Contacts of the helix formed by residues 155 - 181 (chain B) in PDB entry 3DGR
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 SER 155 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 4.0 5.0 - - - -
59B PHE* 5.6 0.7 - - - -
60B TYR 5.0 0.2 - - - -
61B GLY 4.9 0.2 - - - -
62B LEU* 4.7 17.5 - - - -
65B ILE* 3.8 17.0 - - - +
132B PHE* 3.7 20.6 - - - -
152B LEU 2.9 20.7 + - - -
153B VAL 2.8 1.4 + - - -
154B GLN* 1.3 72.0 - - - +
156B TRP* 1.3 66.5 + - - +
157B TYR 3.0 3.3 + - - -
158B PRO* 3.2 11.9 - - - +
159B ILE* 3.1 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ARG 3.2 22.6 + - - -
197A GLY 3.3 22.8 - - - -
198A VAL 2.9 29.2 + - - -
199A SER 4.2 0.2 - - - -
388A GLN* 3.8 11.9 - - - -
37B PHE* 4.3 4.6 - - - -
153B VAL 2.8 20.7 + - - +
154B GLN* 3.8 4.7 - - - -
155B SER* 1.3 77.8 + - - +
157B TYR* 1.3 78.2 + + + +
159B ILE* 3.5 2.5 - - - +
160B THR* 2.6 56.3 + - - -
390B LEU* 3.5 21.1 - - + -
391B THR* 3.3 31.6 - - - -
392B ARG* 3.7 17.7 - - + -
397B CYS* 3.6 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A SER* 3.5 35.4 - - - +
388A GLN* 4.8 4.3 - - - -
154B GLN 3.2 7.6 + - - +
155B SER 3.0 3.0 + - - -
156B TRP* 1.3 109.9 - + + +
158B PRO* 1.3 66.1 - - + +
160B THR* 3.3 0.9 + - - -
161B VAL* 2.9 50.9 + - + +
203B THR* 3.4 28.4 + - + +
206B ILE* 3.8 10.3 - - + -
207B GLY* 3.6 26.9 - - - -
387B LEU* 2.6 42.2 + - - +
390B LEU* 4.8 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A SER 5.3 0.4 - - - +
60B TYR* 3.5 35.4 - - + +
61B GLY* 3.9 13.9 - - - +
64B TYR* 6.3 1.3 - - + -
65B ILE* 5.7 1.1 - - + -
154B GLN 3.4 9.2 - - - +
155B SER* 3.2 17.0 - - - +
157B TYR* 1.3 96.7 - - + +
159B ILE* 1.3 62.5 + - - +
161B VAL* 4.6 0.2 - - + -
162B ALA* 3.1 26.0 + - - +
206B ILE* 3.9 23.3 - - + -
210B ALA* 3.6 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 3.7 29.8 - - + -
39B CYS* 4.2 13.7 - - - -
57B THR* 4.2 5.8 - - - +
58B VAL 3.6 17.8 - - - +
59B PHE* 4.0 20.9 - - + -
60B TYR 3.6 23.8 + - - +
131B LEU* 4.7 1.8 - - + -
155B SER* 3.1 34.3 + - - +
156B TRP* 3.5 3.4 - - - +
158B PRO* 1.3 75.1 - - - +
160B THR* 1.3 56.8 + - - +
162B ALA* 3.8 0.2 - - - +
163B THR* 2.7 38.7 + - - +
395B LEU* 3.9 18.6 - - + -
397B CYS* 5.0 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B TRP* 2.6 42.0 + - + -
157B TYR 3.9 2.7 - - - -
159B ILE* 1.3 70.8 - - - +
161B VAL* 1.3 60.0 + - - +
163B THR* 3.8 0.9 - - - -
164B ASN* 2.9 33.4 + - - +
390B LEU* 4.2 15.5 - - + -
391B THR 4.2 13.4 + - - +
394B LEU* 3.7 31.0 - - + -
395B LEU* 3.5 24.4 - - + +
397B CYS* 4.1 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B TYR* 2.9 56.8 + - + +
160B THR* 1.3 75.1 - - - +
162B ALA* 1.3 58.4 + - - +
164B ASN* 4.0 1.0 - - - +
165B SER* 2.9 30.9 + - - -
207B GLY* 3.5 24.0 - - - +
210B ALA* 3.7 12.6 - - + -
211B HIS* 3.9 9.6 - - + +
386B LEU* 4.0 9.2 - - + +
387B LEU* 3.6 13.9 - - + -
390B LEU* 3.6 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B VAL* 3.9 26.2 - - + +
60B TYR* 4.3 10.5 - - + -
158B PRO 3.1 20.1 + - - +
159B ILE 3.8 3.4 - - - +
161B VAL* 1.3 77.2 - - - +
163B THR* 1.3 58.3 + - - +
166B ARG* 3.0 15.1 + - - +
210B ALA* 3.8 22.9 - - + +
