Contacts of the helix formed by residues 151 - 180 (chain D) in PDB entry 5X11
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 ASP 151 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D LEU* 4.1 22.9 - - + +
141D SER* 4.7 12.8 - - - +
145D MET* 4.0 19.0 - - + +
149D SER* 3.1 3.1 - - - -
150D PRO* 1.3 86.9 - - - +
152D PHE* 1.3 56.9 + - - +
153D GLY 3.4 2.7 - - - -
154D HIS* 3.4 14.1 + - + +
155D TYR* 2.9 28.9 + - - +
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Residues in contact with PHE 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ILE* 3.7 34.8 - - + -
175C ILE* 4.2 10.3 - - + -
178C MET* 4.3 20.9 - - + -
179C ILE* 4.2 9.2 - - + -
145D MET* 3.8 14.5 - - + -
146D SER 3.5 21.8 - - - +
147D PHE* 3.8 34.8 - + - +
149D SER 3.2 17.9 + - - +
150D PRO 3.3 1.0 - - - -
151D ASP* 1.3 77.0 - - - +
153D GLY* 1.3 51.6 + - - +
155D TYR* 3.2 20.2 + + - +
156D LEU* 2.8 64.9 + - + +
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Residues in contact with GLY 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C ALA 3.6 20.9 - - - -
103C TYR* 3.8 20.2 - - - -
105C ILE* 3.9 7.8 - - - +
13D ARG* 6.0 0.2 - - - -
150D PRO 4.8 2.4 + - - -
151D ASP 3.4 0.4 - - - -
152D PHE* 1.3 73.5 - - - +
154D HIS* 1.3 66.0 + - - +
156D LEU* 3.2 4.6 + - - +
157D VAL* 3.1 27.0 + - - +
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Residues in contact with HIS 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C TYR* 4.0 14.6 - - + -
29D GLU* 3.0 43.3 + - + +
138D LEU* 4.2 19.9 - - + +
151D ASP* 3.4 22.3 + - + +
153D GLY* 1.3 76.0 - - - +
155D TYR* 1.3 61.3 + - - +
157D VAL* 3.4 2.9 - - - +
158D LEU* 3.0 44.2 + - + +
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Residues in contact with TYR 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C ILE* 4.4 8.4 - - + +
178C MET* 3.6 37.9 - - + +
135D TYR* 3.9 15.6 + + - -
138D LEU* 3.9 11.4 - - + +
139D MET* 3.7 30.9 - - + +
145D MET* 3.6 28.7 - - + -
151D ASP 2.9 14.1 + - - +
152D PHE* 3.2 18.8 + + - +
154D HIS* 1.3 74.3 - - - +
156D LEU* 1.3 62.3 + - + +
158D LEU* 3.3 2.6 + - - +
159D THR* 2.8 62.6 + - + +
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Residues in contact with LEU 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C MET* 4.0 2.7 - - - -
102C ALA* 3.4 38.8 - - + +
105C ILE* 3.8 15.0 - - + -
117C PHE* 4.3 3.1 - - + -
171C TRP* 3.5 9.1 - - + -
175C ILE* 3.6 46.2 - - + -
152D PHE* 2.8 49.9 + - + +
153D GLY 3.2 6.3 + - - +
155D TYR* 1.3 74.0 - - + +
157D VAL* 1.3 56.8 + - - +
159D THR* 3.2 5.3 + - - -
160D LYS* 3.0 30.7 + - - +
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Residues in contact with VAL 157 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C MET* 3.8 25.8 - - + +
103C TYR* 3.7 40.4 - - + +
29D GLU* 3.6 38.1 - - + +
30D LEU* 4.7 4.9 - - + -
32D GLN* 6.2 0.2 - - - -
33D PHE* 3.2 27.5 - - + -
153D GLY 3.1 5.7 + - - +
154D HIS 3.4 10.8 - - - +
156D LEU* 1.3 73.4 - - - +
158D LEU* 1.3 60.5 + - - +
161D ALA* 3.0 24.8 + - - +
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Residues in contact with LEU 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D GLU* 4.8 13.0 - - + -
32D GLN* 6.3 0.4 - - + -
