Contacts of the helix formed by residues 355 - 373 (chain B) in PDB entry 5AO3
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 GLU 355 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ASN* 4.5 2.1 + - - -
333B ARG* 2.5 48.8 + - - +
334B PHE* 3.5 20.4 + - + +
337B PHE* 3.7 28.8 - - + -
351B ALA* 4.6 12.1 - - + -
352B ARG* 2.8 18.8 + - + +
354B LYS* 1.3 77.5 - - - +
356B VAL* 1.3 59.4 + - - +
357B GLY 3.3 1.8 - - - -
358B ASN* 3.2 28.8 + - - +
359B LEU* 3.0 30.0 + - - +
520B PHE* 4.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A TYR* 3.1 44.4 - - + +
352B ARG 4.4 0.2 + - - -
353B ASP 3.3 12.4 + - - +
355B GLU* 1.3 76.2 - - - +
357B GLY* 1.3 58.8 + - - +
359B LEU* 3.5 7.1 - - - +
360B TYR* 2.9 27.0 + - - +
515B ILE* 4.0 30.1 - - + -
520B PHE* 4.2 15.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A GLY* 3.5 28.2 - - - +
360A TYR* 3.6 14.9 - - - -
361A ASP* 3.7 15.0 - - - -
354B LYS 4.0 1.4 + - - -
355B GLU 3.3 0.8 - - - -
356B VAL* 1.3 84.7 - - - +
358B ASN* 1.3 60.3 + - - +
360B TYR* 3.4 6.9 + - - -
361B ASP* 3.4 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A ASP* 4.9 0.2 - - - -
328B ASN 3.9 8.7 - - - +
329B PHE* 3.7 16.6 - - + -
330B ASP* 3.0 50.7 + - - +
333B ARG* 3.3 34.2 + - - +
334B PHE* 4.1 2.5 - - + +
355B GLU* 3.2 27.3 + - - +
357B GLY* 1.3 74.6 - - - +
359B LEU* 1.3 58.8 + - + +
361B ASP* 3.0 11.6 + - - +
362B MET 2.9 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ILE* 3.9 17.9 - - + -
329B PHE* 5.0 0.9 - - + -
334B PHE* 3.6 33.4 - - + -
351B ALA* 4.7 1.1 - - + -
355B GLU 3.0 15.0 + - - +
356B VAL* 3.3 10.3 + - - +
358B ASN* 1.3 74.3 - - - +
360B TYR* 1.3 65.1 + - - +
362B MET* 3.2 17.4 + - + +
363B PHE* 3.1 37.8 + - + -
515B ILE* 4.8 9.0 - - + -
518B VAL* 3.6 33.2 - - + -
520B PHE* 3.8 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ASP* 3.5 23.3 + - - -
354A LYS* 3.3 17.3 - - - -
356A VAL* 3.3 26.6 - - + +
357A GLY* 3.5 21.8 - - - -
356B VAL* 2.9 15.2 + - + +
357B GLY* 3.4 5.1 + - - +
358B ASN 3.3 0.4 - - - -
359B LEU* 1.3 76.8 - - - +
361B ASP* 1.3 61.3 - - - +
363B PHE* 3.5 3.2 + - + +
364B HIS* 2.8 56.4 + + + +
515B ILE* 4.0 31.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ARG* 3.4 34.3 + - - -
354A LYS 4.1 5.5 - - - +
357A GLY* 4.0 8.2 - - - +
358A ASN* 5.0 0.2 - - - -
361A ASP* 5.1 1.9 - - - +
328B ASN* 3.9 31.7 + - + +
329B PHE* 4.1 5.6 + - - +
357B GLY 3.4 15.8 + - - +
358B ASN* 3.0 12.9 + - - +
360B TYR* 1.3 87.4 - - - +
362B MET* 1.3 65.4 + - - +
364B HIS* 4.3 3.9 + - - +
365B THR* 3.4 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B GLY 4.3 7.2 - - - +
308B ILE* 3.8 23.3 - - + -
312B LYS* 5.8 0.4 - - - -
313B TRP* 3.6 27.6 - - - -
316B PHE* 4.3 22.5 - - + -
329B PHE* 3.5 41.0 - - + +
358B ASN 2.9 7.6 + - - +
359B LEU* 3.2 15.8 + - + +
361B ASP* 1.3 77.1 - - - +
363B PHE* 1.3 105.7 + - + +
365B THR* 3.2 8.2 + - - +
366B ARG* 3.2 19.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B ASN 4.3 17.3 - - - -
307B GLY* 5.1 3.6 - - - -
308B ILE* 4.5 7.2 - - + -
359B LEU* 3.1 33.5 + - + +
360B TYR* 4.0 5.6 - - + +
362B MET* 1.3 104.6 - - + +
364B HIS* 1.3 65.7 + - - +
366B ARG* 3.3 39.5 + - - +
