Contacts of the helix formed by residues 289 - 296 (chain L) in PDB entry 3J0S
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 ILE 289 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149L THR* 6.0 3.8 - - + -
166L TYR* 4.4 40.8 - - + +
171L LEU* 5.6 8.7 - - + -
285L CYS* 5.0 2.9 - - + -
286L ASP* 3.2 36.5 - - + +
288L ASP* 1.3 84.1 - - + +
290L ARG* 1.3 64.1 + - - +
291L LYS 3.3 1.3 - - - -
292L ASP* 3.2 19.9 + - + +
293L LEU* 3.0 43.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 290 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244J ASP* 3.6 30.6 + - + +
246J GLN* 5.5 3.6 + - - +
282L ILE* 3.7 33.3 + - + +
283L MET* 3.0 49.7 + - - +
285L CYS 3.8 2.6 + - - -
286L ASP 3.4 10.2 + - - +
287L VAL* 3.2 45.8 + - - +
289L ILE* 1.3 76.7 - - - +
291L LYS* 1.3 61.6 + - - +
293L LEU* 3.2 19.1 + - + +
294L TYR* 2.9 29.9 + - + -
322L PRO* 5.8 5.9 - - - +
325L MET* 6.1 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 291 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243J PRO* 2.2 46.2 + - - +
244J ASP* 5.8 0.6 - - - +
287L VAL 4.6 0.6 + - - -
288L ASP 3.8 15.7 - - - +
290L ARG* 1.3 79.3 - - - +
292L ASP* 1.3 67.8 + - - +
294L TYR* 3.4 19.1 + - - +
295L ALA* 3.6 10.2 + - - +
325L MET* 4.6 22.6 - - + +
326L LYS 4.9 2.8 - - - +
151X GLU* 3.4 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 292 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149L THR* 4.9 9.9 - - + +
288L ASP* 4.9 2.1 - - - +
289L ILE* 3.2 22.0 + - + +
291L LYS* 1.3 82.0 - - - +
293L LEU* 1.3 59.4 + - - +
295L ALA* 3.1 7.3 + - - +
296L ASN* 2.6 40.9 + - - +
151X GLU* 3.4 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 293 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149L THR* 5.1 5.4 - - + -
150L GLY* 3.7 33.9 - - - +
151L ILE* 4.0 16.8 - - + +
164L PRO* 5.3 5.4 - - + -
171L LEU* 6.3 1.3 - - + -
282L ILE* 4.6 18.2 - - + -
285L CYS* 4.2 24.9 - - + -
289L ILE* 3.0 41.2 + - + +
290L ARG* 3.2 16.8 + - - +
292L ASP* 1.3 77.2 - - - +
294L TYR* 1.3 62.2 + - + +
296L ASN* 3.1 15.2 + - - +
297L THR* 3.2 15.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 294 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279L PHE* 3.7 22.2 - + - -
282L ILE* 4.4 30.2 - - + +
290L ARG* 2.9 34.5 + - + -
291L LYS* 3.7 10.1 - - - +
292L ASP 3.3 0.4 - - - -
293L LEU* 1.3 79.9 - - + +
295L ALA* 1.3 52.4 + - - +
296L ASN 3.2 0.9 + - - -
297L THR* 3.5 9.3 + - - -
317L ILE* 3.8 22.0 - - + -
321L ALA* 3.6 25.2 - - + +
322L PRO* 4.3 5.2 - - + +
325L MET* 4.5 17.3 - - - -
326L LYS 3.7 17.5 - - - +
327L ILE* 3.7 26.6 - - + +
328L LYS 2.6 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 295 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147L ARG* 4.1 2.8 + - - -
291L LYS 3.6 7.0 + - - +
292L ASP* 3.1 11.2 + - - +
294L TYR* 1.3 77.8 - - - +
296L ASN* 1.3 66.2 + - - +
297L THR 3.5 0.9 - - - -
326L LYS* 4.6 19.0 + - - +
328L LYS* 3.9 29.1 + - + +
330L ILE* 3.8 14.7 - - - +
142X GLU* 4.8 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 296 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142L LEU* 3.9 2.9 - - - +
147L ARG* 3.0 26.9 - - - +
149L THR* 2.9 42.7 - - - +
150L GLY* 3.3 11.6 - - - -
151L ILE 3.8 10.5 + - - +
292L ASP* 2.6 32.5 + - - +
293L LEU* 3.1 5.7 + - - +
295L ALA* 1.3 83.7 + - - +
297L THR* 1.3 60.5 + - - +
298L VAL* 3.5 8.1 + - - +
330L ILE* 3.5 9.8 - - - +
136X GLN 5.9 1.0 + - - -
----------------------------------------------------------
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