Contacts of the helix formed by residues 158 - 173 (chain D) in PDB entry 3GTU
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 PHE 158 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU* 4.3 11.9 - - + -
77D ASN* 5.1 0.7 - - + -
80D LEU* 4.2 20.9 - - + +
81D ARG* 3.5 35.4 - - + -
84D ALA* 3.7 24.5 - - + -
89D MET* 3.1 18.6 + - - +
90D CYS* 3.5 20.4 - - + -
100D VAL* 3.6 27.8 - - + -
104D GLU* 3.5 17.5 - - - -
157D THR* 1.3 74.2 - - - +
159D VAL* 1.3 75.0 + - + +
160D ASP 3.1 0.2 - - - -
161D PHE* 3.1 26.4 + - - +
162D LEU* 3.3 25.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 159 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D ARG 5.7 0.2 - - - -
100D VAL* 3.2 50.5 - - + +
103D ILE* 3.6 17.5 - - + -
104D GLU* 3.9 13.5 - - - +
151D PHE* 4.5 12.8 - - + -
152D ALA* 4.7 2.5 - - + +
157D THR* 3.0 24.3 + - - +
158D PHE* 1.3 88.8 - - + +
160D ASP* 1.3 60.4 + - - +
162D LEU* 3.2 9.5 + - + +
163D THR* 2.8 34.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 160 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D TRP* 3.4 23.7 - - + +
151D PHE* 3.0 29.5 + - - -
152D ALA 4.5 0.3 + - - -
155D LYS 3.8 0.3 - - - +
156D LEU* 3.5 16.1 - - + +
157D THR* 3.0 36.4 + - - +
159D VAL* 1.3 76.8 - - - +
161D PHE* 1.3 53.2 + - + +
163D THR* 4.4 2.5 - - - -
164D TYR* 2.8 35.3 + - - +
187D PHE* 3.3 29.6 - - + -
191D PHE* 4.3 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 161 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ALA* 3.8 23.6 - - + +
22D LEU* 3.9 23.4 - - + +
23D LEU* 3.7 36.8 - - + -
26D PHE* 4.0 18.8 - + + -
80D LEU* 5.3 1.8 - - + -
89D MET* 3.6 21.5 - - + -
156D LEU* 3.5 27.8 - - + -
157D THR 3.5 12.1 - - - -
158D PHE* 3.1 13.7 + - - +
160D ASP* 1.3 74.1 - - - +
162D LEU* 1.3 63.1 + - - +
164D TYR* 3.8 3.8 - - - +
165D ASP* 3.2 23.2 + - - +
191D PHE* 3.4 32.8 - + - -
197D ILE* 4.2 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ALA* 4.1 8.7 - - + -
76D SER* 6.3 0.7 - - - -
77D ASN* 4.3 17.0 - - - +
80D LEU* 3.5 28.9 - - + -
104D GLU* 4.4 11.4 - - + -
107D VAL* 4.0 24.4 - - + +
111D ARG* 3.4 30.6 + - - +
158D PHE* 3.3 31.1 + - + +
159D VAL* 3.2 13.1 + - - +
161D PHE* 1.3 76.7 - - - +
163D THR* 1.3 64.0 + - - +
165D ASP* 3.3 4.4 + - - +
166D ILE* 3.3 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 163 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D ILE* 3.4 21.8 - - - +
107D VAL* 3.9 2.9 - - - +
141D PHE* 4.1 15.3 - - + -
151D PHE* 3.5 41.3 - - + -
159D VAL 2.8 26.3 + - - -
160D ASP 3.9 3.4 - - - -
162D LEU* 1.3 69.6 - - - +
164D TYR* 1.3 67.3 + - - +
166D ILE* 3.1 10.7 - - + +
167D LEU* 3.0 41.6 + - + +
187D PHE* 4.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 164 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D HIS* 3.9 10.5 - - - -
22D LEU* 3.8 25.4 - - + -
160D ASP 2.8 19.1 + - - +
161D PHE 3.8 4.5 - - - +
162D LEU 3.3 0.2 - - - -
163D THR* 1.3 77.1 - - - +
165D ASP* 1.3 56.7 + - - +
167D LEU* 3.7 0.7 - - - +
168D ASP* 2.8 57.2 + - + +
171D ARG* 4.1 11.0 - - - -
187D PHE* 4.1 11.8 - + + -
188D MET* 3.8 17.3 - - - -
191D PHE* 3.4 37.0 - + + -
192D GLU* 3.4 43.4 + - + +
197D ILE* 5.3 0.2 - - + -
201D LEU* 3.7 17.2 - - + +
206D PHE* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 165 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ARG* 3.1 30.6 + - - +
15D GLY 4.1 9.6 - - - +
16D LEU* 5.6 0.3 - - - -
18D HIS* 3.2 26.1 - - + +
19D ALA* 4.7 7.3 - - + +
111D ARG* 3.9 19.9 + - - +
161D PHE 3.2 12.2 + - - +
162D LEU* 3.6 9.4 - - - +
163D THR 3.3 0.2 - - - -
