Contacts of the helix formed by residues 170 - 192 (chain U) in PDB entry 3A68
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 TYR 170 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56U GLU* 4.3 5.6 - - - -
94U HIS* 2.7 55.2 + + + -
97U LYS* 3.4 21.8 - - + +
98U LEU* 3.2 24.5 + - + +
147U LEU* 3.8 33.7 - - + +
150U LEU* 6.3 0.2 - - + -
165U PHE* 3.7 31.6 - + - -
166U VAL* 3.0 20.5 + - + +
168U THR 3.5 0.4 - - - -
169U GLU* 1.3 92.9 - - + +
171U LEU* 1.3 61.4 + - - +
172U GLY 3.5 2.0 - - - -
173U GLU* 3.4 6.2 + - - +
174U GLN* 2.9 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 171 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160P VAL* 3.6 31.9 - - + -
161P GLN* 3.7 19.1 - - + +
164P ASP* 5.9 0.9 - - + +
144U ASN* 4.3 9.6 - - - +
147U LEU* 3.8 30.5 - - + -
148U LEU* 3.8 23.3 - - + -
151U HIS* 4.2 7.6 - - + -
166U VAL* 3.0 23.2 + - + +
167U GLU* 3.5 22.3 + - + +
170U TYR* 1.3 75.5 - - - +
172U GLY* 1.3 63.7 + - - +
174U GLN* 3.3 4.6 + - - +
175U VAL* 3.2 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 172 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161P GLN* 3.7 22.7 - - - +
167U GLU 3.8 5.9 + - - -
170U TYR 3.5 0.2 - - - -
171U LEU* 1.3 74.1 - - - +
173U GLU* 1.3 71.8 + - - +
175U VAL* 3.2 5.4 + - - +
176U GLU* 3.0 30.1 + - - +
214U CA 4.7 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 173 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94U HIS* 5.9 9.4 - - + +
168U THR 3.5 3.3 - - - +
169U GLU* 3.3 31.4 - - - +
170U TYR* 3.6 7.5 + - - +
172U GLY* 1.3 76.1 + - - +
174U GLN* 1.3 57.7 + - - +
176U GLU* 3.3 14.7 + - - +
177U ALA* 2.9 29.0 + - - +
214U CA 2.7 28.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 174 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94U HIS* 5.6 2.9 - - - -
140U GLU* 2.7 56.0 + - - +
143U THR* 3.8 12.1 - - - +
144U ASN* 3.5 34.8 - - + +
147U LEU* 3.9 18.3 - - + +
170U TYR* 2.9 18.3 + - - +
171U LEU* 3.6 5.4 - - - +
172U GLY 3.2 0.2 - - - -
173U GLU* 1.3 75.3 - - - +
175U VAL* 1.3 65.8 + - - +
177U ALA* 3.3 5.0 + - - +
178U ILE* 3.0 29.7 + - + +
213U CA 4.2 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 175 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101P TYR* 5.1 2.2 - - + -
104P LYS* 3.8 39.1 - - + +
105P ARG* 3.8 23.1 - - - +
161P GLN* 3.8 27.1 - - + +
144U ASN* 5.2 11.9 - - - +
171U LEU 3.2 12.4 + - - +
172U GLY* 3.2 9.4 + - - +
174U GLN* 1.3 77.8 - - - +
176U GLU* 1.3 62.4 + - + +
178U ILE* 3.3 8.7 + - + +
179U LYS* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 176 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104P LYS* 3.0 39.6 + - + +
172U GLY 3.0 19.2 + - - +
173U GLU* 3.7 16.4 - - - +
175U VAL* 1.3 79.0 - - + +
177U ALA* 1.3 57.8 + - - +
179U LYS* 3.3 7.0 + - - +
180U ARG* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 177 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140U GLU* 4.0 24.0 - - + +
173U GLU 2.9 16.7 + - - +
174U GLN* 3.7 7.6 - - - +
176U GLU* 1.3 76.3 - - - +
178U ILE* 1.3 62.6 + - - +
180U ARG* 3.3 9.7 + - - +
