Contacts of the helix formed by residues 167 - 192 (chain D) in PDB entry 3GV5
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 167 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D ASN* 3.1 27.7 + - + +
166D LEU* 1.3 77.7 - - - +
168D VAL* 1.3 66.7 + - - +
169D LEU* 2.9 29.1 + - - +
170D HIS* 3.1 29.2 + - + +
171D ILE* 3.1 22.4 + - - +
223D PRO* 5.8 0.5 - - - +
224D GLU* 3.8 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 168 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D LEU* 5.7 1.3 - - + -
166D LEU 3.6 4.9 + - - -
167D ASP* 1.3 73.4 + - - +
169D LEU* 1.3 69.7 + - + +
171D ILE* 2.9 19.9 - - + +
172D ARG* 2.7 47.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 169 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D SER* 3.8 31.4 - - - +
167D ASP* 2.9 19.9 + - - +
168D VAL* 1.3 79.3 - - + +
170D HIS* 1.3 67.1 + - - +
172D ARG* 3.5 10.8 + - - +
173D LEU* 3.1 31.7 + - + +
223D PRO* 4.1 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 170 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D GLN* 3.5 12.0 + - - -
162D SER 4.0 3.0 + - - -
163D ILE* 4.0 5.2 - - + -
164D ASN* 3.1 53.9 + - + +
165D LEU* 5.3 0.2 - - - -
167D ASP* 3.1 17.5 + - + +
169D LEU* 1.3 72.1 - - - +
171D ILE* 1.3 67.1 + - - +
173D LEU* 3.2 2.8 + - - +
174D LEU* 2.9 29.8 + - + +
222D LEU* 3.7 27.4 - - + +
223D PRO* 3.8 17.4 - - + +
224D GLU* 2.9 39.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 171 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D LEU* 3.3 25.8 - - + -
148D LEU* 3.5 27.6 - - + -
151D VAL* 3.3 37.7 - - + -
164D ASN 4.8 0.8 + - - -
165D LEU* 4.5 17.9 - - + +
167D ASP 3.1 9.5 + - - +
168D VAL* 2.9 37.7 - - + +
170D HIS* 1.3 78.0 - - - +
172D ARG* 1.3 70.2 + - + +
174D LEU* 3.4 3.7 + - - +
175D VAL* 3.1 22.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 172 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D SER* 3.4 41.2 + - - -
28D ARG 5.8 0.4 + - - -
29D VAL* 3.6 19.6 - - + +
133D THR* 4.2 6.9 - - - +
136D VAL* 3.7 20.4 - - + +
137D GLU* 3.8 23.6 + - - +
140D LEU* 3.1 33.4 - - - +
168D VAL* 2.7 33.4 + - - +
169D LEU* 3.9 15.4 - - - +
170D HIS 3.3 0.2 - - - -
171D ILE* 1.3 76.9 - - - +
173D LEU* 1.3 58.3 + - + +
175D VAL 3.4 0.3 + - - -
176D GLY* 2.9 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 173 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D ARG 4.7 1.1 - - - +
29D VAL* 4.3 14.6 - - + -
169D LEU* 3.1 21.1 + - + +
170D HIS 3.2 4.0 + - - +
172D ARG* 1.3 78.9 - - + +
174D LEU* 1.3 57.9 + - - +
176D GLY* 3.2 2.5 + - - +
177D SER* 3.0 22.0 + - - -
199D VAL* 3.7 16.7 - - + +
200D ALA* 3.8 36.6 - - - +
201D SER* 4.2 9.6 - - - +
220D VAL* 3.8 18.4 - - + +
221D LEU 3.5 19.5 - - - +
222D LEU* 4.1 8.1 - - + -
223D PRO* 4.0 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 174 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D VAL* 3.9 25.4 - - + +
152D THR* 4.2 4.8 - - - +
153D VAL* 3.1 45.5 - - + +
157D VAL* 5.1 0.2 - - + -
163D ILE* 3.6 33.9 - - + -
165D LEU* 4.0 8.5 - - + -
170D HIS* 2.9 21.5 + - - +
171D ILE 3.8 4.0 - - - +
173D LEU* 1.3 76.3 - - - +
175D VAL* 1.3 63.8 + - - +
177D SER* 2.7 23.0 + - - -
178D GLN* 3.2 11.7 + - - +
220D VAL* 4.4 9.6 - - + -
