Contacts of the helix formed by residues 254 - 265 (chain B) in PDB entry 5J3V
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 MET 254 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B LEU* 6.2 2.5 - - + -
247B MET* 4.0 24.0 - - + -
250B LEU* 3.3 23.6 - - + +
251B LEU* 3.5 30.5 - - + +
252B PRO 2.9 8.6 + - - +
253B HIS* 1.3 71.6 - - - +
255B HIS* 1.3 62.1 + - + +
256B ASN 3.0 4.5 - - - +
257B ILE* 2.8 11.8 + - + +
258B VAL* 2.6 58.6 + - + +
279B PHE* 5.0 6.5 - - + -
283B LEU* 5.4 5.8 - - + -
292B VAL* 3.9 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B PRO 4.9 0.6 + - - -
254B MET* 1.3 91.8 - - + +
256B ASN* 1.3 61.2 + - - +
258B VAL* 4.1 3.8 - - + -
259B GLU* 3.3 23.7 + - - +
291B ASP 5.5 1.0 + - - -
292B VAL* 4.1 21.3 + - + +
295B ARG* 3.1 49.4 + - + +
296B HIS* 4.0 23.1 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B HIS* 4.3 29.7 + - + +
254B MET 3.0 1.2 - - - +
255B HIS* 1.3 83.4 - - - +
257B ILE* 1.3 59.8 + - + +
258B VAL 3.4 0.2 - - - -
259B GLU* 4.0 4.3 - - - +
260B TYR* 3.3 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B PHE* 4.0 29.2 - - + -
239B LEU* 3.6 39.7 - - + -
243B LEU* 6.1 0.4 - - + -
250B LEU* 4.7 9.6 - - + +
253B HIS* 3.3 19.1 - - + +
254B MET* 2.8 32.2 + - + +
256B ASN* 1.3 80.9 - - + +
258B VAL* 1.3 61.2 + - - +
260B TYR* 3.8 12.3 - - + +
261B MET* 3.2 31.3 + - + +
279B PHE* 4.2 13.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B MET* 2.6 47.8 + - + +
255B HIS* 4.4 5.4 - - + -
257B ILE* 1.3 74.5 - - + +
259B GLU* 1.3 58.5 + - - +
260B TYR 3.2 0.2 - - - -
261B MET 3.5 1.0 + - - -
262B LEU* 3.0 29.5 + - + +
279B PHE* 4.4 15.3 - - + -
280B TRP* 3.9 10.8 - - + -
283B LEU* 5.2 0.4 - - + -
292B VAL* 4.0 14.1 - - + -
293B LEU* 4.3 13.9 - - + -
296B HIS* 3.6 35.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B HIS 3.3 21.3 + - - +
256B ASN* 4.2 4.7 - - - +
258B VAL* 1.3 79.2 - - - +
260B TYR* 1.3 62.0 + - - +
262B LEU* 3.4 28.3 - - - +
263B GLN* 3.8 13.2 + - - +
296B HIS* 3.3 24.1 + - + -
299B LYS* 5.6 7.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ALA* 3.8 27.3 - - + -
225B GLY* 3.6 18.4 + - - -
232B ARG* 3.7 11.4 - - - +
235B VAL* 4.5 10.6 - - + +
236B CYS* 4.6 5.1 - - - -
239B LEU* 4.3 13.0 - - + -
256B ASN 3.3 18.3 + - - +
257B ILE* 4.0 12.6 - - + +
258B VAL 3.2 0.6 - - - -
259B GLU* 1.3 75.4 - - - +
261B MET* 1.3 79.4 + - + +
262B LEU 3.1 4.5 - - - -
263B GLN* 3.2 25.3 - - - +
264B ARG* 3.2 60.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B CYS* 4.2 20.6 - - + +
239B LEU* 3.5 26.7 - - + -
240B VAL* 4.5 0.9 - - + -
257B ILE 3.2 19.9 + - - +
258B VAL 3.5 0.2 + - - -
260B TYR* 1.3 87.1 - - + +
262B LEU* 1.3 62.5 + - - +
263B GLN 3.2 0.4 + - - -
264B ARG* 3.8 6.4 - - - +
265B THR* 3.3 28.6 + - - +
275B GLU 4.0 7.0 - - - +
276B ALA* 3.6 28.7 - - + +
279B PHE* 3.6 47.8 - - + -
280B TRP* 3.3 8.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B VAL* 3.0 17.5 + - + +
259B GLU* 3.4 30.1 - - - +
260B TYR 3.1 0.6 - - - -
261B MET* 1.3 78.9 - - - +
263B GLN* 1.3 57.3 + - - +
265B THR* 3.2 13.4 + - - -
266B GLN* 3.7 13.0 - - - +
280B TRP* 4.0 6.5 - - + -
296B HIS* 4.4 17.7 - - + +
299B LYS* 4.0 31.9 - - + +
300B LEU* 3.8 44.2 - - + +
303B VAL* 4.3 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B GLU* 3.8 10.8 + - - +
260B TYR* 3.2 25.3 + - - +
262B LEU* 1.3 76.9 - - + +
264B ARG* 1.3 97.3 + - - +
265B THR 3.2 2.7 - - - -
266B GLN* 3.2 26.8 + - - +
267B ASP* 3.6 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B GLY* 4.9 6.5 - - - -
232B ARG* 3.5 25.9 - - - +
236B CYS* 4.1 10.1 - - - -
260B TYR* 3.2 61.6 + - + +
261B MET* 4.0 5.6 - - - -
262B LEU 3.5 0.4 - - - -
263B GLN* 1.3 113.7 + - - +
265B THR* 1.3 61.2 + - - +
266B GLN 3.1 0.9 - - - -
267B ASP* 3.0 47.7 + - - +
272B VAL* 4.3 2.4 - - + +
273B ALA* 3.3 11.8 + - - -
276B ALA* 3.6 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B MET 3.3 14.4 + - - +
262B LEU* 3.2 20.1 + - - -
264B ARG* 1.3 77.6 - - - +
266B GLN* 1.3 58.2 + - - +
267B ASP 3.3 1.3 - - - -
273B ALA* 3.3 20.6 - - - +
276B ALA* 3.4 22.9 - - - +
277B CYS* 3.7 9.9 - - + +
280B TRP* 3.4 26.3 + - - +
303B VAL* 3.2 21.7 - - + +
304B LEU* 5.8 0.7 - - + -
375B LEU* 4.7 9.4 - - - +
----------------------------------------------------------
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