Contacts of the helix formed by residues 163 - 186 (chain B) in PDB entry 4MZ7
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 ASN 163 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TYR* 3.1 34.1 + - - +
161A SER* 3.9 6.3 + - - +
144B LEU 3.5 12.3 - - - +
145B ARG 3.1 16.4 + - - +
146B TYR 4.6 0.9 - - - -
147B ILE 3.3 9.1 + - - +
148B LYS* 3.5 29.3 + - - +
149B GLN* 3.8 5.5 - - - +
161B SER 3.6 10.4 + - - +
162B HIS* 1.3 75.6 - - - +
164B ARG* 1.3 66.8 + - - +
165B PHE 3.1 1.5 + - - -
166B GLU* 2.8 23.6 + - - +
167B HIS* 3.5 8.0 + - - +
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Residues in contact with ARG 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU* 3.3 23.3 + - + +
147B ILE* 2.9 28.3 + - + +
149B GLN* 2.9 56.9 + - - +
163B ASN* 1.3 72.4 - - - +
165B PHE* 1.3 58.3 + - - +
167B HIS* 3.4 1.6 + - - +
168B SER* 2.8 35.8 + - - +
207B ASP* 2.7 38.9 + - + -
210B HIS* 3.4 32.9 + - + -
214B SER* 2.9 25.8 + - - +
215B HIS* 5.0 0.8 - - - +
803B ZN 3.9 4.2 - - - -
804B DGT 3.0 28.1 + - - -
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Residues in contact with PHE 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TYR* 4.3 0.2 - - - -
158A PRO* 4.1 11.2 - - + -
136B ILE* 4.2 4.3 - - + -
141B PHE* 3.7 36.3 - + - -
142B GLN* 3.5 24.0 - - - -
144B LEU* 3.0 29.4 + - - +
145B ARG* 3.3 40.4 - - + +
163B ASN 3.1 0.4 - - - -
164B ARG* 1.3 76.2 - - - +
166B GLU* 1.3 78.7 + - - +
168B SER* 3.1 14.6 + - - -
169B LEU* 3.1 39.0 + - + +
801B DGT 3.3 23.6 - + - -
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Residues in contact with GLU 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TYR* 2.6 25.9 + - - -
158A PRO* 3.5 31.5 - - + +
159A GLY* 5.3 1.7 - - - -
161A SER* 3.5 22.0 + - - -
120B ASP* 4.7 2.7 - - - +
162B HIS* 3.5 6.5 - - + +
163B ASN* 2.8 35.2 + - - +
165B PHE* 1.3 79.3 - - - +
167B HIS* 1.3 65.2 + - - +
169B LEU* 3.4 9.1 + - - +
170B GLY 3.1 16.6 + - - -
318B ARG* 3.5 32.1 + - - +
322B HIS* 5.9 1.1 - - + -
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Residues in contact with HIS 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B GLN* 3.3 41.6 + - - +
163B ASN 3.5 3.3 + - - +
164B ARG* 3.4 8.0 + - - +
165B PHE 3.3 0.4 - - - -
166B GLU* 1.3 81.2 - - - +
168B SER* 1.3 60.4 + - - +
170B GLY* 3.0 3.3 + - - -
171B VAL* 2.9 41.9 + - + +
206B HIS* 3.4 5.2 + + - -
207B ASP* 3.1 12.1 - - - -
311B ASP* 3.1 19.5 - - - -
314B ASP* 2.8 21.2 + - - +
315B TYR* 3.9 9.5 - + + +
318B ARG* 3.5 16.5 - - - +
803B ZN 2.1 37.4 - - - -
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Residues in contact with SER 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B PHE* 3.9 10.3 - - - -
144B LEU* 3.6 15.6 - - - +
164B ARG 2.8 23.1 + - - -
165B PHE 3.4 5.4 - - - -
167B HIS* 1.3 74.6 - - - +
169B LEU* 1.3 64.1 + - - +
171B VAL 3.2 0.2 + - - -
172B GLY 3.0 19.2 + - - -
203B GLY 3.7 0.9 - - - +
204B LEU* 3.4 33.4 + - - -
206B HIS* 4.2 10.8 - - - -
207B ASP* 3.9 16.3 - - - +
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PRO* 4.0 13.5 - - + -
118B ILE* 3.8 28.0 - - + -
120B ASP* 6.1 1.6 - - + +
126B ILE* 4.5 12.7 - - + +
128B LEU* 4.8 10.2 - - + +
136B ILE* 3.7 34.8 - - + -
141B PHE* 4.3 8.1 - - + -
165B PHE* 3.1 45.1 + - + +
166B GLU* 3.7 7.6 - - - +
168B SER* 1.3 75.6 - - - +
170B GLY* 1.3 58.3 - - - +
172B GLY* 3.3 1.7 + - - -
173B TYR* 2.9 29.2 + - - +
204B LEU* 3.9 12.1 - - + +
