Contacts of the helix formed by residues 287 - 297 (chain L) in PDB entry 3J8B
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 TYR 287 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87K CYS* 4.5 27.7 + - + +
282L SER* 6.4 0.2 - - - +
285L GLY 3.8 1.9 + - - -
286L ASP* 1.3 73.9 - - - +
288L TYR* 1.3 58.6 + - - +
290L ALA* 3.6 5.9 + - - +
291L ILE* 3.1 26.9 + - - +
325L MET* 5.4 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 288 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286L ASP* 3.5 2.7 - - + +
287L TYR* 1.3 75.4 - - - +
289L GLN* 1.3 62.1 + - - +
291L ILE* 3.2 8.6 + - - +
292L LYS* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 289 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281L HIS* 6.2 3.4 - - + -
286L ASP* 3.8 14.5 + - + +
287L TYR 3.5 0.4 - - - -
288L TYR* 1.3 77.6 - - - +
290L ALA* 1.3 58.4 + - - +
292L LYS* 3.2 8.2 + - - +
293L VAL* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 290 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278L LEU* 4.3 24.7 - - + +
281L HIS* 5.0 5.3 - - + +
282L SER* 4.7 14.8 - - - +
286L ASP 3.5 16.7 + - - +
287L TYR* 3.7 5.8 - - - +
289L GLN* 1.3 78.4 - - - +
291L ILE* 1.3 58.3 + - - +
293L VAL* 3.2 9.7 + - - +
294L LEU* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 291 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287L TYR 3.1 15.5 + - - +
288L TYR* 3.2 11.9 + - - +
290L ALA* 1.3 77.8 - - - +
292L LYS* 1.3 57.1 + - - +
294L LEU* 3.2 9.2 + - - +
295L GLU* 2.9 27.4 + - - +
322L ALA* 5.8 5.2 - - + -
325L MET* 6.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 292 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288L TYR 2.9 13.3 + - - +
289L GLN* 3.5 11.4 - - - +
291L ILE* 1.3 71.9 - - - +
293L VAL* 1.3 65.6 + - - +
295L GLU* 3.2 9.8 + - - +
296L ASN* 3.0 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 293 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274L LEU* 5.1 8.7 - - + +
278L LEU* 4.1 21.1 - - + -
289L GLN 2.9 13.4 + - - +
290L ALA* 3.2 9.8 + - - +
292L LYS* 1.3 75.9 - - - +
294L LEU* 1.3 57.4 + - - +
296L ASN* 3.2 8.5 + - - +
297L ILE* 2.8 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 294 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278L LEU* 5.3 4.0 - - + +
290L ALA 2.9 13.0 + - - +
291L ILE* 3.2 12.3 + - - +
293L VAL* 1.3 76.0 - - - +
295L GLU* 1.3 63.1 + - - +
297L ILE* 3.0 21.8 + - - +
298L GLU* 3.7 7.1 + - - +
318L TYR* 5.8 2.7 - - + +
319L VAL* 6.5 0.4 - - - -
322L ALA* 4.6 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 295 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291L ILE 2.9 12.9 + - - +
292L LYS* 3.4 12.8 - - - +
294L LEU* 1.3 74.4 - - - +
296L ASN* 1.3 65.4 + - - +
298L GLU* 4.4 4.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
292L LYS 3.0 12.9 + - - +
293L VAL* 3.6 9.9 - - - +
295L GLU* 1.3 76.7 - - - +
297L ILE* 1.3 63.9 + - - +
298L GLU 3.3 9.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 297 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271L TYR* 4.3 13.9 - - - +
274L LEU* 4.9 18.4 - - + -
275L VAL* 5.4 8.3 - - + +
293L VAL 2.8 17.5 + - - +
294L LEU* 3.0 15.5 + - - +
296L ASN* 1.3 77.2 - - - +
298L GLU* 1.3 66.4 + - - +
299L LEU* 3.3 8.8 + - - +
----------------------------------------------------------
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