181U ILE* 3.0 32.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 178 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P ALA* 3.6 34.3 - - + +
39P GLN* 3.5 25.6 - - + +
104P LYS 5.7 0.4 - - - +
137U LEU* 3.8 16.3 - - + +
140U GLU* 3.9 35.0 - - + +
141U LYS* 4.1 7.4 - - + +
144U ASN* 3.9 14.1 - - + +
174U GLN* 3.0 22.4 + - + +
175U VAL* 3.7 7.6 - - + +
176U GLU 3.2 0.2 - - - -
177U ALA* 1.3 77.8 - - - +
179U LYS* 1.3 60.5 + - - +
181U ILE 3.5 0.2 + - - -
182U SER* 2.8 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 179 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P ALA* 4.2 4.4 - - + +
100P GLU 5.4 0.4 + - - -
103P ASN* 3.8 22.6 - - - +
104P LYS* 4.0 27.3 - - + +
71T ASP* 2.9 47.9 + - - -
73T ASP* 4.0 19.5 - - + +
175U VAL 3.1 13.5 + - - +
176U GLU* 3.3 8.9 + - - +
178U ILE* 1.3 75.6 - - - +
180U ARG* 1.3 64.4 + - - +
182U SER* 3.2 5.6 + - - -
183U GLU* 2.9 53.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 180 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83U PHE* 3.6 29.8 - - - -
86U GLU* 5.8 1.8 + - - -
87U SER* 5.5 0.8 + - - -
176U GLU 2.9 17.2 + - - +
177U ALA* 3.5 10.3 - - - +
179U LYS* 1.3 77.2 - - - +
181U ILE* 1.3 63.2 + - - +
183U GLU* 3.3 16.9 + - - +
184U TYR* 2.8 57.6 + - + +
204U LEU* 5.2 1.2 - - - +
207U GLU* 4.2 6.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 181 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63U TYR* 3.9 10.8 - - - +
83U PHE* 4.3 24.2 - - + -
133U MET* 3.5 35.4 - - + +
136U ALA* 4.1 9.2 - - + +
137U LEU* 3.6 19.3 - - + +
140U GLU* 3.5 34.1 - - + +
177U ALA* 3.0 16.7 + - + +
178U ILE* 4.1 2.2 - - - +
180U ARG* 1.3 76.9 - - + +
182U SER* 1.3 66.2 + - - +
184U TYR* 3.0 9.4 + - + +
185U VAL* 2.9 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 182 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36P LEU* 3.5 9.2 - - - +
37P ALA* 3.3 21.3 + - - -
73T ASP* 3.6 28.0 - - - -
137U LEU* 3.4 18.6 - - - +
178U ILE 2.8 23.7 + - - -
179U LYS 3.5 4.9 - - - -
181U ILE* 1.3 76.6 - - - +
183U GLU* 1.3 57.4 + - - +
185U VAL* 3.2 5.2 + - - +
186U ALA* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 183 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71T ASP* 4.6 3.1 - - - +
72T ARG 5.2 0.5 - - - +
73T ASP* 3.7 24.7 - - + +
76T ALA* 4.1 10.9 - - + -
78T ARG* 4.6 21.2 - - - +
179U LYS* 2.9 50.5 + - - +
180U ARG* 3.4 16.1 - - - +
181U ILE 3.2 0.2 - - - -
182U SER* 1.3 77.4 - - - +
184U TYR* 1.3 57.5 + - + +
186U ALA* 3.3 2.4 + - - +
187U GLN* 2.9 46.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 184 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78T ARG* 6.0 0.4 - - - -
83U PHE* 3.7 25.1 - + - -
133U MET* 3.5 35.0 - - + -
180U ARG* 2.8 47.0 + - + +
181U ILE* 3.0 11.7 + - - +
183U GLU* 1.3 74.5 - - + +
185U VAL* 1.3 67.2 + - - +
187U GLN* 3.3 15.9 + - - +
188U LEU* 2.9 28.9 + - - +
200U PHE* 3.7 22.1 - + + -
203U MET* 4.8 0.9 - - + -
204U LEU* 3.4 20.4 - - + +
207U GLU* 2.7 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 185 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28P VAL* 5.4 0.2 - - + -
36P LEU* 3.9 13.0 - - + -
130U LEU* 3.9 13.2 - - + +
133U MET* 3.7 35.7 - - + +