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Residues in contact with GLY 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B HIS* 3.7 13.9 - - - -
126B ILE* 4.8 2.4 - - - +
166B GLU 3.1 7.3 + - - -
167B HIS 3.0 5.3 + - - -
169B LEU* 1.3 76.8 - - - +
171B VAL* 1.3 56.5 + - - +
173B TYR* 3.3 4.9 + - - +
174B LEU* 3.0 33.8 + - - +
314B ASP* 3.3 24.0 - - - -
318B ARG* 3.8 4.5 - - - -
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Residues in contact with VAL 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B HIS* 2.9 46.4 + - + +
168B SER 3.2 0.6 + - - +
170B GLY* 1.3 72.8 - - - +
172B GLY* 1.3 61.3 + - - +
174B LEU* 3.4 3.8 + - - -
175B ALA* 2.9 29.8 + - - +
203B GLY* 3.5 21.5 - - - +
206B HIS* 3.6 22.9 - - + +
301B VAL* 4.7 3.6 - - + -
310B VAL* 3.8 18.9 - - + +
311B ASP* 3.8 15.5 - - + +
314B ASP* 3.8 11.7 - - + -
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Residues in contact with GLY 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LEU* 6.5 0.9 - - - -
132B LEU* 6.4 0.9 - - - -
168B SER 3.0 12.0 + - - -
169B LEU 3.7 3.6 - - - -
171B VAL* 1.3 76.6 - - - +
173B TYR* 1.3 61.2 + - - +
175B ALA* 3.6 2.4 - - - +
176B GLY 3.2 17.5 + - - -
200B GLN* 3.7 21.7 - - - +
203B GLY* 3.6 3.0 - - - -
204B LEU* 3.6 28.9 - - - -
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Residues in contact with TYR 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B HIS* 3.6 47.2 + + + -
125B HIS 4.9 4.7 + - - -
126B ILE* 3.7 43.3 - - + -
127B GLU 5.2 3.1 - - - -
128B LEU* 6.1 1.9 - - - +
169B LEU 2.9 14.1 + - - +
170B GLY 3.5 5.8 - - - +
171B VAL 3.3 0.2 - - - -
172B GLY* 1.3 75.7 - - - +
174B LEU* 1.3 70.1 + - + +
176B GLY* 3.3 4.2 + - - -
177B CYS* 2.9 51.9 + - - -
200B GLN* 5.3 4.3 + - - +
331B TYR* 4.3 5.6 + - - -
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B HIS* 3.7 23.3 - - + +
170B GLY 3.0 16.1 + - - +
171B VAL 4.0 1.1 - - - +
173B TYR* 1.3 82.7 - - + +
175B ALA* 1.3 60.3 + - - +
177B CYS* 3.1 7.3 + - + +
178B LEU* 2.9 31.7 + - - +
310B VAL* 3.7 25.4 - - + +
313B TRP* 3.9 14.1 - - + -
314B ASP* 3.7 30.7 - - + +
331B TYR* 3.3 41.3 - - + +
335B ILE* 5.0 1.1 - - + +
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Residues in contact with ALA 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B VAL 2.9 18.1 + - - +
172B GLY 3.6 5.2 - - - +
174B LEU* 1.3 75.5 - - - +
176B GLY* 1.3 63.9 + - - +
179B VAL* 3.1 29.5 + - - +
199B VAL* 3.6 35.7 - - + +
203B GLY* 4.5 0.9 - - - -
300B ILE* 3.7 18.3 - - + +
301B VAL* 4.0 9.4 - - + -
310B VAL* 3.9 3.5 - - + +
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Residues in contact with GLY 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B GLY 3.2 8.7 + - - -
173B TYR 3.6 3.4 - - - -
175B ALA* 1.3 79.7 - - - +
177B CYS* 1.3 54.4 + - - +
179B VAL* 4.1 2.1 - - - +
180B HIS* 2.9 33.9 + - - +
196B VAL* 4.7 9.7 - - - +
200B GLN* 3.6 29.3 - - - +
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Residues in contact with CYS 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B TYR* 2.9 59.7 + - - +
174B LEU* 3.1 14.3 + - + +
176B GLY* 1.3 76.5 - - - +
178B LEU* 1.3 58.4 + - - +
180B HIS* 3.8 4.9 - - - +
181B ALA* 3.0 28.9 + - - +
331B TYR* 5.3 1.8 - - - -
335B ILE* 4.4 14.5 - - + +
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Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LEU 2.9 15.2 + - - +
175B ALA 4.0 2.9 - - - +
177B CYS* 1.3 74.2 - - - +
179B VAL* 1.3 68.1 + - - +
181B ALA* 3.2 3.3 + - + +