222D LEU* 4.6 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 175 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D VAL* 4.2 21.1 - - + +
139D ARG* 4.1 33.0 - - + +
140D LEU* 3.8 20.9 - - + -
143D LEU* 5.3 3.1 - - + -
151D VAL* 4.6 8.7 - - + -
171D ILE* 3.1 25.4 + - + +
172D ARG 3.9 3.4 - - - +
174D LEU* 1.3 73.0 - - - +
176D GLY* 1.3 65.7 + - - +
178D GLN* 3.1 24.1 + - - +
179D ILE* 3.0 21.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 176 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D VAL* 3.8 20.4 - - - -
132D LEU* 3.8 9.0 - - - +
136D VAL* 3.9 8.1 - - - +
172D ARG 2.9 15.7 + - - -
173D LEU 3.5 5.4 - - - -
174D LEU 3.2 0.4 - - - -
175D VAL* 1.3 76.5 - - - +
177D SER* 1.3 55.8 + - - +
179D ILE* 3.1 5.1 + - - +
180D ALA* 2.9 27.9 + - - +
199D VAL* 4.0 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 177 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D VAL* 3.8 10.8 - - - +
154D SER* 2.9 38.9 + - - -
173D LEU 3.0 12.6 + - - -
174D LEU* 2.7 20.1 + - - -
176D GLY* 1.3 75.8 - - - +
178D GLN* 1.3 61.1 + - - +
180D ALA 3.3 0.3 + - - -
181D ALA* 3.0 21.5 + - - +
199D VAL* 4.0 9.8 - - - +
218D GLN* 3.0 14.0 - - - +
219D THR 6.1 0.4 - - - -
220D VAL* 4.4 13.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 178 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D ARG* 4.3 12.6 - - - +
151D VAL* 4.3 10.1 - - - +
152D THR* 3.2 38.1 + - + +
154D SER* 4.2 12.6 - - - -
174D LEU 3.5 12.1 - - - +
175D VAL* 3.1 28.9 + - - +
177D SER* 1.3 82.5 + - - +
179D ILE* 1.3 62.2 + - - +
181D ALA* 3.4 3.9 + - - +
182D GLU* 3.2 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 179 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D PHE* 4.4 4.7 - - + -
132D LEU* 3.9 24.7 - - + -
135D MSE 3.8 42.8 - - + -
136D VAL* 3.9 31.6 - - + +
139D ARG* 3.6 32.1 - - - +
175D VAL* 3.0 14.9 + - + +
176D GLY 3.6 5.8 - - - +
178D GLN* 1.3 72.6 - - - +
180D ALA* 1.3 65.3 + - - +
182D GLU* 3.0 9.3 + - - +
183D MSE 3.0 28.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 180 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D VAL* 3.8 27.1 - - + -
33D VAL* 6.2 0.4 - - - +
132D LEU* 4.8 0.6 - - - +
176D GLY 2.9 18.5 + - - +
177D SER 3.7 4.7 - - - +
179D ILE* 1.3 73.0 - - - +
181D ALA* 1.3 56.6 + - - +
183D MSE 3.1 16.3 + - - +
184D ARG* 2.9 31.5 + - - +
197D ALA* 4.0 11.2 - - + -
199D VAL* 3.9 10.1 - - + -
218D GLN* 3.8 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 181 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D SER* 3.1 28.9 - - - +
177D SER 3.0 9.4 + - - +
178D GLN* 3.5 10.1 - - - +
179D ILE 3.1 0.2 - - - -
180D ALA* 1.3 77.8 - - - +
182D GLU* 1.3 56.9 + - - +
184D ARG* 3.5 5.2 + - - +
185D GLU* 3.0 40.2 + - + +
218D GLN* 3.3 14.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 182 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D PHE* 3.7 21.1 - - + -
139D ARG* 2.8 42.1 + - - -
178D GLN* 3.2 13.0 + - - +
179D ILE* 3.0 10.5 + - - +
181D ALA* 1.3 72.8 - - + +
183D MSE 1.3 60.1 + - - +
185D GLU* 3.5 20.9 - - - +
186D ALA* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 183 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D VAL* 4.0 22.2 - - - -
33D VAL* 4.6 8.3 - - + -
112D LEU* 4.3 0.3 - - - +
113D LEU* 4.2 23.3 - - + +
116D PHE* 3.4 54.1 - - + -
130D VAL* 3.9 20.0 - - + -