213B VAL* 4.7 2.2 - - + -
214B ASN* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B TYR* 4.0 21.3 - - + -
56B GLU 3.4 24.7 - - - +
57B THR* 3.4 9.0 - - - -
58B VAL* 2.8 30.0 + - + +
159B ILE 2.7 21.6 + - - -
160B THR 3.8 2.7 - - - -
162B ALA* 1.3 75.8 - - - +
164B ASN* 1.3 54.2 + - - +
166B ARG* 3.2 2.9 + - - +
167B GLU* 2.8 38.0 + - + +
395B LEU* 4.0 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B TYR* 2.6 40.1 + - + -
160B THR 2.9 17.5 + - - +
161B VAL* 4.0 2.9 - - - +
163B THR* 1.3 76.0 - - - +
165B SER* 1.3 62.2 + - - +
167B GLU* 3.3 2.4 + - - +
168B GLN* 3.1 47.0 + - - +
358B ILE* 3.8 15.8 - - - +
385B GLY 4.0 12.9 + - - -
386B LEU* 4.7 5.9 + - - +
390B LEU* 3.9 27.4 - - + +
394B LEU* 4.9 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B VAL 2.9 19.3 + - - -
162B ALA 4.3 0.2 - - - -
164B ASN* 1.3 74.2 - - - +
166B ARG* 1.3 59.3 + - - +
168B GLN* 3.2 15.6 + - - +
169B LYS 3.0 22.5 + - - -
211B HIS* 2.8 36.5 + - - -
214B ASN* 3.2 19.4 + - - +
215B PHE* 3.4 15.6 - - - -
386B LEU* 4.5 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLU* 2.8 31.5 + - - +
58B VAL* 3.5 22.9 - - + +
124B VAL* 3.5 24.9 - - - +
162B ALA 3.0 19.4 + - - +
163B THR* 3.2 4.9 + - - +
165B SER* 1.3 70.9 - - - +
167B GLU* 1.3 67.9 + - - +
169B LYS* 3.2 6.8 + - + +
170B LYS* 3.0 35.7 + - + +
214B ASN* 3.4 19.2 - - - +
480B ALA 2.7 22.4 + - - +
481B GLN 3.0 22.6 + - - -
482B LEU* 3.7 25.4 - - + +
483B ASN* 4.7 6.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B TYR* 3.8 31.2 - - + -
55B GLU 5.5 1.8 + - - -
56B GLU* 4.5 10.9 - - - +
163B THR* 2.8 24.7 + - + +
164B ASN 3.6 2.7 - - - +
165B SER 3.3 0.2 - - - -
166B ARG* 1.3 74.7 + - - +
168B GLN* 1.3 62.5 + - - +
170B LYS* 2.8 45.9 + - - +
171B ILE* 3.3 24.6 + - - +
358B ILE* 3.6 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ASN* 3.1 42.1 + - - +
165B SER 3.2 6.3 + - - +
167B GLU* 1.3 73.8 - - - +
169B LYS* 1.3 58.9 + - - +
171B ILE* 3.4 10.1 + - - +
172B LEU* 2.9 33.8 + - - +
190B LEU* 3.7 23.0 - - + +
356B VAL* 4.7 2.4 - - - +
357B ASP* 3.8 6.6 - - - -
358B ILE* 3.6 35.8 + - + -
361B LEU* 3.5 24.4 - - + +
382B SER* 5.0 2.1 + - - -
385B GLY 5.4 0.8 + - - -
386B LEU* 3.6 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B SER 3.0 7.3 + - - +
166B ARG* 3.2 11.2 + - - +
168B GLN* 1.3 72.7 - - - +
170B LYS* 1.3 56.1 + - - +
172B LEU* 3.8 3.8 - - - +
173B ALA* 2.8 33.3 + - - +
186B LEU* 3.9 26.9 - - + +
187B GLU* 5.3 7.3 - - - +
213B VAL 5.2 1.0 + - - -
214B ASN* 2.9 43.7 + - + +
215B PHE* 3.4 29.7 - - + -
480B ALA 5.7 1.2 + - - -
481B GLN* 5.4 6.1 - - - +
482B LEU* 3.8 29.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLU* 2.7 33.4 + - - +
166B ARG* 3.0 28.3 + - - +
167B GLU* 2.8 44.0 + - - +
168B GLN 3.2 0.2 - - - -
169B LYS* 1.3 74.4 - - - +
171B ILE* 1.3 62.9 + - + +
173B ALA* 3.3 3.7 + - - +
174B LYS* 3.0 23.3 + - - +
482B LEU* 3.9 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLU 3.3 12.0 + - - +
168B GLN* 3.4 7.8 + - - +
170B LYS* 1.3 73.6 - - + +
172B LEU* 1.3 66.3 + - - +
174B LYS* 3.3 7.4 + - + +
175B TYR* 3.2 32.0 + - + -
358B ILE* 3.8 33.9 - - + +