182B LEU* 3.0 52.1 + - + +
299B GLU 5.2 1.1 - - - +
300B ILE* 3.8 25.4 - - + -
309B ASP* 6.4 0.9 - - - -
310B VAL* 4.2 12.6 - - + -
313B TRP* 4.1 20.6 - - + -
334B PHE* 5.4 1.8 - - + -
335B ILE* 4.1 31.0 - - + +
338B ALA* 4.4 13.2 - - + -
349B ILE* 4.3 12.3 - - + -
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Residues in contact with VAL 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ALA 3.1 17.6 + - - +
176B GLY* 4.1 4.0 - - - +
178B LEU* 1.3 77.0 - - - +
180B HIS* 1.3 60.3 + - - +
182B LEU* 3.3 8.9 + - - +
183B GLY* 3.1 18.7 + - - -
191B ILE* 3.6 32.5 - - + +
196B VAL* 4.1 16.8 - - + +
199B VAL* 3.4 20.6 - - + -
296B PHE* 5.4 0.4 - - + -
297B LEU* 3.8 15.7 - - + -
300B ILE* 3.2 29.4 - - + -
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Residues in contact with HIS 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B GLY 2.9 19.2 + - - +
177B CYS* 3.8 4.9 - - - +
179B VAL* 1.3 76.9 - - - +
181B ALA* 1.3 63.3 + - - +
183B GLY* 3.3 2.6 + - - -
184B GLU* 3.0 62.9 + - + +
191B ILE* 6.0 0.2 - - - -
196B VAL* 4.9 16.9 - - + +
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Residues in contact with ALA 181 (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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177B CYS 3.0 18.9 + - - +
178B LEU* 3.2 5.4 + - + +
180B HIS* 1.3 77.7 - - - +
182B LEU* 1.3 64.0 + - + +
184B GLU* 3.4 5.5 + - - +
185B LYS* 3.1 27.4 + - - +
335B ILE* 3.7 29.2 - - + +
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Residues in contact with LEU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B LEU* 3.0 35.3 + - + +
179B VAL* 3.8 7.9 - - - +
181B ALA* 1.3 77.1 - - + +
183B GLY* 1.3 57.6 + - - +
185B LYS* 3.4 4.9 + - - +
186B GLN* 2.9 34.0 + - - +
189B LEU* 4.0 1.1 - - - +
191B ILE* 4.2 8.7 - - + -
296B PHE* 4.2 11.9 - - + -
300B ILE* 4.9 2.7 - - + -
335B ILE 5.7 0.9 - - - +
338B ALA* 3.8 39.3 - - + +
339B ARG* 4.0 15.9 - - - +
340B VAL* 4.1 20.0 - - + -
349B ILE* 4.1 21.5 - - + -
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Residues in contact with GLY 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B VAL 3.1 11.9 + - - -
180B HIS* 3.7 3.1 - - - -
182B LEU* 1.3 75.8 - - - +
184B GLU* 1.3 65.7 + - - +
186B GLN 3.4 5.1 - - - +
187B PRO* 3.3 26.0 - - - +
191B ILE* 3.6 26.9 - - - +
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Residues in contact with GLU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B HIS* 3.0 55.6 + - + +
181B ALA* 3.9 5.4 - - - +
183B GLY* 1.3 76.6 - - - +
185B LYS* 1.3 66.0 + - + +
187B PRO* 4.1 9.1 - - - +
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Residues in contact with LYS 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ALA 3.1 17.6 + - - +
182B LEU* 3.9 4.9 - - - +
184B GLU* 1.3 81.8 + - + +
186B GLN* 1.3 71.1 + - + +
187B PRO* 3.6 6.3 - - - +
188B GLU* 4.9 0.2 - - - +
336B LYS 6.1 1.8 - - - +
338B ALA 5.6 7.6 - - - +
339B ARG* 4.5 19.4 + - + +
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Residues in contact with GLN 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LEU* 2.9 14.8 + - - +
183B GLY* 3.4 8.3 - - - +
185B LYS* 1.3 87.1 - - + +
187B PRO* 1.3 66.5 - - - +
188B GLU* 3.0 33.6 + - - +
189B LEU* 3.0 33.0 + - + +
190B GLN 4.6 0.2 + - - -
339B ARG* 3.5 38.1 - - - +
340B VAL* 2.8 51.3 + - - +
527B ASN* 4.2 4.0 + - - -
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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