Contacts of the helix formed by residues 396 - 407 (chain B) in PDB entry 2RIO
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 PRO 396 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A GLN 3.8 9.0 - - - +
427A ILE* 5.3 1.3 - - - -
430A GLU* 3.3 40.6 - - + +
302B LYS* 5.4 0.4 - - - -
303B SER* 3.8 22.7 - - - -
306B LEU* 3.9 18.1 - - + +
394B PRO* 3.6 1.6 - - + -
395B VAL* 1.4 90.0 - - + +
397B ASP* 1.3 69.3 + - - +
398B GLY 3.5 2.5 - - - -
399B PHE* 3.4 3.3 + - - +
400B TYR* 2.9 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A GLU* 5.0 2.5 - - - +
302B LYS* 3.6 32.8 + - + +
303B SER* 4.0 5.2 + - - -
394B PRO* 3.7 5.2 + - + +
395B VAL 4.0 0.2 - - - -
396B PRO* 1.3 89.9 - - - +
398B GLY* 1.3 57.9 + - - +
400B TYR* 3.8 4.6 - - - +
401B ASP* 3.0 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B LEU 5.3 0.9 - - - +
392B MET 3.9 6.2 - - - +
393B GLY 3.5 16.8 - - - +
394B PRO* 2.7 23.9 + - - +
397B ASP* 1.3 73.6 - - - +
399B PHE* 1.3 58.5 + - - +
401B ASP* 3.3 6.3 + - - +
402B TYR* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B LEU* 3.8 32.3 - - + -
374B LEU* 3.3 31.6 - - + -
377B LYS* 3.8 13.0 - - + -
378B TYR* 3.4 31.0 - + + -
381B PHE* 3.9 18.2 - + - -
392B MET* 3.1 29.9 + - + +
394B PRO 2.9 6.0 + - - +
395B VAL* 3.9 22.2 - - + -
396B PRO 3.7 6.3 - - - +
397B ASP 3.4 0.2 - - - -
398B GLY* 1.3 75.8 - - - +
400B TYR* 1.3 66.7 + - - +
402B TYR* 3.2 18.2 + - - +
403B PHE* 3.5 27.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ASP* 6.0 0.9 - - - -
267B SER* 5.1 4.1 + - - -
271B GLU* 4.4 1.7 + - - -
302B LYS* 3.8 28.9 - - + +
305B LYS* 3.4 34.6 - - + +
306B LEU* 3.7 28.5 - - + -
309B LEU* 4.0 15.0 - - + -
374B LEU* 6.0 2.0 - - + -
396B PRO 2.9 18.8 + - - +
397B ASP* 3.8 5.4 - - - +
399B PHE* 1.3 84.5 - - - +
401B ASP* 1.3 70.7 + - - +
403B PHE* 3.1 7.9 + - - +
404B THR* 3.1 52.9 + - + +
411B LEU* 3.3 33.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ASP* 4.5 5.9 - - - +
302B LYS* 2.7 37.9 + - - +
397B ASP* 3.0 22.7 + - - +
398B GLY* 3.7 7.0 - - - +
400B TYR* 1.3 82.2 - - - +
402B TYR* 1.3 61.2 + - - +
404B THR* 3.8 8.3 + - - -
405B LYS* 2.8 36.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B PHE* 3.6 27.3 - + - -
349B ASP* 5.2 9.9 + - - +
352B PHE* 3.9 21.3 - + - -
391B LEU* 3.4 36.1 - - + +
392B MET* 3.8 30.5 - - + +
398B GLY 2.9 13.4 + - - +
399B PHE 3.2 12.8 - - - +
401B ASP* 1.3 80.2 - - - +
403B PHE* 1.3 73.4 + + + +
406B ARG* 2.8 66.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B PHE* 3.5 32.5 - + - -
352B PHE* 3.6 24.9 - + - -
370B LEU* 4.8 9.9 - - + -
373B ALA* 5.4 0.4 - - + -
374B LEU* 3.6 53.6 - - + -
377B LYS* 4.0 6.5 - - + -
392B MET* 4.7 1.6 - - - -
399B PHE* 3.5 43.7 - + - -
400B TYR* 3.1 7.6 + - + +
402B TYR* 1.3 93.7 - + + +
404B THR* 1.3 59.6 + - + +
406B ARG* 3.3 6.6 + - - +
407B PHE* 2.9 29.7 + + - +
410B LEU* 4.3 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ASP* 5.0 4.5 + - - +
266B ARG* 5.7 0.9 - - - +
267B SER* 3.9 25.1 + - - -
400B TYR* 3.1 56.1 + - + +
401B ASP* 3.8 9.0 + - - -
403B PHE* 1.3 73.7 - - + +
405B LYS* 1.3 67.5 + - - +
406B ARG 3.2 0.9 - - - -
407B PHE 3.6 9.0 - - - +
408B PRO* 3.1 24.5 - - - +
410B LEU* 4.4 18.4 - - + -
411B LEU* 5.0 3.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ARG* 5.9 1.7 - - - +
347B LYS* 5.3 1.2 + - - -
401B ASP* 2.8 22.1 + - + +
402B TYR* 3.9 3.4 - - - +
404B THR* 1.3 79.6 + - - +
406B ARG* 1.3 78.2 + - + +
408B PRO* 3.9 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LYS* 3.2 65.1 + - + +
348B PHE* 3.6 21.5 - - - +
402B TYR* 2.8 61.8 + - - +
403B PHE* 3.3 10.1 + - - +
404B THR 3.2 0.2 - - - -
405B LYS* 1.3 97.9 - - + +
407B PHE* 1.4 81.1 + - + +
408B PRO* 3.8 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B VAL* 3.5 26.0 - - + -
339B ILE* 4.4 8.5 - - + -
340B PRO* 5.7 1.8 - - + -
341B SER* 5.8 0.9 - - - -
343B ASP 5.6 0.2 - - - -
344B TRP* 3.5 33.2 - - + -
347B LYS* 3.4 28.9 - - + -
348B PHE* 3.8 16.8 - + - -
370B LEU* 3.6 32.1 - - + -
403B PHE* 2.9 18.5 + + - +
404B THR* 3.3 9.8 - - - +
405B LYS 3.3 0.2 - - - -
406B ARG* 1.4 91.5 - - + +
408B PRO* 1.3 67.2 - - - +
409B ASN 3.0 4.6 + - - -
410B LEU* 3.0 29.1 + - + +
----------------------------------------------------------
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