361B LEU* 3.6 21.3 - - + -
362B GLN* 3.5 41.1 - - + +
365B VAL* 3.8 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B GLN 2.9 20.4 + - - +
169B LYS 3.8 0.7 - - - +
171B ILE* 1.3 76.2 - - - +
173B ALA* 1.3 57.4 + - - +
175B TYR* 3.4 3.1 + - - +
176B LEU* 2.9 33.2 + - + +
186B LEU* 3.7 15.5 - - + -
189B LYS* 3.7 28.5 - - + +
190B LEU* 4.0 13.2 - - + -
215B PHE* 4.0 21.1 - - + -
361B LEU* 3.9 20.2 - - + -
365B VAL* 4.3 7.9 - - + -
375B ILE* 4.7 10.4 - - + +
380B PHE* 3.7 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B LYS 2.8 21.8 + - - +
170B LYS* 3.6 4.5 - - - +
172B LEU* 1.3 71.1 - - - +
174B LYS* 1.3 66.8 + - - +
176B LEU* 4.6 0.7 - - - -
177B LEU* 3.0 28.7 + - - +
183B LEU* 3.5 19.4 - - + +
186B LEU* 3.8 21.5 - - + +
482B LEU* 4.0 12.8 - - + -
484B ILE* 6.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LYS 3.0 12.4 + - - +
171B ILE* 3.5 11.0 - - + +
173B ALA* 1.3 75.5 - - - +
175B TYR* 1.3 83.6 + - + +
177B LEU* 3.8 5.7 - - - +
178B GLU* 2.7 63.8 + - - +
362B GLN* 5.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ILE* 3.2 19.7 + - + +
172B LEU 4.2 1.6 - - - +
174B LYS* 1.3 103.0 + - + +
176B LEU* 1.3 62.9 + - - +
178B GLU* 3.9 9.0 - - - -
179B THR* 2.8 34.3 + - - +
362B GLN* 3.0 32.6 + - - -
365B VAL* 3.7 33.2 - - + -
366B GLU* 3.0 40.8 + - + +
369B LYS* 4.1 22.9 - - + -
375B ILE* 3.6 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B LEU* 2.9 19.7 + - + +
173B ALA* 4.0 3.1 - - - +
175B TYR* 1.3 77.1 - - - +
177B LEU* 1.3 57.7 + - - +
179B THR* 4.0 1.8 - - - -
180B SER* 2.7 47.4 + - - +
182B ASN* 3.5 9.4 - - - +
183B LEU* 3.9 18.8 - - + +
184B ASP 3.5 23.6 - - - +
186B LEU* 4.2 15.5 - - + +
189B LYS* 4.0 20.9 - - + -
375B ILE* 3.8 12.7 - - + +
376B GLU* 3.7 34.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ALA 3.0 19.6 + - - +
174B LYS* 3.8 4.7 - - - +
176B LEU* 1.3 74.4 - - - +
178B GLU* 1.3 62.3 + - - +
181B GLY* 2.8 34.2 + - - +
182B ASN* 3.7 28.8 + - - +
183B LEU* 3.9 17.7 - - + -
339B LYS* 4.8 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LYS* 2.7 53.7 + - - +
175B TYR* 3.9 13.8 - - - +
177B LEU* 1.3 77.2 - - - +
179B THR* 1.3 63.2 + - + +
339B LYS* 4.0 11.3 - - - +
341B TYR* 3.9 13.0 + - - +
369B LYS* 2.7 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B TYR* 2.8 26.4 + - - +
176B LEU* 3.7 2.1 + - - -
178B GLU* 1.3 79.0 - - + +
180B SER* 1.3 58.1 + - - +
337B ASN* 2.9 21.0 + - - +
339B LYS* 3.7 3.0 - - - +
341B TYR* 3.4 42.5 - - + +
369B LYS* 4.2 21.3 - - + -
373B TRP 4.1 7.9 - - - +
374B SER* 3.6 7.3 + - - -
375B ILE* 2.9 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B LEU* 2.7 25.5 + - - +
179B THR* 1.3 77.5 - - - +
181B GLY* 1.3 62.1 + - - +
182B ASN* 3.2 32.5 + - - -
337B ASN* 3.8 7.7 + - - +
338B SER* 4.5 8.5 + - - -
339B LYS* 3.9 8.7 - - - +
374B SER* 4.0 1.3 - - - -
376B GLU* 3.4 36.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LEU* 2.8 28.2 + - - +
180B SER* 1.3 76.5 + - - +
182B ASN* 1.3 62.5 + - - +
339B LYS* 3.9 23.5 - - - +
----------------------------------------------------------
Back to top of page
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