Contacts of the helix formed by residues 152 - 163 (chain D) in PDB entry 2PI8
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 152 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D TYR* 3.5 7.1 - - - -
150D SER* 3.1 15.7 + - - -
151D ASN* 1.3 85.5 + - - +
153D LEU* 1.3 61.6 + - - +
154D MSE 3.3 11.3 + - - +
155D ASP* 3.2 41.1 + - - +
156D ASN* 3.3 13.3 + - - +
212D ARG* 5.6 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D TYR* 3.7 40.3 - - + -
119D PRO* 6.4 0.2 - - + -
137D TYR* 3.8 35.7 + - + +
152D SER* 1.3 73.3 + - - +
154D MSE 1.3 58.2 + - - +
156D ASN* 3.5 10.7 + - + +
157D PHE* 3.1 25.5 + - - +
220D GLU* 3.6 23.3 - - - +
223D VAL* 5.3 3.6 - - + -
224D ARG* 4.1 24.2 - - + +
227D LEU* 3.8 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 154 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D SER* 3.2 8.2 + - - +
153D LEU* 1.3 77.2 - - - +
155D ASP* 1.3 61.7 + - - +
157D PHE* 3.1 7.9 + - - +
158D ILE* 2.9 51.6 + - + +
211D ILE* 3.7 40.2 - - + +
212D ARG* 5.0 16.2 - - + +
214D TRP* 5.3 3.8 - - + -
215D GLY* 4.2 11.9 - - - -
223D VAL* 3.9 28.2 - - + +
226D LEU* 5.4 1.8 - - + -
227D LEU* 4.0 24.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 155 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D PRO* 5.6 0.3 - - - +
106D ILE* 3.3 45.5 - - + +
151D ASN* 4.2 4.9 - - - +
152D SER* 3.2 28.0 + - - +
153D LEU 3.4 0.2 - - - -
154D MSE 1.3 76.8 - - - +
156D ASN* 1.3 57.0 + - - +
158D ILE* 3.3 6.7 + - - +
159D MSE 2.9 25.1 + - - -
212D ARG* 3.1 33.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 156 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D ILE* 4.4 3.1 - - - +
118D TYR* 3.3 27.7 + - - +
119D PRO 3.7 13.1 + - - +
120D ILE* 4.0 16.5 - - + +
133D ARG* 5.5 2.2 - - - +
137D TYR* 6.1 0.4 - - - +
150D SER* 2.6 36.3 + - - -
152D SER 3.3 3.2 + - - +
153D LEU* 3.6 14.8 - - + +
154D MSE 3.2 0.4 - - - -
155D ASP* 1.3 76.6 - - - +
157D PHE* 1.3 57.8 + - - +
159D MSE 3.5 16.4 + - + +
160D ASP* 2.9 27.7 + - - +
236D PHE* 5.3 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 157 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D ARG* 3.5 24.7 - - - +
137D TYR* 4.3 0.4 - - - +
153D LEU 3.1 13.9 + - - +
154D MSE 3.1 14.8 + - - +
156D ASN* 1.3 74.9 - - - +
158D ILE* 1.3 66.5 + - + +
160D ASP* 3.1 8.4 - - - +
161D VAL* 3.0 42.4 + - + +
188D TYR* 5.2 2.9 - + - -
191D ILE* 3.2 37.0 - - + -
211D ILE* 6.2 2.0 - - + -
227D LEU* 3.4 52.5 - - + -
230D ASN* 3.6 24.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 158 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D TYR* 3.9 19.7 - - + +
104D PRO* 5.1 3.8 - - + -
154D MSE 2.9 38.3 + - + +
155D ASP* 3.8 5.6 - - - +
157D PHE* 1.3 74.6 - - + +
159D MSE 1.3 60.9 + - - +
161D VAL* 3.0 8.2 + - - +
162D GLN* 2.9 51.9 + - + +
208D MSE 4.2 33.9 - - + -
211D ILE* 6.2 0.9 - - + -
212D ARG* 3.4 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 159 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D PRO* 4.1 13.4 - - + +
106D ILE* 3.7 19.5 - - + -
120D ILE* 3.9 27.8 - - + -
155D ASP 2.9 17.5 + - - +
156D ASN* 3.7 20.4 - - + +
158D ILE* 1.3 76.2 - - - +
160D ASP* 1.3 61.5 + - - +
162D GLN* 3.3 1.0 + - - -
163D GLY 3.1 19.4 + - - -
164D SER 3.5 25.3 + - - +
165D GLY* 4.2 13.7 - - - +
167D ILE* 4.0 18.6 - - - -
178D PHE* 5.1 2.5 - - - -
236D PHE* 3.6 33.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
133D ARG* 2.9 33.3 + - - +
156D ASN 2.9 16.4 + - - +
157D PHE* 3.1 14.8 - - - +
159D MSE 1.3 79.6 - - - +
161D VAL* 1.3 59.7 + - + +
163D GLY* 3.5 6.4 + - - -
188D TYR* 6.0 1.2 - - - -
230D ASN* 4.8 3.5 + - - -
232D SER* 4.3 2.6 + - - +
233D PHE* 3.9 6.6 - - - -
234D VAL* 2.9 57.2 + - - +
236D PHE* 4.0 11.8 - - + -
3H NAG 5.2 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 161 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D PHE* 3.0 37.4 + - + +
158D ILE* 3.0 10.2 + - - +
160D ASP* 1.3 78.6 - - + +
162D GLN* 1.3 68.4 + - - +
163D GLY 3.4 0.3 + - - -
188D TYR* 4.3 22.2 - - + +
208D MSE 6.4 0.7 - - + -
230D ASN* 5.4 0.4 - - - +
1H NAG 4.8 1.8 - - - +
2H NAG 3.2 35.2 + - - +
3H NAG 2.8 40.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 162 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D TYR* 3.4 23.1 - - - +
102D TYR* 3.2 51.8 + - + +
104D PRO* 3.9 12.1 - - + -
158D ILE* 2.9 42.2 + - + +
159D MSE 3.3 5.6 + - - +
161D VAL* 1.3 83.5 - - - +
163D GLY* 1.3 58.2 + - - +
164D SER 3.4 11.1 + - - +
208D MSE 5.2 1.0 - - - +
2H NAG 3.0 32.7 + - - +
3H NAG 3.4 20.5 + - - +
4H NAG 4.1 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 163 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D MSE 3.1 5.8 + - - -
160D ASP 3.5 6.9 + - - -
161D VAL 3.3 3.2 - - - -
162D GLN* 1.3 78.6 - - - +
164D SER* 1.3 62.3 + - - +
180D TYR* 3.2 35.2 - - - +
236D PHE* 3.4 17.0 - - - -
3H NAG 3.9 10.8 - - - -
4H NAG 3.4 9.4 - - - -
----------------------------------------------------------
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