Contacts of the strand formed by residues 174 - 178 (chain D) 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 LYS 174 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C SER* 3.6 25.8 + - - +
172D GLY 3.9 9.4 - - - +
173D HIS* 1.3 76.1 - - - +
175D VAL* 1.3 60.3 + - - +
197D ALA* 3.9 10.3 - - - -
198D GLN* 3.4 34.9 - - + +
239D LEU* 4.1 18.9 + - + -
241D CYS* 3.8 28.1 - - - -
243D PRO* 3.1 16.3 - - + +
244D GLU* 2.8 38.0 + - - +
245D VAL 3.7 3.1 + - - -
264D ARG* 4.3 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 175 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D VAL* 4.0 18.8 - - + -
173D HIS* 4.0 12.8 - - + -
174D LYS* 1.3 78.1 - - - +
176D LEU* 1.3 71.3 + - - +
177D VAL* 4.2 7.6 - - + -
191D ALA* 4.6 5.4 - - + -
196D ALA* 4.0 22.0 - - + -
198D GLN 2.9 11.9 + - - +
199D VAL* 3.2 11.8 - - + +
200D VAL* 2.8 30.2 + - - +
239D LEU* 5.3 0.4 - - - +
243D PRO* 4.2 2.5 - - - -
245D VAL* 3.3 16.8 - - + +
247D ILE* 4.1 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D VAL* 1.3 74.9 - - - +
177D VAL* 1.3 64.0 + - - +
178D CYS* 3.9 11.2 - - - -
200D VAL* 3.5 15.0 - - + +
202D THR* 3.7 27.8 - - + -
231D ILE* 6.0 2.5 - - + -
235D VAL* 4.0 25.8 - - + -
243D PRO* 3.9 11.8 - - + +
245D VAL 2.9 7.1 + - - +
246D THR* 3.2 33.5 - - + +
247D ILE 2.8 26.5 + - - -
258D ALA* 5.2 1.8 - - + +
259D GLY* 4.8 2.9 - - - -
262D ALA* 3.9 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 177 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D VAL* 4.2 8.7 - - + -
176D LEU* 1.3 78.5 - - - +
178D CYS* 1.3 61.9 + - - +
179D GLY 3.6 14.0 + - - +
184D GLY* 3.6 27.4 - - - +
187D THR* 3.9 22.0 - - + +
188D LEU* 4.5 6.3 - - - +
191D ALA* 5.5 0.4 - - + -
199D VAL* 3.8 22.9 - - + -
200D VAL 2.7 12.4 + - - +
201D VAL* 3.2 11.6 - - + +
202D THR* 3.0 24.4 + - - -
247D ILE* 3.4 9.0 - - + +
249D CYS* 4.2 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 178 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D LEU* 3.9 17.0 - - - -
177D VAL* 1.3 69.9 - - - +
179D GLY* 1.3 60.2 + - - +
202D THR* 3.2 14.1 - - - +
231D ILE* 6.4 1.3 - - - -
246D THR* 3.9 26.0 - - - -
247D ILE 3.0 7.5 + - - -
248D GLU* 3.5 13.2 - - - +
249D CYS* 2.7 34.0 + - - +
250D THR* 3.2 5.0 - - + +
255D SER* 3.1 35.7 - - - +
258D ALA* 5.7 2.5 - - - -
259D GLY* 5.2 1.3 - - - -
----------------------------------------------------------
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