132D LEU* 3.7 24.5 - - + -
179D ILE* 3.0 16.8 + - + +
180D ALA* 3.1 17.0 + - - +
182D GLU* 1.3 74.3 - - - +
184D ARG* 1.3 60.8 + - + +
186D ALA* 3.2 3.5 + - - +
187D MSE 2.9 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 184 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D VAL* 5.4 4.3 - - + -
180D ALA 2.9 14.7 + - - +
181D ALA* 3.8 7.0 + - - +
183D MSE 1.3 77.3 - - + +
185D GLU* 1.3 61.9 + - - +
187D MSE 3.4 15.4 + - - +
188D TYR* 3.0 24.1 + - - +
193D LEU 4.5 1.2 - - - +
195D GLY* 2.9 23.1 + - - +
196D CYS 5.1 0.9 - - - +
197D ALA* 3.9 23.1 - - + +
216D ASN* 2.8 52.1 + - - +
217D GLN* 3.3 10.2 + - - +
218D GLN* 2.9 38.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 185 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D ALA* 3.0 35.7 + - + +
182D GLU* 3.5 20.7 + - - +
183D MSE 3.3 0.2 - - - -
184D ARG* 1.3 76.9 - - - +
186D ALA* 1.3 57.5 + - - +
188D TYR* 3.4 5.2 + - - +
189D ASN* 2.8 44.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 186 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D LEU* 4.0 14.6 - - + -
116D PHE* 4.2 12.3 - - + -
182D GLU 3.0 18.2 + - - +
183D MSE 3.7 4.0 - - - +
185D GLU* 1.3 72.3 - - - +
187D MSE 1.3 60.1 + - - +
189D ASN* 4.4 6.5 - - - +
190D GLN* 2.8 55.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 187 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D VAL* 3.6 26.2 - - - -
35D LEU* 3.0 44.0 - - + -
109D VAL* 4.2 19.7 - - + -
112D LEU* 3.8 24.9 - - + -
113D LEU* 4.4 8.3 - - + -
183D MSE 2.9 23.2 + - - +
184D ARG* 3.7 13.5 - - + +
186D ALA* 1.3 76.4 - - - +
188D TYR* 1.3 56.3 + - - +
191D LEU* 2.9 36.2 + - + +
192D GLY 3.3 2.1 + - - -
193D LEU* 3.4 16.7 + - + +
194D THR 5.0 2.5 - - - -
195D GLY* 5.1 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 188 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D ARG 3.0 17.2 + - - +
185D GLU* 3.6 5.6 - - - +
187D MSE 1.3 76.1 - - - +
189D ASN* 1.3 70.7 + - - +
192D GLY* 2.8 39.6 + - - -
193D LEU 3.2 18.7 + - - +
194D THR* 3.7 24.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 189 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D GLU* 2.8 34.7 + - - +
186D ALA* 3.9 6.7 - - - +
188D TYR* 1.3 86.1 - - - +
190D GLN* 1.3 65.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 190 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D LEU* 3.7 25.9 - - + +
115D GLU* 4.4 11.4 + - - +
186D ALA* 2.8 33.9 + - - +
189D ASN* 1.3 83.7 - - + +
191D LEU* 1.3 69.4 + - + +
192D GLY 3.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 191 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D ILE* 3.8 7.8 - - - +
105D MSE 3.5 27.6 - - + +
108D LYS* 4.0 26.5 - - + +
109D VAL* 4.0 37.9 - - + +
112D LEU* 3.8 24.9 - - + -
187D MSE 2.9 16.2 + - + +
190D GLN* 1.3 88.6 - - + +
192D GLY* 1.3 60.0 + - - +
193D LEU* 3.1 18.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 192 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D GLN* 3.9 4.2 - - - +
45D ILE* 3.5 19.7 - - - +
51D LYS* 5.4 3.5 + - - -
188D TYR* 2.8 36.8 + - - -
190D GLN 3.8 0.6 - - - -
191D LEU* 1.3 78.5 - - - +
193D LEU* 1.3 59.7 + - - +
194D THR* 4.0 0.5 + - - -
----------------------------------------------------------
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