - -
136D ALA* 3.1 11.4 + - - -
138D ASP* 1.3 79.2 - - - +
140D ILE* 1.3 57.3 + - - +
142D ASN* 3.6 5.1 - - - +
143D GLU* 2.9 28.2 + - - +
173D SER* 4.4 2.0 + - - -
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Residues in contact with ILE 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D ALA 3.8 11.0 - - - +
137D SER* 3.0 14.7 + - - +
139D GLY* 1.3 76.3 - - - +
141D VAL* 1.3 66.7 + - + +
143D GLU* 3.3 5.1 + - - -
144D ASN* 3.0 19.6 + - - +
197D ILE* 4.0 19.5 - - + -
207D ALA* 3.8 38.8 - - + +
210D ALA* 3.7 27.4 - - + -
211D LEU* 3.8 22.0 - - + +
214D ILE* 3.4 23.7 - - + +
228D PHE* 4.2 2.6 - - + -
231D VAL* 6.3 0.7 - - + -
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Residues in contact with VAL 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D SER 3.0 18.5 + - - +
138D ASP* 3.6 9.9 - - - +
140D ILE* 1.3 75.0 - - - +
142D ASN* 1.3 56.2 + - - +
144D ASN* 3.2 4.7 + - - +
145D LEU* 3.0 37.9 + - + +
165D GLN* 4.0 6.1 - - - +
169D GLU* 3.8 19.1 - - - +
228D PHE* 4.2 15.3 - - + -
231D VAL* 3.9 26.2 - - + -
232D GLU* 3.8 36.1 - - + +
236D PHE* 4.5 7.2 - - + -
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Residues in contact with ASN 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PHE* 4.3 11.2 - - + -
159A ARG* 5.5 4.0 - - - +
138D ASP 2.8 20.4 + - - +
139D GLY* 3.6 9.2 - - - +
141D VAL* 1.3 70.5 - - - +
143D GLU* 1.3 67.4 + - - +
145D LEU* 3.1 10.4 + - - +
146D VAL* 2.8 44.0 + - - +
166D ILE* 3.3 26.9 + - - +
169D GLU* 3.4 15.4 - - + +
170D ASN* 3.0 28.4 + - - +
173D SER* 5.9 0.2 + - - -
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Residues in contact with GLU 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 4.4 5.2 + - - -
80A PHE* 3.5 41.1 - - + -
139D GLY 2.9 19.8 + - - +
140D ILE* 3.3 5.2 + - - +
142D ASN* 1.3 75.1 - - - +
144D ASN* 1.3 58.2 + - - +
146D VAL* 3.3 0.4 + - - -
147D GLU* 2.8 58.2 + - - +
211D LEU* 3.7 23.2 - - - +
214D ILE* 4.0 17.5 - - + +
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Residues in contact with ASN 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D ILE 3.0 8.6 + - - +
141D VAL 3.6 7.6 + - - +
143D GLU* 1.3 77.3 - - - +
145D LEU* 1.3 59.7 + - - +
148D ARG* 2.9 43.0 + - - +
149D PHE* 3.1 54.0 + - - -
213D TRP 4.7 1.6 - - - +
214D ILE* 3.7 19.0 - - + +
224D ARG* 4.8 1.0 + - - -
228D PHE* 3.3 42.0 - - + -
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Residues in contact with LEU 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D VAL* 3.0 27.1 + - + +
142D ASN* 3.1 6.7 + - - +
144D ASN* 1.3 78.4 - - - +
146D VAL* 1.3 54.5 + - - +
149D PHE* 3.7 17.4 + - + -
150D SER* 2.8 39.0 + - - +
162D TYR* 3.5 37.5 - - + +
165D GLN* 3.5 40.4 - - + +
166D ILE* 3.5 27.8 - - + +
169D GLU* 4.2 6.3 - - + -
232D GLU* 5.8 0.2 - - - +
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Residues in contact with VAL 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PHE* 4.8 4.3 - - + -
150A SER* 4.5 9.2 - - - +
151A GLN* 3.2 29.8 + - - +
159A ARG* 4.0 26.9 - - + +
142D ASN* 2.8 38.6 + - - +
143D GLU* 3.9 4.3 - - - +
145D LEU* 1.3 73.7 - - - +
147D GLU* 1.3 61.9 + - + +
150D SER* 3.4 5.1 + - - -
151D GLN* 3.1 27.9 + - - -
166D ILE* 3.9 24.7 - - + -
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Residues in contact with GLU 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 3.4 34.3 + - - -
80A PHE* 4.0 2.8 - - + -
151A GLN* 4.0 16.4 - - - +
159A ARG* 5.6 0.7 - - - +
143D GLU* 2.8 47.5 + - + +
146D VAL* 1.3 80.0 - - + +
148D ARG* 1.3 70.1 + - + +
151D GLN* 3.4 15.3 - - - +
214D ILE* 4.1 8.4 - - + +
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Residues in contact with ARG 148 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D ASN* 2.9 28.3 + - - +
146D VAL 3.6 0.6 - - - -
147D GLU* 1.3 89.5 - - + +
149D PHE* 1.3 66.5 + - - +
150D SER 3.4 1.3 - - - -
151D GLN* 3.1 4.8 + - - +
152D GLU* 3.0 33.2 + - - +
213D TRP 3.6 3.4 + - - -
214D ILE* 3.0 33.8 + - + -
215D GLY 4.7 0.2 - - - -
216D ASP 2.9 28.9 + - - -
217D LYS* 5.0 5.6 + - - +
219D ALA 4.7 2.6 + - - -
224D ARG* 3.2 48.3 - - - +
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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