367B ASN* 3.1 27.5 + - - +
514B PRO* 4.2 13.5 - - + -
515B ILE* 3.9 39.0 - - + -
518B VAL* 5.2 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ARG* 4.9 14.0 + - - -
353A ASP* 6.1 0.2 - - - -
354A LYS* 3.9 27.5 + - + +
360B TYR* 2.8 53.1 + + + +
361B ASP* 4.3 5.6 - - - +
362B MET 3.3 0.2 - - - -
363B PHE* 1.3 75.9 - - - +
365B THR* 1.3 60.8 + - - +
367B ASN* 3.2 11.5 + - + +
368B SER* 3.0 45.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B PHE* 4.1 20.6 - - + -
320B CYS* 3.7 23.6 - - - -
325B ILE* 6.1 0.9 - - - -
326B GLN 3.9 5.5 + - - -
327B ASN* 3.1 38.0 + - - +
328B ASN 4.1 2.1 + - - -
361B ASP 3.4 9.8 + - - -
362B MET* 3.2 9.5 + - - -
364B HIS* 1.3 79.6 + - - +
366B ARG* 1.3 60.5 + - - +
368B SER* 3.1 7.8 + - - +
369B LEU* 2.9 33.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B GLY 6.2 0.4 - - - -
312B LYS* 6.0 2.7 - - + -
316B PHE* 3.5 38.1 - - + -
362B MET* 3.2 9.1 + - - +
363B PHE* 3.3 40.7 + - + +
365B THR* 1.3 76.2 - - - +
367B ASN* 1.3 86.7 + - - +
369B LEU* 3.6 1.7 + - - +
370B HIS* 2.9 48.9 + - + +
505B MET* 6.2 3.8 - - - +
514B PRO* 6.0 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B PHE* 3.1 13.9 + - - +
364B HIS* 3.5 13.5 - - + +
365B THR 3.1 0.4 - - - -
366B ARG* 1.3 112.3 + - - +
368B SER* 1.3 59.3 + - - +
370B HIS* 3.5 4.5 + - - +
371B ARG* 3.0 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ILE* 4.5 18.6 - - - +
364B HIS* 3.0 34.2 + - - -
365B THR* 3.7 8.7 - - - -
367B ASN* 1.3 73.8 - - - +
369B LEU* 1.3 59.2 + - - +
371B ARG* 4.8 9.2 + - - +
372B ARG* 2.7 60.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B TYR 4.2 2.7 - - - +
316B PHE* 3.7 43.5 - - + +
319B ASP* 4.1 8.5 - - + -
320B CYS* 4.1 11.9 - - - +
323B LEU* 3.9 27.8 - - + -
325B ILE* 4.1 14.6 - - + -
365B THR* 2.9 20.0 + - + +
366B ARG* 4.0 3.6 - - - +
368B SER* 1.3 75.9 - - - +
370B HIS* 1.3 57.7 + - - +
373B ALA* 2.8 27.3 + - + +
374B TYR* 2.9 44.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B TYR* 5.7 3.6 - - - -
316B PHE* 5.5 3.1 - + - -
366B ARG* 2.9 44.9 + - + +
367B ASN* 4.0 4.7 - - - +
369B LEU* 1.3 80.2 - - - +
371B ARG* 1.3 63.4 + - - +
374B TYR* 3.3 39.1 + + + -
375B GLN* 3.0 43.5 + - + +
505B MET* 3.8 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ARG* 5.6 6.3 - - - +
524A THR* 6.2 1.8 - - - +
367B ASN 3.0 18.5 + - - +
368B SER* 4.2 9.8 + - - +
370B HIS* 1.3 78.6 - - - +
372B ARG* 1.3 94.9 + - - +
375B GLN* 3.8 19.4 - - - +
376B HIS* 4.7 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ARG* 5.6 6.1 - - - +
157B PHE* 3.6 16.1 - - - -
324B GLY 4.9 6.3 + - - -
325B ILE* 4.2 42.8 - - + +
368B SER* 2.7 32.4 + - - +
371B ARG* 1.3 111.6 - - - +
373B ALA* 1.3 58.3 + - - +
376B HIS* 3.8 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B LEU* 5.6 1.8 - - + -
157B PHE* 4.0 16.8 - - + -
323B LEU* 3.6 30.7 - - + -
325B ILE* 5.4 0.9 - - + -
369B LEU* 2.8 22.0 + - + +
371B ARG 3.5 0.6 - - - -
372B ARG* 1.3 76.7 - - + +
374B TYR* 1.3 75.8 + - + +
375B GLN 3.1 1.8 - - - -
376B HIS* 3.0 21.5 + - - +
380B ASN* 5.0 0.2 + - - -
----------------------------------------------------------
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