131D LEU* 4.1 28.7 - - + +
134D SER* 3.9 39.9 - - - +
135D TYR* 4.4 13.9 - - + +
138D LEU* 4.0 15.7 - - + -
154D HIS* 3.0 44.6 + - + +
155D TYR* 3.7 4.5 - - - +
157D VAL* 1.3 75.1 - - - +
159D THR* 1.3 61.1 + - - +
161D ALA* 3.1 5.1 + - + +
162D LEU* 2.8 33.0 + - + +
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Residues in contact with THR 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C TRP* 3.0 24.1 + - - -
175C ILE* 4.5 3.0 - - - +
135D TYR* 4.1 13.9 - - + -
155D TYR* 2.8 60.1 + - + +
156D LEU* 3.2 10.7 + - - -
158D LEU* 1.3 71.5 - - - +
160D LYS* 1.3 63.3 + - - +
162D LEU* 3.3 9.3 + - + +
163D GLU* 2.9 30.3 + - - +
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Residues in contact with LYS 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ASP* 4.8 1.1 - - - -
99C MET* 3.5 25.6 - - + -
167C ASN* 4.2 18.0 + - - -
168C TYR* 3.7 53.6 - - - +
171C TRP* 3.5 33.6 - - + +
33D PHE* 3.8 17.3 - - + -
156D LEU 3.0 19.1 + - - +
159D THR* 1.3 78.2 + - - +
161D ALA* 1.3 53.6 + - - +
163D GLU* 3.2 2.0 + - - +
164D ARG* 2.8 46.4 + - + +
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Residues in contact with ALA 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D GLN* 3.9 15.9 - - + +
33D PHE* 3.5 17.7 - - + -
131D LEU* 3.5 27.3 - - + +
157D VAL 3.0 17.4 + - - +
158D LEU* 3.5 4.3 - - + +
160D LYS* 1.3 79.2 - - - +
162D LEU* 1.3 60.9 + - - +
164D ARG* 3.7 9.2 + - - +
165D GLU* 3.3 24.3 + - - +
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Residues in contact with LEU 162 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D LEU* 3.2 30.3 - - + +
131D LEU* 3.7 28.0 - - + +
132D GLN* 3.8 27.8 - - - +
135D TYR* 4.0 35.9 - - + -
158D LEU* 2.8 20.4 + - + +
159D THR* 3.6 7.6 - - + +
161D ALA* 1.3 70.6 - - - +
163D GLU* 1.3 60.4 + - + +
165D GLU* 3.1 3.6 + - - +
166D LYS* 2.9 46.5 + - - +
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Residues in contact with GLU 163 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C ASN* 3.3 33.0 + - - +
170C SER* 5.0 7.5 + - - -
171C TRP* 4.2 26.0 - - + +
174C SER* 6.1 1.2 - - - -
159D THR* 2.9 22.2 + - - +
160D LYS* 3.6 5.6 - - - +
162D LEU* 1.3 73.1 - - + +
164D ARG* 1.3 67.4 + - - +
166D LYS* 3.4 15.6 + - + +
167D ASN* 2.9 26.5 + - - +
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Residues in contact with ARG 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C GLU 4.4 5.1 + - - -
94C VAL* 3.0 47.9 + - - +
96C ASP* 5.5 1.2 - - - +
160C LYS* 5.8 0.3 + - - -
167C ASN* 3.9 8.2 + - - -
32D GLN* 3.0 47.3 + - - +
33D PHE* 3.6 22.7 - - - -
124D ARG* 6.3 0.4 - - - +
127D LYS* 4.7 4.0 - - - +
160D LYS* 2.8 27.4 + - - +
161D ALA* 3.7 8.1 + - - +
163D GLU* 1.3 76.1 - - - +
165D GLU* 1.3 67.0 + - - +
167D ASN* 3.5 4.8 + - - +
168D TYR* 3.1 32.4 + - + +
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Residues in contact with GLU 165 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D GLN* 5.2 0.5 - - - +
124D ARG* 2.8 53.8 + - - +
127D LYS* 3.4 31.4 + - + +
128D LEU* 3.8 34.1 - - + +
131D LEU* 4.2 5.5 - - + +
161D ALA 3.3 14.8 + - - +
162D LEU 3.1 4.9 + - - +
164D ARG* 1.3 86.5 + - - +
166D LYS* 1.3 61.9 + - - +
