Contacts of the helix formed by residues 291 - 301 (chain A) in PDB entry 1PS9
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 ASP 291 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ARG* 3.8 20.6 + - - +
289A ILE* 3.8 1.1 - - - +
290A ASN* 1.3 86.4 - - - +
292A PRO* 1.3 75.2 - - - +
293A GLN* 2.7 39.7 + - - +
294A VAL* 3.2 19.7 + - + +
295A ALA* 3.0 24.0 + - - +
309A MET* 4.8 4.4 - - - -
319A LEU* 5.9 0.7 - - - -
426A GLU* 4.8 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A TYR* 3.6 29.9 - - + +
5A LEU* 3.9 12.2 - - + +
290A ASN 4.7 0.9 - - - +
291A ASP* 1.3 94.6 - - - +
293A GLN* 1.3 55.4 + - - +
295A ALA* 3.5 3.0 + - + +
296A ASP* 2.8 31.7 + - - +
309A MET* 6.0 1.8 - - + -
319A LEU* 4.7 6.1 - - + -
320A LEU* 6.5 0.2 - - + -
323A ALA* 3.9 16.6 - - + -
328A ALA* 4.4 11.2 - - + -
331A ILE* 3.5 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A SER* 5.1 3.4 + - - +
2A TYR* 3.5 24.2 + - + +
291A ASP* 2.7 17.6 + - - +
292A PRO* 1.3 72.4 - - - +
294A VAL* 1.3 57.0 + - + +
296A ASP* 3.7 11.7 + - - -
297A ASP* 2.7 73.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ARG* 4.1 37.5 - - + +
266A GLY* 4.7 7.9 - - - +
289A ILE* 4.6 10.5 - - + -
290A ASN* 5.3 0.2 - - - +
291A ASP* 3.2 30.6 + - + +
293A GLN* 1.3 78.3 - - + +
295A ALA* 1.3 62.8 + - - +
297A ASP* 3.7 6.6 - - - +
298A ILE* 3.0 39.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 3.7 21.5 - - + -
289A ILE* 3.7 23.1 - - + +
291A ASP 3.0 16.1 + - - +
292A PRO* 3.8 2.9 - - + +
294A VAL* 1.3 78.0 - - - +
296A ASP* 1.3 63.1 + - - +
298A ILE* 3.2 5.0 + - - +
299A LEU* 3.0 29.8 + - - +
307A VAL* 3.9 14.5 - - + +
309A MET* 4.5 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A SER 4.4 1.6 - - - +
2A TYR* 2.9 40.3 - - + -
3A PRO* 4.0 7.1 - - - +
4A SER* 3.1 8.6 + - - -
5A LEU* 2.9 33.4 + - + +
292A PRO 2.8 23.0 + - - +
293A GLN* 3.7 12.5 + - - +
295A ALA* 1.3 73.3 - - - +
297A ASP* 1.3 54.3 + - - +
299A LEU* 3.2 5.3 + - - +
300A SER* 2.7 38.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A GLN* 2.7 58.8 + - - +
294A VAL* 3.7 6.1 - - - +
296A ASP* 1.3 71.6 - - - +
298A ILE* 1.3 62.0 + - - +
300A SER* 3.5 8.7 + - - -
301A ARG* 2.9 57.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLY* 4.4 3.4 - - - -
269A SER* 3.0 27.4 - - - +
285A THR* 3.8 19.5 - - + -
289A ILE* 3.6 31.9 - - + -
294A VAL* 3.0 28.0 + - + +
295A ALA* 3.2 8.3 + - - +
297A ASP* 1.3 76.4 - - - +
299A LEU* 1.3 62.1 + - + +
301A ARG* 3.6 13.9 + - - +
302A GLY 3.3 2.9 + - - -
303A ASP* 2.9 52.1 + - + +
304A ALA* 4.0 4.0 + - + +
307A VAL* 4.0 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER* 3.5 20.4 - - - +
5A LEU* 3.3 46.4 - - + +
19A ARG* 3.8 13.5 - - + +
295A ALA 3.0 13.5 + - - +
296A ASP 3.2 2.7 + - - +
298A ILE* 1.3 75.9 - - + +
300A SER* 1.3 61.0 + - - +
302A GLY* 3.0 19.1 + - - -
304A ALA 3.7 13.6 - - - +
305A ASP 3.6 33.2 - - - +
306A MET* 3.8 9.2 - - - +
307A VAL* 4.0 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER* 3.3 19.7 + - - -
296A ASP* 2.7 22.3 + - - -
297A ASP* 3.2 16.3 + - - -
299A LEU* 1.3 74.4 - - - +
301A ARG* 1.3 65.8 + - - +
302A GLY* 3.1 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A SER* 5.3 1.4 - - - -
273A ARG* 5.2 3.3 + - - -
297A ASP* 2.9 54.8 + - - +
298A ILE* 4.0 17.7 - - - +
300A SER* 1.3 80.8 + - - +
302A GLY* 1.3 60.4 + - - +
303A ASP* 3.1 31.1 + - - +
524A ILE* 6.4 0.4 - - - +
----------------------------------------------------------
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