Contacts of the helix formed by residues 302 - 312 (chain B) in PDB entry 1PL8
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 THR 302 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B TYR* 4.7 0.4 + - - -
158B SER* 2.6 45.9 + - - +
161B ILE* 3.7 27.2 - - + +
162B HIS* 4.2 5.2 - - + +
165B ARG* 3.8 8.5 - - - +
299B TYR* 4.0 10.7 - - + +
300B CYS 3.5 15.4 - - - +
301B ASN* 1.3 76.0 - - - +
303B TRP* 1.3 74.7 + - - +
304B PRO* 3.5 2.7 - - - -
305B VAL* 3.5 4.0 + - - +
306B ALA* 2.8 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ALA* 3.8 19.8 - - + +
93B ILE 3.7 19.5 + - - -
94B GLU* 3.4 33.6 + - + +
95B PRO* 3.8 8.1 - - + -
140B TYR* 3.5 39.5 - + + -
151B GLY 4.8 0.8 + - - -
154B ILE* 3.5 24.5 - - + +
155B GLU* 3.7 29.6 - - + -
158B SER* 3.3 11.7 - - - -
299B TYR* 3.5 41.7 - + - -
302B THR* 1.3 99.9 + - - +
304B PRO* 1.3 70.3 - - + +
306B ALA* 3.2 1.2 + - - +
307B ILE* 2.8 36.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B TYR* 3.7 25.6 - - + +
301B ASN* 4.7 5.8 - - - -
302B THR* 3.8 5.6 - - - +
303B TRP* 1.3 94.3 - - + +
305B VAL* 1.3 58.6 + - + +
307B ILE* 3.3 10.6 + - + +
308B SER* 2.9 32.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LEU* 3.5 46.2 - - + +
172A GLY* 4.1 6.7 - - - +
173A HIS* 5.8 4.0 - - + -
244A GLU* 5.9 2.5 - - - +
161B ILE* 4.3 12.3 - - + -
165B ARG* 3.5 29.4 - - - +
301B ASN 4.6 2.7 - - - +
302B THR* 3.5 6.9 + - - +
303B TRP 3.2 0.4 - - - -
304B PRO* 1.3 79.4 - - + +
306B ALA* 1.3 66.6 - - - +
308B SER* 3.2 8.1 + - - -
309B MET* 2.9 22.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ILE* 3.5 30.1 - - + -
157B LEU* 4.0 13.6 - - + +
158B SER* 4.6 0.4 - - - +
161B ILE* 3.9 18.8 - - + -
302B THR 2.8 23.5 + - - +
303B TRP 3.6 0.9 - - - +
305B VAL* 1.3 72.6 - - - +
307B ILE* 1.3 59.7 + - - +
309B MET* 3.1 6.0 + - - +
310B LEU* 2.9 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ALA* 4.7 1.1 - - + -
140B TYR* 3.5 35.7 - - + +
141B LYS 3.7 13.5 - - - +
142B LEU* 4.3 9.2 - - + -
143B PRO* 3.5 33.0 - - + -
146B VAL* 4.7 1.5 - - + +
154B ILE* 3.6 20.4 - - + -
303B TRP* 2.8 22.4 + - + +
304B PRO* 3.6 8.3 - - + +
306B ALA* 1.3 77.0 - - - +
308B SER* 1.3 57.6 + - - +
310B LEU* 3.3 7.5 + - - +
311B ALA* 2.8 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A GLY* 3.7 21.3 + - - -
174A LYS* 3.6 19.9 + - - +
197A ALA* 3.7 9.8 - - - +
304B PRO 2.9 20.5 + - - -
305B VAL* 3.2 6.8 + - - -
307B ILE* 1.3 77.4 - - - +
309B MET* 1.3 61.0 + - - +
311B ALA* 4.1 4.5 - - - +
312B SER* 2.8 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LEU* 3.3 32.5 - - + -
172A GLY* 3.3 7.4 - - - +
195A GLY* 3.2 22.4 - - - +
197A ALA* 3.1 46.0 - - + -
157B LEU* 5.7 1.8 - - + -
161B ILE* 6.0 1.1 - - + -
193B ALA* 5.2 2.9 - - + -
305B VAL* 2.9 19.9 + - + +
306B ALA* 3.1 6.5 + - - +
308B SER* 1.3 76.7 - - - +
310B LEU* 1.3 61.2 + - - +
312B SER* 3.3 0.5 + - - -
313B LYS 3.2 1.7 + - - -
314B SER* 2.8 50.4 + - - +
315B VAL* 3.7 19.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B VAL* 4.0 18.6 - - + +
150B GLU* 3.8 38.0 - - + +
154B ILE* 3.6 35.2 - - + -
157B LEU* 4.7 6.7 - - + -
306B ALA 2.9 19.1 + - - +
307B ILE* 3.8 4.0 - - - +
309B MET* 1.3 75.6 - - - +
311B ALA* 1.3 63.5 + - - +
313B LYS* 3.1 27.7 + - - +
315B VAL* 4.0 27.0 - - + +
317B VAL* 4.0 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B PRO* 3.8 26.7 - - + -
145B ASN* 2.8 28.4 + - - +
146B VAL* 3.7 9.1 - - - +
307B ILE 2.8 21.8 + - - +
308B SER* 4.1 4.9 - - - +
310B LEU* 1.3 73.7 - - - +
312B SER* 1.3 57.4 + - - +
313B LYS* 3.2 2.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LYS* 5.7 0.4 - - - -
197A ALA* 3.3 28.8 + - - +
198A GLN* 4.4 11.0 - - - -
218A ASP* 5.8 0.4 - - - -
308B SER 2.8 21.8 + - - -
309B MET* 3.3 2.9 + - - -
311B ALA* 1.3 76.2 - - - +
313B LYS* 1.3 71.7 + - - +
314B SER* 2.5 26.7 + - - -
----------------------------------------------------------
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