Contacts of the helix formed by residues 326 - 333 (chain B) in PDB entry 1SHY
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 GLY 326 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B PRO* 1.3 74.1 - - - +
327B ALA* 1.3 60.8 + - - -
328B GLN 3.2 2.8 + - - -
329B LEU 3.3 2.8 + - - -
330B ALA* 2.8 28.5 + - - +
337B LEU* 4.4 2.9 - - - -
446B ILE* 3.6 21.8 - - - +
448B GLY 4.9 0.7 - - - -
449B ASP 3.8 8.7 - - - -
450B LEU 4.5 0.2 - - - -
451B THR* 2.8 19.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B GLY* 1.3 71.4 - - - -
328B GLN* 1.3 62.9 + - - +
330B ALA* 3.3 7.1 - - - +
331B ARG* 2.9 44.1 + - - +
337B LEU* 3.9 19.1 - - + +
448B GLY 4.7 1.8 + - - +
449B ASP* 3.7 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ALA* 1.3 77.4 - - - +
329B LEU* 1.3 64.2 + - - +
331B ARG* 3.6 15.0 - - - +
332B GLN* 3.1 32.7 + - - +
449B ASP* 3.2 24.5 + - + +
450B LEU* 3.4 27.3 - - + +
451B THR 5.6 0.7 - - - +
466B VAL* 5.3 2.5 - - - +
467B VAL 4.2 4.1 - - - +
468B SER* 2.9 33.1 + - - -
470B SER 4.3 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B PRO* 4.7 6.3 - - + -
326B GLY 3.3 2.7 + - - +
328B GLN* 1.3 78.9 - - - +
330B ALA* 1.3 68.4 + - - +
332B GLN* 3.0 29.1 + - - +
333B ILE* 3.1 39.4 + - + +
341B ILE* 6.0 0.7 - - + -
343B PHE* 3.8 20.0 - - + -
364B ALA* 5.5 2.2 - - + -
429B LEU* 4.0 19.3 - - + -
449B ASP 4.5 0.8 + - - -
451B THR* 3.7 33.6 - - + +
467B VAL* 3.7 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B PRO* 4.1 15.2 - - + +
326B GLY 2.8 23.2 + - - +
327B ALA* 3.1 11.8 + - - +
329B LEU* 1.3 74.6 - - - +
331B ARG* 1.3 68.2 + - - +
332B GLN 2.7 0.3 + - - -
333B ILE* 3.0 16.3 + - - +
335B ALA* 3.0 35.9 + - + +
336B SER 4.5 1.8 - - - +
337B LEU* 4.8 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ALA* 2.9 37.9 + - - +
328B GLN* 3.6 12.6 + - - +
330B ALA* 1.3 76.0 - - - +
332B GLN* 1.3 62.7 + - + +
334B GLY* 4.1 5.4 + - - -
335B ALA* 3.9 10.4 - - - +
449B ASP* 5.1 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B GLN* 3.1 44.4 - - - +
329B LEU* 3.0 14.9 + - + +
330B ALA 2.7 4.8 + - - -
331B ARG* 1.3 81.8 - - + +
333B ILE* 1.3 60.2 + - - +
334B GLY 3.6 0.6 + - - -
468B SER* 3.3 9.3 + - - +
469B ARG* 2.6 58.2 - - + +
470B SER* 4.3 11.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B PRO* 4.9 2.9 - - + -
329B LEU* 3.1 40.8 - - + +
330B ALA* 3.0 15.9 + - - +
332B GLN* 1.3 74.7 - - - +
334B GLY* 1.3 58.1 + - - +
335B ALA* 3.7 10.1 - - - +
341B ILE* 4.6 18.4 - - + -
364B ALA* 5.0 15.5 - - + +
366B PRO* 4.2 22.3 - - + +
369B TYR* 3.7 14.0 - - - -
426B ARG* 4.6 10.9 + - - +
429B LEU* 5.0 5.8 - - + -
469B ARG* 4.4 24.0 - - + +
----------------------------------------------------------
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