167D ASN 3.2 0.7 - - - -
168D TYR* 3.7 2.3 - - - +
169D VAL* 2.9 34.8 + - - +
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Residues in contact with LYS 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D LEU* 3.7 27.3 - - + +
132D GLN* 4.1 21.0 + - - +
162D LEU* 2.9 31.3 + - - +
163D GLU* 3.8 16.0 - - + +
165D GLU* 1.3 74.6 - - - +
167D ASN* 1.3 57.7 + - - +
169D VAL* 3.3 2.5 + - - +
170D SER* 2.9 31.9 + - - -
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Residues in contact with ASN 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C LYS* 4.5 9.7 + - - -
163C GLU* 3.6 50.2 + - - +
164C ARG* 4.0 5.2 + - - -
167C ASN* 3.7 26.8 - - - +
163D GLU 2.9 18.9 + - - +
164D ARG* 3.5 6.0 - - - +
166D LYS* 1.3 74.1 - - - +
168D TYR* 1.3 60.6 + - - +
170D SER* 3.4 6.9 + - - -
171D TRP* 2.9 28.9 + - - +
----------------------------------------------------------
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Residues in contact with TYR 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C LYS* 3.7 34.7 - - - +
96D ASP* 2.5 37.2 + - - -
98D PHE* 3.7 20.2 - + - +
99D MET* 4.2 2.8 - - - +
120D GLN* 4.3 2.9 - - - -
124D ARG* 3.4 51.6 + - - -
164D ARG* 3.1 22.0 + - + +
165D GLU* 3.7 7.9 - - - +
167D ASN* 1.3 73.5 + - - +
169D VAL* 1.3 64.3 + - - +
171D TRP* 2.8 19.4 + + - +
172D LEU* 2.9 39.3 + - + +
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Residues in contact with VAL 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D LEU* 3.5 19.8 - - + +
124D ARG* 3.7 38.1 - - + +
125D LYS* 3.8 19.7 - - + +
128D LEU* 4.2 14.8 - - + -
165D GLU 2.9 22.9 + - - +
166D LYS* 3.7 4.7 - - - +
168D TYR* 1.3 71.9 - - - +
170D SER* 1.3 61.8 + - - +
172D LEU* 3.5 3.3 + - - +
173D GLU* 3.3 35.3 + - - +
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Residues in contact with SER 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D LYS 2.9 18.5 + - - -
167D ASN* 3.7 7.1 + - - -
169D VAL* 1.3 75.1 - - - +
171D TRP* 1.3 65.9 + - - +
173D GLU* 3.4 15.6 + - - +
174D SER* 3.3 22.3 + - - -
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Residues in contact with TRP 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C LEU* 3.5 29.6 - - + -
159C THR* 3.2 23.3 + - - -
160C LYS* 3.3 44.4 - - + +
163C GLU* 4.3 20.2 - - + -
98D PHE* 4.2 3.4 - + - -
99D MET* 3.7 25.6 - - + -
102D ALA* 4.6 1.6 - - + -
117D PHE* 4.0 15.7 - + - -
167D ASN* 2.9 15.3 + - - +
168D TYR* 2.8 8.6 + + - +
170D SER* 1.3 78.1 + - - +
172D LEU* 1.3 98.9 + - + +
174D SER* 3.2 10.9 + - - -
175D ILE* 3.0 44.0 + - + +
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Residues in contact with LEU 172 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D PHE* 3.9 13.2 - - + -
117D PHE* 3.6 29.9 - - + +
120D GLN* 3.7 25.1 - - + +
121D LEU* 3.8 29.2 - - + +
124D ARG* 4.1 5.6 - - + -
168D TYR* 2.9 39.0 + - + +
169D VAL* 3.8 7.4 - - - +
171D TRP* 1.3 91.4 - - + +
173D GLU* 1.3 50.7 + - - +
175D ILE* 3.1 3.8 + - - +
176D LEU* 2.7 39.6 + - - +
----------------------------------------------------------
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Residues in contact with GLU 173 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D LEU* 3.9 20.6 - - + +
