Contacts of the helix formed by residues 396 - 406 (chain B) in PDB entry 2AY6
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 396 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 3.8 41.0 - - + +
391B GLY 3.8 2.9 + - - +
392B LEU* 3.5 13.3 - - - +
393B ASN* 2.8 38.2 + - - +
395B ASN* 1.3 78.3 - - + +
397B ILE* 1.3 64.8 + - - +
398B PRO* 3.4 1.1 - - - -
399B ILE* 3.3 11.6 + - + +
400B LEU* 2.9 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B LEU* 3.8 21.3 - - + +
336B GLN* 3.2 40.6 - - + +
337B LEU* 3.9 31.7 - - + +
340B GLU* 4.1 16.4 - - + +
392B LEU* 3.8 14.8 - - + -
393B ASN 2.7 34.6 + - - +
394B ASP* 4.7 1.8 - - - +
396B THR* 1.3 71.9 - - - +
398B PRO* 1.3 63.0 - - + +
400B LEU* 3.1 9.0 + - - +
401B ALA* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B GLU* 3.7 28.0 - - + +
344B LEU* 6.0 0.2 - - - +
394B ASP 3.1 20.9 - - - +
395B ASN 3.4 13.2 - - - +
396B THR 3.4 0.9 - - - -
397B ILE* 1.3 95.3 - - + +
399B ILE* 1.3 65.3 + - + +
401B ALA* 3.1 3.8 + - - +
402B ARG* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 4.7 15.7 - - + -
377B PHE* 5.9 4.3 - - + -
379B ILE* 6.1 1.8 - - + -
395B ASN 3.4 24.0 - - - +
396B THR* 3.3 15.9 + - + +
398B PRO* 1.3 78.6 - - + +
400B LEU* 1.3 51.0 + - - +
402B ARG* 3.4 21.6 + - - +
403B ALA* 2.7 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 5.6 2.2 - - + +
35B LEU* 3.8 17.5 - - + -
337B LEU* 3.6 31.0 - - + -
363B LEU* 5.3 5.2 - - + -
379B ILE* 3.6 36.3 - - + -
381B MET* 5.0 3.4 - - + -
387B ILE* 5.1 6.5 - - + -
392B LEU* 3.6 28.7 - - + -
396B THR* 2.9 13.9 + - - +
397B ILE 3.3 7.6 - - - +
399B ILE* 1.3 74.0 - - - +
401B ALA* 1.3 64.6 + - - +
403B ALA* 3.0 6.2 + - - +
404B ILE* 2.9 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B LEU* 4.9 2.9 - - + -
340B GLU* 3.6 27.6 - - + -
341B LEU* 3.6 29.1 - - + +
344B LEU* 4.0 11.7 - - + -
397B ILE 2.9 8.9 + - - +
398B PRO 3.4 7.9 - - - +
400B LEU* 1.3 76.9 - - - +
402B ARG* 1.3 62.1 + - - +
404B ILE* 3.2 20.3 - - - +
405B ILE* 3.2 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LEU* 4.1 12.7 - - + +
377B PHE* 6.1 1.6 - - + -
398B PRO 2.9 16.4 + - - +
399B ILE* 3.8 20.5 + - - +
401B ALA* 1.3 76.3 - - - +
403B ALA* 1.3 52.6 + - - +
405B ILE* 3.1 6.2 + - + +
406B GLU* 2.7 56.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B ILE* 4.0 15.5 - - + -
377B PHE* 3.6 32.9 - - + -
379B ILE* 4.9 7.4 - - + -
399B ILE* 2.7 23.9 + - + +
400B LEU* 3.0 12.5 + - - +
402B ARG* 1.3 72.6 - - - +
404B ILE* 1.3 56.5 + - + +
406B GLU* 3.3 2.1 + - - +
407B VAL* 2.8 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU* 3.3 37.2 - - + -
350B PHE* 4.0 24.0 - - + -
363B LEU* 4.0 32.3 - - + -
373B ILE* 4.7 11.7 - - + -
400B LEU* 2.9 30.3 + - + +
401B ALA* 3.2 15.7 - - - +
403B ALA* 1.3 72.6 - - + +
405B ILE* 1.3 60.8 + - + +
407B VAL* 3.3 12.2 - - + +
408B GLY* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU* 5.1 2.0 - - + -
344B LEU* 3.5 34.1 - - + +
345B SER* 4.6 11.4 - - - -
349B ARG* 5.6 3.4 - - - +
350B PHE* 5.2 8.3 - - + -
401B ALA 3.2 15.0 - - - +
402B ARG* 3.1 11.6 + - + +
404B ILE* 1.3 84.3 - - + +
406B GLU* 1.3 59.7 + - + +
408B GLY* 2.8 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B ARG* 5.0 3.3 + - - -
377B PHE* 3.4 31.9 - - + -
402B ARG* 2.7 40.6 + - + +
405B ILE* 1.3 74.9 - - + +
407B VAL* 1.3 59.4 + - - +
408B GLY* 3.5 0.5 + - - -
----------------------------------------------------------
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