Contacts of the helix formed by residues 148 - 160 (chain D) in PDB entry 3PII
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 CYS 148 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D CYS* 3.8 4.7 - - - -
61D HIS* 3.6 4.3 - - + +
62D GLU* 3.6 16.2 - - + +
144D ALA 4.2 0.2 + - - -
145D PRO 3.1 1.6 + - - -
146D ILE 3.2 0.4 - - - -
147D PHE* 1.3 81.2 - - - +
149D ALA* 1.3 66.1 + - - +
150D GLY 3.3 0.9 - - - -
151D VAL* 4.2 1.9 - - - +
152D THR* 2.9 34.6 + - - -
176D PHE* 4.5 9.9 - - - -
286D VAL* 4.8 2.9 - - - -
331D ARG* 3.9 6.3 - - - +
340D ZN 2.4 36.6 - - - -
400D BMD 2.8 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 149 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D PRO* 2.8 18.8 + - + +
148D CYS* 1.3 76.1 - - - +
150D GLY* 1.3 58.5 + - - +
153D THR* 2.9 31.5 + - - -
175D GLY 4.0 13.9 - - - +
176D PHE* 3.5 23.1 - - + -
179D VAL* 3.4 13.9 - - + +
331D ARG* 3.6 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 150 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D PRO 3.4 6.7 + - - -
146D ILE* 3.5 16.9 + - - +
148D CYS 3.3 0.4 - - - -
149D ALA* 1.3 75.8 - - - +
151D VAL* 1.3 54.3 + - - +
153D THR* 3.0 3.6 + - - +
154D TYR* 2.7 38.1 + - - +
179D VAL* 4.1 4.2 - - - +
183D TYR* 3.7 25.4 - - - -
295D ALA* 4.2 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D ILE 3.1 17.9 + - - +
147D PHE 3.7 17.0 - - - +
148D CYS* 4.1 2.0 - - - +
150D GLY* 1.3 72.0 - - - +
152D THR* 1.3 64.6 + - - +
154D TYR* 4.3 1.8 - - + -
155D LYS* 2.9 28.9 + - - +
286D VAL* 4.2 10.5 - - + -
287D GLY* 4.2 12.3 - - - +
288D THR 4.5 0.2 - - - +
291D ASP* 3.5 18.6 - - + +
292D LEU* 3.3 52.3 - - + +
295D ALA* 3.9 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 152 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D CYS* 2.9 29.8 + - - -
149D ALA 4.2 2.2 - - - -
151D VAL* 1.3 76.9 - - - +
153D THR* 1.3 57.1 + - - +
155D LYS* 4.3 1.0 - - - +
156D ALA* 3.0 25.6 + - - +
176D PHE* 4.4 12.9 - - + -
260D VAL* 3.8 28.7 - - + +
284D SER* 5.0 1.7 + - - +
285D ILE* 3.8 25.0 - - + +
286D VAL* 3.1 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D ALA 2.9 17.4 + - - +
150D GLY 3.4 7.2 - - - +
151D VAL 2.9 0.2 - - - -
152D THR* 1.3 82.1 - - - +
154D TYR* 1.3 63.6 + - - +
156D ALA* 3.4 5.4 + - - +
157D LEU* 2.9 31.5 + - - +
176D PHE* 3.7 18.2 + - - +
179D VAL* 3.7 2.7 - - + -
180D ALA* 3.4 38.3 - - - +
183D TYR* 3.4 23.6 - - + -
235D VAL* 5.1 2.4 - - - +
237D THR* 4.8 3.3 - - - +
260D VAL* 5.4 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 154 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C LYS* 4.3 2.6 - - - +
164C PRO 4.0 10.4 + - - -
150D GLY 2.7 17.6 + - - +
151D VAL* 3.9 2.0 - - - +
153D THR* 1.3 76.4 - - - +
155D LYS* 1.3 73.4 + - - +
157D LEU* 2.8 17.8 + - - +
158D LYS* 2.9 37.7 + - + +
