Contacts of the strand formed by residues 288 - 294 (chain A) in PDB entry 1PG0
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 GLU 288 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LYS* 3.1 43.5 + - - +
6A LYS 2.9 11.7 + - - +
7A ILE* 3.5 8.5 - - + +
8A LEU* 2.9 29.2 + - - +
34A TRP* 5.5 0.2 - - - -
280A TYR* 4.8 0.2 - - - -
286A THR 4.6 6.4 - - - +
287A ALA* 1.3 76.8 - - - +
289A LEU* 1.3 59.5 + - - +
290A TYR* 2.4 46.5 + - + +
315A ARG* 4.5 0.9 - - - -
318A SER* 3.4 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.5 35.9 - - + -
10A THR* 5.0 0.4 - - + -
281A TRP* 3.6 36.6 - - + -
288A GLU* 1.3 72.8 - - - +
290A TYR* 1.3 64.4 + - - +
291A HIS* 3.9 26.5 - - + +
315A ARG* 3.7 28.4 - - - +
316A LYS 4.3 0.2 - - - -
317A PRO* 3.7 23.5 - - + -
318A SER* 2.7 40.2 + - - +
319A ASN 3.3 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 3.6 22.7 - - + -
8A LEU 2.9 9.4 + - - +
9A VAL* 3.4 11.2 - - + +
10A THR* 3.0 26.2 + - - +
34A TRP* 3.7 23.3 - + - -
288A GLU* 2.4 49.1 + - + +
289A LEU* 1.3 78.6 - - - +
291A HIS* 1.3 64.6 + - - +
318A SER* 3.8 11.1 - - - -
319A ASN* 3.5 26.7 - - + -
321A PHE* 3.4 38.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A THR* 2.8 30.5 - - + +
260A TYR* 3.5 26.6 - + - +
281A TRP* 4.8 0.4 - - - -
289A LEU* 3.9 19.3 - - + +
290A TYR* 1.3 77.1 - - - +
292A PHE* 1.3 64.0 + - - +
293A ILE* 3.7 15.7 + - + +
301A HIS* 4.3 3.8 - + + -
305A TRP* 2.8 36.0 + + - -
317A PRO* 3.4 24.5 - - + +
319A ASN 3.3 6.3 + - - -
320A LEU* 3.6 19.4 - - + +
321A PHE* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.3 35.2 - - + -
10A THR 2.9 14.6 + - - +
11A CYS* 3.6 5.1 - - - -
12A ALA 3.2 20.8 + - - -
27A GLU* 3.8 10.8 - - + +
30A GLN* 3.7 37.5 - - + +
31A ALA* 3.8 25.8 - - + -
34A TRP* 3.9 33.7 - + + -
290A TYR 5.0 0.2 - - - -
291A HIS* 1.3 71.0 - - - +
293A ILE* 1.3 66.7 + - - +
321A PHE* 3.3 43.7 - + + -
323A HIS* 5.4 0.2 - - - +
435A ARG* 4.5 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA* 4.4 1.6 - - + -
27A GLU* 3.7 5.6 - - - -
260A TYR* 4.2 6.1 - - - +
291A HIS* 4.3 10.1 - - + +
292A PHE* 1.3 80.4 - - - +
294A GLY* 1.3 62.4 + - - +
297A ILE* 3.8 12.6 - - + +
298A VAL* 4.1 19.1 - - + -
301A HIS* 3.6 57.2 - - + +
320A LEU* 4.7 10.1 - - + -
321A PHE 3.0 5.1 + - - +
322A VAL* 3.2 28.3 - - + -
323A HIS* 3.0 32.4 + - - -
553A MOD 4.0 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ILE* 1.3 78.1 - - - +
295A LYS* 1.3 62.6 + - - -
296A ASP* 3.1 8.7 + - - -
297A ILE* 3.3 15.2 + - - +
298A VAL* 3.7 6.6 - - - +
322A VAL* 3.8 2.0 - - - -
323A HIS* 3.4 17.0 - - - -
325A TYR* 4.9 1.6 - - - -
553A MOD 3.0 30.5 + - - -
----------------------------------------------------------
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