Contacts of the helix formed by residues 283 - 294 (chain A) in PDB entry 3SA0
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 283 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ASN* 3.5 37.5 + - - +
222A LEU* 5.3 1.2 - - - +
281A ASN 3.8 1.4 + - - -
282A ALA* 1.3 73.4 - - - +
284A SER* 1.3 66.3 + - - +
285A LYS* 2.7 39.5 + - - +
286A ALA* 3.1 20.7 + - + +
287A LEU* 3.2 12.3 + - - +
312A TYR* 4.2 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ALA 3.5 4.5 + - - -
283A ASP* 1.3 76.1 + - - +
285A LYS* 1.3 68.7 + - - +
287A LEU* 3.3 10.7 + - - +
288A ASP* 3.0 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ASP* 2.7 19.7 + - - +
284A SER* 1.3 75.3 + - - +
286A ALA* 1.3 63.8 + - - +
288A ASP* 3.3 6.3 + - - -
289A LEU* 3.1 18.9 + - - +
310A HIS* 3.2 14.2 - - + -
311A PRO* 4.0 33.2 + - + +
312A TYR* 3.7 20.1 - - + +
314A GLU* 5.0 6.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ASN* 4.9 0.2 - - - +
218A LEU* 3.8 8.5 - - + +
222A LEU* 4.7 17.9 - - + -
283A ASP* 3.1 19.0 + - + +
285A LYS* 1.3 78.8 - - - +
287A LEU* 1.3 58.8 + - + +
289A LEU* 3.3 3.7 + - - +
290A LEU* 2.9 27.5 + - - +
312A TYR* 3.5 42.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LEU* 4.0 10.3 - - + -
275A TRP* 4.0 18.1 - - + +
276A ASN* 3.7 37.7 - - + +
279A PHE* 3.9 26.9 - - + +
282A ALA* 3.6 31.4 - - + +
283A ASP 3.2 11.3 + - - +
284A SER* 3.7 11.0 - - - +
285A LYS 3.2 0.4 - - - -
286A ALA* 1.3 74.7 - - - +
288A ASP* 1.3 65.7 + - - +
290A LEU* 3.6 7.8 - - + +
291A ASP* 2.9 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A SER 3.0 13.4 + - - +
285A LYS* 3.3 10.1 + - - +
287A LEU* 1.3 77.8 - - - +
289A LEU* 1.3 61.7 + - - +
291A ASP* 3.4 7.5 + - - +
292A LYS* 2.9 50.5 + - - +
310A HIS* 2.8 24.8 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
130A LEU* 3.7 28.7 - - + -
218A LEU* 4.8 1.1 - - + -
285A LYS 3.1 15.6 + - - +
286A ALA* 3.7 4.5 - - - +
288A ASP* 1.3 73.0 - - - +
290A LEU* 1.3 66.4 + - - +
292A LYS* 3.0 3.5 + - + +
293A MET* 3.0 51.6 + - + +
302A ILE* 4.0 21.5 - - + -
307A ALA* 4.1 10.3 - - + +
310A HIS* 3.6 41.8 + - + +
312A TYR* 4.3 7.4 - - + -
313A LEU* 4.2 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A GLY* 3.2 30.1 - - - +
218A LEU* 3.9 15.4 - - + +
219A ALA* 4.0 10.3 - - + +
222A LEU* 4.2 7.2 - - + -
275A TRP* 3.7 30.5 - - + -
279A PHE* 3.8 23.1 - - + -
286A ALA 2.9 17.8 + - - +
287A LEU* 3.6 14.6 - - + +
288A ASP 3.3 0.2 - - - -
289A LEU* 1.3 77.0 - - - +
291A ASP* 1.3 56.7 + - - +
293A MET* 3.1 4.9 + - - +
294A LEU* 2.8 50.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LYS* 4.5 6.4 - - - -
275A TRP* 2.9 38.8 + - + +
287A LEU 2.9 15.1 + - - +
288A ASP* 3.5 8.7 - - - +
289A LEU 3.2 0.2 - - - -
290A LEU* 1.3 78.0 - - - +
292A LYS* 1.3 68.0 + - - +
294A LEU 3.5 11.6 - - - +
295A THR* 2.9 16.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ASP* 2.9 44.1 + - - +
289A LEU* 3.0 7.6 + - - +
291A ASP* 1.3 85.1 + - - +
293A MET* 1.3 62.1 + - - +
295A THR* 3.2 15.3 + - - -
300A LYS 4.9 0.2 - - - +
301A ARG* 3.8 0.3 - - - +
302A ILE* 3.2 52.2 + - + +
310A HIS* 4.3 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LEU* 4.2 7.6 - - + -
134A LEU* 3.9 24.5 - - + -
211A ILE* 4.0 12.3 - - + +
212A TRP* 3.8 8.1 - - - -
214A VAL* 4.2 6.1 - - + -
215A GLY* 3.8 31.0 - - - -
218A LEU* 4.4 12.6 - - - -
289A LEU* 3.0 41.3 + - + +
290A LEU* 3.6 5.6 - - - +
292A LYS* 1.3 76.3 - - - +
294A LEU* 1.3 60.6 + - - +
295A THR 3.2 2.2 + - - -
301A ARG* 3.2 27.4 + - - -
302A ILE* 3.8 16.6 - - + -
307A ALA* 3.8 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A TRP* 3.5 56.5 - - + +
215A GLY* 3.8 8.5 - - - +
216A CYS* 3.8 10.3 - - - +
227A ILE* 4.1 8.3 - - + -
228A PHE* 4.0 15.7 - - + -
244A LEU* 3.4 22.4 - - + +
275A TRP* 3.8 27.6 - - + -
290A LEU* 2.8 41.0 + - + +
291A ASP* 3.5 7.9 - - - +
293A MET* 1.3 77.6 - - - +
295A THR* 1.3 58.4 + - - +
----------------------------------------------------------
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