134U GLU* 4.0 12.3 - - + +
137U LEU* 4.4 12.1 - - + -
181U ILE 2.9 18.5 + - - +
182U SER* 3.5 6.7 - - - +
184U TYR* 1.3 76.3 - - - +
186U ALA* 1.3 63.9 + - - +
188U LEU* 3.3 3.4 + - - +
189U ARG* 3.0 52.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 186 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36P LEU* 4.1 7.6 - - + +
73T ASP 3.4 26.5 - - - +
74T ASN* 3.8 20.2 - - - +
75T VAL 4.7 2.0 - - - +
76T ALA* 3.8 7.9 - - + -
182U SER 2.9 8.2 + - - +
183U GLU 3.6 6.5 - - - +
185U VAL* 1.3 77.2 - - - +
187U GLN* 1.3 62.2 + - - +
189U ARG* 3.3 9.7 + - - +
190U ARG* 3.0 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 187 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76T ALA* 3.9 19.9 - - + +
78T ARG* 2.9 38.7 + - - +
198T TRP* 2.9 34.9 + - + +
183U GLU* 2.9 35.0 + - - +
184U TYR* 3.7 20.2 - - - +
185U VAL 3.2 0.2 - - - -
186U ALA* 1.3 75.4 - - - +
188U LEU* 1.3 58.9 + - - +
190U ARG* 3.1 8.3 + - - +
191U VAL* 3.0 35.0 + - - +
200U PHE* 3.8 12.3 - - + -
203U MET* 3.7 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 188 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80U LEU* 5.5 0.2 - - + -
129U ALA* 3.8 44.2 - - + +
130U LEU* 4.0 17.7 - - + +
133U MET* 3.9 19.7 - - + -
184U TYR 2.9 19.5 + - - +
185U VAL 3.7 3.8 - - - +
187U GLN* 1.3 77.6 - - - +
189U ARG* 1.3 61.2 + - - +
191U VAL* 3.6 4.5 - - + +
192U GLY* 3.3 22.2 + - - -
197U VAL* 4.0 21.6 - - + +
200U PHE* 3.6 43.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 189 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28P VAL* 3.9 13.7 + - - +
29P PRO 3.0 29.6 + - - -
30P THR* 4.2 15.9 + - - +
31P VAL 5.6 2.0 + - - -
32P PRO* 6.3 0.6 - - - +
36P LEU* 3.5 15.3 - - - +
130U LEU* 3.9 20.1 - - + +
134U GLU* 2.8 32.1 + - - -
185U VAL* 3.0 29.0 + - - +
186U ALA* 3.6 11.0 - - - +
188U LEU* 1.3 78.0 - - - +
190U ARG* 1.3 63.0 + - - +
192U GLY* 3.9 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 190 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74T ASN 5.0 1.4 + - - -
75T VAL* 3.1 28.5 + - - +
76T ALA 5.3 0.6 + - - -
77T LEU* 3.6 26.9 - - - +
128T ASP* 3.3 36.4 + - - -
194T GLY* 3.3 45.4 - - - +
197T VAL* 3.9 11.1 - - - +
198T TRP* 4.1 18.8 - - + +
186U ALA 3.0 14.0 + - - +
187U GLN* 3.1 11.2 + - - +
189U ARG* 1.3 80.0 - - - +
191U VAL* 1.3 63.1 + - + +
192U GLY 3.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 191 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195T HIS* 3.7 26.6 + - + +
198T TRP* 3.5 49.8 - - + -
187U GLN 3.0 18.1 + - - +
188U LEU* 3.6 12.8 - - - +
190U ARG* 1.3 77.0 - - - +
192U GLY* 1.3 66.6 + - - +
193U LYS 4.9 0.5 - - - +
196U GLY* 3.4 38.2 + - - +
197U VAL* 3.8 5.2 - - - +
200U PHE* 4.4 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 192 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188U LEU 3.3 10.1 + - - -
189U ARG 3.9 5.3 + - - -
190U ARG 3.4 3.4 - - - -
191U VAL* 1.3 82.2 - - - +
193U LYS* 1.3 68.2 + - - +
196U GLY* 3.6 0.2 - - - -
197U VAL* 3.1 27.1 + - - +
----------------------------------------------------------
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