164D TYR* 1.3 82.3 - - - +
166D ILE* 1.3 59.0 + - - +
169D GLN* 2.9 51.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 166 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D VAL* 4.3 17.3 - - + +
110D PHE* 3.8 32.3 - - + +
111D ARG* 3.7 36.3 - - + +
114D LEU* 3.6 31.2 - - + -
141D PHE* 5.4 0.9 - - + -
162D LEU 3.3 10.2 + - - +
163D THR* 3.1 21.8 - - + +
165D ASP* 1.3 77.5 - - - +
167D LEU* 1.3 64.7 + - + +
169D GLN* 3.4 12.2 + - - +
170D ASN* 3.1 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D PHE* 4.8 8.5 - - + -
138D LEU* 3.5 32.1 - - + -
141D PHE* 5.0 8.7 - - + -
151D PHE* 4.8 0.4 - - + -
163D THR* 3.0 41.0 + - + +
164D TYR 3.8 0.2 - - - +
166D ILE* 1.3 78.0 - - + +
168D ASP* 1.3 59.8 + - - +
170D ASN* 3.4 5.9 + - - +
171D ARG* 2.9 29.3 + - - +
178D LEU* 4.3 7.3 - - + +
184D LEU* 4.4 24.2 - - + -
187D PHE* 4.2 11.2 - - + -
188D MET* 3.5 30.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 168 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ARG* 3.1 25.8 + - - +
18D HIS* 4.5 1.6 + - - -
164D TYR* 2.8 41.6 + - + +
165D ASP 3.5 5.2 - - - +
167D LEU* 1.3 73.8 - - - +
169D GLN* 1.3 66.2 + - - +
171D ARG* 3.1 28.6 + - - +
172D ILE* 2.9 31.8 + - - +
188D MET* 3.5 10.7 - - + +
206D PHE* 5.4 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 169 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ARG* 3.8 15.7 - - - +
15D GLY* 5.2 5.4 - - - +
111D ARG* 5.1 6.2 + - - +
114D LEU* 3.8 27.5 - - + +
115D ILE* 5.9 4.4 - - - +
165D ASP* 2.9 46.0 + - - +
166D ILE* 3.4 12.1 + - - +
168D ASP* 1.3 75.7 - - - +
170D ASN* 1.3 57.3 + - - +
172D ILE* 3.1 13.7 + - - +
173D PHE* 3.0 26.0 + - - +
211D ILE* 3.9 24.0 - - + +
212D ASN* 4.4 8.3 + - - +
218D TRP* 3.9 11.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 170 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D PHE* 3.3 22.9 - - - -
114D LEU* 4.2 5.0 - - - +
130D TYR* 3.1 23.9 + - - -
134D LEU* 3.1 38.5 - - + +
138D LEU* 5.0 4.3 - - + -
166D ILE* 3.1 26.1 + - - +
167D LEU* 3.7 6.7 - - - +
169D GLN* 1.3 72.5 - - - +
171D ARG* 1.3 55.1 + - - +
173D PHE* 2.8 9.4 + - - +
174D ASP* 2.8 34.7 + - - +
177D CYS* 3.7 13.3 - - - -
178D LEU* 5.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 171 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D TYR* 4.1 2.6 - - - -
167D LEU 2.9 14.7 + - - +
168D ASP* 3.2 30.5 + - - +
170D ASN* 1.3 74.6 - - - +
172D ILE* 1.3 60.7 + - - +
174D ASP 4.0 0.2 - - - -
175D PRO* 3.0 45.1 - - + +
177D CYS* 3.7 12.0 - - - -
178D LEU* 4.4 12.6 - - + +
188D MET* 3.1 37.2 - - - +
192D GLU* 3.1 39.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 172 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ARG* 3.6 28.0 - - - +
168D ASP* 2.9 29.6 + - - +
169D GLN* 3.3 10.1 - - - +
171D ARG* 1.3 78.8 - - - +
173D PHE* 1.3 64.1 + - - +
174D ASP 3.4 0.2 + - - -
175D PRO* 4.2 8.2 - - - +
211D ILE* 3.9 19.7 - - + -
218D TRP* 4.0 16.4 - - + -
223D VAL* 5.0 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 173 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D LEU* 5.0 4.7 - - + -
117D LEU* 3.6 21.1 - - + -
118D CYS* 5.0 1.3 - - - -
123D HIS* 3.7 22.9 - + - -
127D LYS* 3.7 34.5 + - + -
130D TYR* 3.9 30.7 - + - -
131D LEU* 3.9 27.1 - - + +
134D LEU* 5.4 0.7 - - + -
169D GLN 3.0 12.2 + - - +
170D ASN* 2.8 15.3 + - - +
172D ILE* 1.3 76.9 - - - +
174D ASP* 1.3 61.6 + - + +
175D PRO* 4.2 1.8 - - - +
218D TRP* 3.5 39.9 - + + +
----------------------------------------------------------
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