Contacts of the helix formed by residues 252 - 266 (chain W) in PDB entry 5IY8
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 THR 252 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126W PHE* 4.7 10.5 - - + -
250W ASN* 3.9 14.1 - - - +
251W LEU* 1.3 86.8 - - - +
253W ARG* 1.3 65.1 + - - +
254W ARG* 4.7 2.0 - - - -
255W THR* 2.6 41.0 + - - -
256W LEU* 3.3 11.8 + - - +
429W ALA 5.5 7.6 - - - +
431W PRO 5.8 2.2 - - - -
432W ILE* 3.9 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 253 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251W LEU* 4.7 5.1 - - - +
252W THR* 1.3 70.6 - - - +
254W ARG* 1.4 58.6 + - - +
256W LEU* 3.3 17.1 + - + +
257W ASP* 2.9 28.5 + - - +
286W ARG* 4.4 10.7 + - - +
289W VAL* 5.5 5.8 - - + -
290W GLU* 2.8 48.7 + - + +
293W ARG* 3.3 36.0 - - - +
294W GLU* 5.4 2.6 + - - -
428W ILE* 5.9 1.1 - - + -
429W ALA 5.6 3.0 + - - +
430W ASN* 4.1 31.6 + - + +
431W PRO 5.3 7.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 254 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126W PHE* 3.4 62.8 - - + +
252W THR* 3.4 2.0 - - - -
253W ARG* 1.4 78.5 - - - +
255W THR* 1.3 56.8 + - - +
257W ASP* 3.2 7.9 + - - +
258W ARG* 2.9 54.9 + - - +
428W ILE* 3.7 62.7 + - + +
429W ALA* 5.6 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 255 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126W PHE* 3.5 18.0 - - - -
127W GLY* 5.8 6.5 - - - -
252W THR* 2.6 29.9 + - - -
254W ARG* 1.3 76.1 - - - +
256W LEU* 1.3 57.4 + - - +
258W ARG* 3.5 6.9 + - + +
259W CYS* 3.0 26.4 + - - +
395W SER* 3.3 28.2 - - - +
398W THR* 4.8 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 256 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251W LEU* 5.8 6.1 - - + -
252W THR 3.3 8.4 + - - +
253W ARG* 3.3 16.5 + - + +
255W THR* 1.3 74.4 - - - +
257W ASP* 1.3 59.9 + - - +
259W CYS* 3.1 6.6 + - + +
260W GLN* 3.0 31.7 + - - +
282W ARG* 4.3 21.5 - - + +
285W TYR* 6.1 2.9 - - + -
286W ARG* 3.9 43.3 - - + +
289W VAL* 4.2 14.4 - - + -
399W LEU* 3.8 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 257 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253W ARG 2.9 17.4 + - - +
254W ARG* 3.5 10.1 - - - +
256W LEU* 1.3 74.9 - - - +
258W ARG* 1.3 88.0 + - - +
260W GLN* 3.5 9.3 + - - +
261W GLY* 3.4 14.9 + - - -
286W ARG* 2.7 40.7 + - - +
428W ILE* 5.3 4.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 258 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126W PHE* 5.4 8.8 - - + +
127W GLY* 5.6 11.2 - - - +
254W ARG* 2.9 54.3 + - + +
255W THR* 3.7 7.9 - - - +
257W ASP* 1.3 96.5 + - - +
259W CYS* 1.3 53.6 + - - +
261W GLY* 3.3 4.4 + - - -
262W ASN* 3.1 26.5 + - - +
395W SER* 4.8 3.4 - - - +
428W ILE* 4.0 18.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 259 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255W THR 3.0 14.3 + - - +
256W LEU* 3.1 8.3 + - - +
258W ARG* 1.3 69.7 - - - +
260W GLN* 1.3 60.2 + - - +
262W ASN* 3.7 6.6 - - - +
263W LEU* 2.9 39.0 + - - +
282W ARG* 6.2 0.2 - - - -
330W LEU* 6.2 0.7 - - - -
337W LEU* 4.9 3.1 - - - -
395W SER* 3.4 21.2 + - - +
396W PRO* 3.6 39.0 - - - -
399W LEU* 4.2 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 260 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256W LEU 3.0 13.7 + - - +
257W ASP* 3.5 9.2 + - - +
259W CYS* 1.3 74.9 - - - +
261W GLY* 1.3 62.8 + - - +
263W LEU* 3.8 4.4 - - - +
264W GLU* 3.1 24.0 + - - +
279W GLN* 3.6 16.8 + - - +
282W ARG* 3.0 50.9 + - - +
286W ARG* 2.8 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 261 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257W ASP 3.4 7.0 + - - -
258W ARG 3.3 7.1 + - - -
260W GLN* 1.3 76.9 - - - +
262W ASN* 1.3 53.4 + - - +
264W GLU* 3.4 6.4 + - - +
265W THR* 2.6 39.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 262 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258W ARG 3.1 14.7 + - - +
259W CYS* 3.7 10.5 - - - +
260W GLN 3.3 0.4 - - - -
261W GLY* 1.3 75.3 - - - +
263W LEU* 1.3 56.8 + - - +
265W THR* 3.3 12.3 - - - +
266W LEU* 3.0 27.4 + - - +
337W LEU* 3.6 24.5 - - + +
340W VAL* 6.2 0.3 - - - +
341W LYS* 6.1 0.8 - - - +
394W PHE* 4.1 24.5 - - - -
395W SER* 5.7 1.3 + - - +
396W PRO* 5.3 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 263 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259W CYS* 2.9 23.6 + - - +
260W GLN* 3.8 1.8 - - - +
262W ASN* 1.3 72.2 - - - +
264W GLU* 1.4 65.6 + - - +
266W LEU* 3.3 20.9 + - - +
268W LYS* 3.4 26.9 + - + +
278W GLU* 4.8 7.9 - - + +
279W GLN* 3.4 40.6 - - + +
282W ARG* 4.3 20.4 - - + -
330W LEU* 5.6 9.2 - - + -
333W LEU* 3.7 31.2 - - + -
337W LEU* 4.1 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 264 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260W GLN 3.1 18.3 + - - +
261W GLY* 3.7 7.4 - - - +
263W LEU* 1.4 75.1 - - - +
265W THR* 1.4 56.3 + - - +
267W GLN* 3.1 26.7 + - - -
268W LYS* 2.7 38.6 + - - +
279W GLN* 2.8 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 265 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261W GLY 2.6 24.4 + - - -
262W ASN* 3.3 14.5 - - - +
264W GLU* 1.4 71.2 - - - +
266W LEU* 1.4 54.7 + - - +
267W GLN* 3.1 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 266 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262W ASN 3.0 13.4 + - - +
263W LEU 3.3 11.7 - - - +
265W THR* 1.4 71.3 - - - +
267W GLN* 1.3 66.7 + - - +
268W LYS 3.7 21.9 - - - +
333W LEU* 3.7 21.8 - - + -
336W LEU* 4.1 28.3 - - + -
337W LEU* 3.9 17.0 - - + +
340W VAL* 3.7 40.2 - - + -
----------------------------------------------------------
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