183D TYR* 3.6 33.0 - + + -
187D MET* 3.7 20.6 - - + -
291D ASP* 3.6 17.5 - - + -
294D GLU* 2.7 44.4 + - + +
295D ALA* 3.9 7.2 - - + -
298D PHE* 3.3 27.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 155 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D GLY 5.1 6.1 + - - -
104D THR* 5.3 6.5 - - - +
151D VAL 2.9 20.8 + - - +
152D THR 4.3 1.3 - - - +
154D TYR* 1.3 74.5 - - - +
156D ALA* 1.3 64.2 + - - +
158D LYS* 2.7 29.6 + - + +
159D VAL* 2.8 45.2 + - + +
284D SER* 4.2 8.5 - - - +
285D ILE 6.1 0.2 - - - -
286D VAL 3.4 20.6 - - - +
287D GLY* 4.0 3.8 - - - -
288D THR* 4.6 4.4 + - - +
291D ASP* 2.7 42.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 156 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D THR 3.0 21.1 + - - +
153D THR* 3.4 6.3 - - - +
154D TYR 3.2 0.6 - - - -
155D LYS* 1.3 79.7 - - - +
157D LEU* 1.3 63.0 + - - +
159D VAL* 3.4 4.8 + - - +
160D THR* 3.1 24.8 + - - +
235D VAL* 3.9 15.3 - - + -
258D VAL* 3.9 13.1 - - + +
260D VAL* 3.6 22.9 - - + -
284D SER* 4.3 7.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 157 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D THR 2.9 18.0 + - - +
154D TYR 2.8 10.3 + - - +
156D ALA* 1.3 76.5 - - - +
158D LYS* 1.3 56.4 + - - +
160D THR* 2.9 27.0 + - + -
161D GLY 4.0 0.3 + - - -
162D ALA* 4.8 5.2 + - - +
168D VAL* 4.0 20.4 - - + -
170D ILE* 4.7 3.6 - - + -
180D ALA* 3.4 17.7 - - + +
183D TYR* 3.7 12.1 - - + -
184D ALA* 3.4 45.3 - - + +
187D MET* 3.8 15.1 - - + +
189D LEU* 4.5 8.3 - - + +
235D VAL* 4.1 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 158 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C LYS* 4.3 18.0 - - + +
154D TYR* 2.9 38.8 + - + +
155D LYS* 2.7 21.6 + - + +
157D LEU* 1.3 68.2 - - - +
159D VAL* 1.3 59.1 + - - +
161D GLY* 2.9 23.4 + - - -
187D MET* 3.9 15.8 - - + +
291D ASP* 3.0 26.9 + - - -
294D GLU* 2.8 28.3 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
280A LYS* 6.2 2.5 - - - +
155D LYS* 2.8 48.0 + - + +
156D ALA* 3.6 9.6 - - - +
158D LYS* 1.3 72.9 - - + +
160D THR* 1.3 63.2 + - - +
161D GLY* 3.0 1.9 + - - -
258D VAL* 4.2 5.2 - - + -
282D ILE* 3.7 44.7 - - + +
283D GLY 5.3 0.2 - - - +
284D SER* 3.8 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 160 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D ALA 3.1 18.0 + - - +
157D LEU* 2.9 19.5 + - + +
158D LYS 3.1 1.6 - - - -
159D VAL* 1.3 76.5 - - - +
161D GLY* 1.3 56.6 + - - +
162D ALA* 3.1 25.1 + - - +
168D VAL* 4.6 2.3 - - + +
232D HIS 5.4 0.2 - - - +
233D ALA* 3.6 24.4 - - + +
234D ALA 4.8 0.4 - - - +
235D VAL* 3.7 24.9 - - + -
256D ALA* 3.6 18.8 - - - +
258D VAL* 3.7 16.8 - - + -
280D LYS* 5.0 3.8 + - - -
----------------------------------------------------------
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