Contacts of the strand formed by residues 282 - 288 (chain A) in PDB entry 1PD6
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 ALA 282 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LYS* 5.3 4.0 - - + -
249A ASN* 3.5 22.4 - - - +
280A ASP* 3.0 11.4 + - - +
281A ASP* 1.3 77.9 - - - +
283A ALA* 1.3 61.0 + - - +
284A TYR* 5.3 3.1 - - + -
296A GLU* 3.6 5.7 - - - +
297A LEU* 2.6 35.6 + - - +
298A PHE* 5.1 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LYS* 4.0 0.3 - - - +
249A ASN* 2.6 49.2 + - + +
282A ALA* 1.3 83.7 - - - +
284A TYR* 1.3 67.1 + - - +
285A GLN* 4.1 6.1 - - - +
294A SER* 5.8 2.2 - - - -
295A THR 3.3 13.7 - - - +
296A GLU* 3.8 11.7 - - + +
297A LEU* 3.5 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A TYR* 6.0 0.2 - - + -
233A LEU* 3.6 31.7 - - + +
246A TRP* 5.1 0.9 - - + -
247A LEU 2.9 6.5 - - - +
248A LYS* 3.1 41.5 + - + -
253A ILE* 3.6 20.8 - - + +
260A TYR* 4.3 4.6 + + - -
271A LEU* 5.1 2.2 - - + -
273A ILE* 3.8 27.0 - - + +
276A CYS* 4.2 2.1 - - - -
280A ASP* 3.2 28.0 + - - +
282A ALA* 5.3 0.2 - - + -
283A ALA* 1.3 84.3 - - - +
285A GLN* 1.3 63.9 + - - +
295A THR* 2.6 38.7 + - + +
297A LEU* 3.4 36.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A GLU* 3.5 20.3 - - + +
246A TRP* 3.4 9.5 - - - +
247A LEU* 2.5 77.6 + - + +
248A LYS 2.9 16.0 + - - -
249A ASN* 3.1 23.7 - - - +
250A GLY 4.1 2.8 + - - +
283A ALA* 4.3 4.4 - - - +
284A TYR* 1.3 76.5 - - - +
286A CYS* 1.3 57.9 + - - +
292A LYS* 4.0 7.4 - - + -
293A CYS 2.8 13.0 - - - +
294A SER* 3.2 30.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A THR* 3.3 1.8 - - - +
215A PHE* 3.4 30.5 - - + -
218A LYS* 3.8 20.2 - - + -
245A LYS 4.0 0.2 - - - -
246A TRP* 3.2 32.8 - - + -
285A GLN* 1.3 73.4 - - - +
287A VAL* 1.3 61.2 + - - +
291A GLU 3.0 1.2 - - - +
292A LYS* 2.8 5.7 - - - -
293A CYS* 2.7 58.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A PHE* 3.2 3.8 - - - -
245A LYS* 2.5 72.7 + - + +
246A TRP 3.5 9.2 - - - +
247A LEU* 3.4 41.3 - - + +
286A CYS* 1.3 77.5 - - - +
288A VAL* 1.3 69.0 + - - +
289A GLY 4.8 2.2 - - - +
290A GLY* 4.8 6.1 - - - +
291A GLU 2.6 24.7 - - - +
292A LYS* 3.9 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A ALA* 3.8 21.8 - - + +
215A PHE* 3.3 28.4 - - + -
237A LEU* 4.5 2.2 - - + -
239A ASP* 3.4 22.9 - - - +
242A ALA* 4.8 4.9 - - + -
243A GLU 4.5 9.0 - - - +
244A VAL* 3.9 18.2 - - + -
245A LYS 4.8 1.6 - - - +
287A VAL* 1.3 76.2 - - - +
289A GLY* 1.3 55.4 + - - +
290A GLY 2.7 17.3 + - - -
291A GLU* 3.2 28.5 + - - +
----------------------------------------------------------
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