125D LYS* 4.5 12.4 + - - +
169D VAL* 3.3 29.5 + - - +
170D SER* 3.4 17.4 - - - +
171D TRP 3.4 0.2 - - - -
172D LEU* 1.3 75.0 - - - +
174D SER* 1.3 54.7 - - - +
176D LEU* 3.2 8.0 + - - +
177D ALA* 2.8 37.0 + - - +
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Residues in contact with SER 174 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D SER 3.3 10.3 + - - -
171D TRP* 3.2 14.6 + - - -
173D GLU* 1.3 79.8 - - - +
175D ILE* 1.3 66.7 + - - +
177D ALA* 3.5 7.5 + - - +
178D MET* 3.1 24.0 + - - +
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Residues in contact with ILE 175 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C PHE* 4.1 13.6 - - + -
155C TYR* 4.5 15.7 - - + +
156C LEU* 3.5 28.7 - - + -
159C THR* 4.6 2.0 - - + +
117D PHE* 3.5 30.5 - - + -
171D TRP* 3.0 53.3 + - + +
172D LEU 3.8 5.2 - - - +
174D SER* 1.3 78.1 - - - +
176D LEU* 1.3 60.1 + - - +
178D MET* 3.2 11.0 + - - +
179D ILE* 3.0 27.5 + - + +
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Residues in contact with LEU 176 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D ALA 4.7 0.2 - - - +
114D SER* 3.9 18.8 - - - +
117D PHE* 3.5 32.0 - - + +
118D THR* 3.4 27.1 - - + +
121D LEU* 4.0 24.0 - - + -
172D LEU 2.7 21.1 + - - +
173D GLU* 3.5 7.0 - - - +
175D ILE* 1.3 72.6 - - - +
177D ALA* 1.3 61.8 + - - +
179D ILE* 3.1 7.3 + - + +
180D ASP* 3.1 35.9 + - - +
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Residues in contact with ALA 177 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D GLU 2.8 19.5 + - - +
174D SER* 3.7 8.3 - - - +
176D LEU* 1.3 73.2 - - - +
178D MET* 1.3 59.0 + - - +
179D ILE 3.7 0.2 + - - -
180D ASP* 3.8 18.6 + - - +
----------------------------------------------------------
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Residues in contact with MET 178 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C MET* 3.3 48.2 - - + +
146C SER* 4.3 3.7 - - - -
147C PHE* 4.1 15.7 + - - +
152C PHE* 4.2 15.3 - - + -
155C TYR* 3.9 29.6 - - + +
110D ARG* 4.8 2.3 + - - -
174D SER* 3.1 18.6 + - - +
175D ILE* 3.5 13.2 - - - +
176D LEU 3.1 0.6 - - - -
177D ALA* 1.3 76.9 - - - +
179D ILE* 1.3 62.9 + - - +
180D ASP 4.5 1.9 - - - +
----------------------------------------------------------
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Residues in contact with ILE 179 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C PHE* 4.4 26.0 - - + -
152C PHE* 5.7 1.1 - - + -
110D ARG* 2.6 47.5 + - + +
113D ALA* 5.5 3.6 - - + +
114D SER* 5.4 4.3 - - - +
175D ILE* 3.0 13.8 + - + +
176D LEU* 3.1 14.6 + - + +
178D MET* 1.3 78.9 - - - +
180D ASP* 1.3 64.2 + - - +
----------------------------------------------------------
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Residues in contact with ASP 180 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D ARG* 4.1 15.1 + - - +
114D SER* 3.2 32.9 + - - -
176D LEU* 3.1 25.7 + - - +
177D ALA* 3.8 14.5 - - - +
178D MET 4.5 2.1 - - - +
179D ILE* 1.3 89.9 - - - +
----------------------------------------------------------
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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