Contacts of the helix formed by residues 336 - 346 (chain C) in PDB entry 4P0S
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 ARG 336 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C ARG* 3.9 22.7 - - - +
335C LYS* 1.3 77.5 - - - +
337C LEU* 1.3 60.4 + - - +
338C ASP* 3.5 29.6 + - - +
339C ASP* 3.2 16.5 + - + +
340C LEU* 2.9 26.2 + - - +
369C GLU* 3.3 39.8 + - + +
370C GLU* 3.1 28.0 + - + -
405C ILE* 5.3 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 337 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C ARG* 1.3 70.7 - - - +
338C ASP* 1.3 64.5 + - - +
340C LEU* 3.2 12.8 + - + +
341C CYS* 3.1 27.2 + - - -
368C VAL* 4.3 15.7 - - + -
369C GLU 3.3 21.6 + - - +
370C GLU* 3.1 35.1 + - + +
371C HIS* 5.5 3.1 - - + +
373C SER* 4.8 11.2 - - - +
375C HIS* 5.2 4.5 - - + +
377C LEU* 3.5 30.5 - - + -
384C LEU* 4.9 9.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 338 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C ARG* 3.9 33.9 + - - +
337C LEU* 1.3 74.9 - - - +
339C ASP* 1.3 87.7 + - - +
340C LEU 3.3 0.3 + - - -
341C CYS* 3.4 5.6 + - - +
342C SER* 3.3 26.2 + - - -
370C GLU* 4.6 7.0 + - - +
376C ASN 5.8 0.7 - - - +
377C LEU* 3.9 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 339 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C ARG* 5.8 2.1 + - - -
335C LYS* 4.1 17.7 + - - +
336C ARG* 3.2 30.0 + - + +
338C ASP* 1.3 88.2 + - - +
340C LEU* 1.3 55.5 + - - +
342C SER* 3.7 4.8 + - - -
343C SER* 2.5 33.7 + - - -
348C ARG* 3.6 17.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 340 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C LYS* 4.1 17.2 - - + +
336C ARG 2.9 13.6 + - - +
337C LEU* 3.4 17.3 - - + +
338C ASP 3.2 0.4 - - - -
339C ASP* 1.3 75.9 - - - +
341C CYS* 1.3 66.8 + - - +
343C SER* 3.1 7.9 + - - -
344C ILE* 2.9 41.5 + - + +
349C PHE* 3.5 34.8 - - + -
366C TYR* 5.3 1.8 - - + +
368C VAL* 6.6 0.2 - - + -
384C LEU* 4.5 17.0 - - + -
387C ALA* 5.2 7.4 - - + -
388C VAL* 5.3 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 341 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C LEU 3.1 12.3 + - - -
338C ASP* 3.4 8.5 + - - +
340C LEU* 1.3 80.1 - - - +
342C SER* 1.3 64.7 + - - +
344C ILE* 3.3 3.4 + - - +
345C ILE* 3.2 27.2 + - - +
377C LEU* 3.8 20.0 - - - -
378C SER* 3.3 20.6 - - - +
379C LEU* 3.8 24.7 - - + -
384C LEU* 3.5 30.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 342 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C ASP 3.3 15.0 + - - -
339C ASP* 4.1 4.9 - - - -
340C LEU 3.3 0.4 - - - -
341C CYS* 1.3 79.6 - - - +
343C SER* 1.3 62.4 + - - +
345C ILE* 3.3 10.7 + - - +
346C ASP* 3.1 31.0 + - - +
348C ARG* 4.4 12.6 - - - -
378C SER* 4.6 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 343 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C LYS* 3.4 11.2 - - - -
339C ASP 2.5 20.7 + - - -
340C LEU* 3.1 14.5 + - - -
342C SER* 1.3 76.8 - - - +
344C ILE* 1.3 59.4 + - - +
346C ASP* 3.1 9.0 - - - +
348C ARG* 2.7 57.6 + - - +
349C PHE* 2.9 21.6 + - - -
352C GLN* 5.0 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 344 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C LEU* 2.9 47.5 + - + +
341C CYS 3.3 3.3 + - - +
343C SER* 1.3 76.1 - - - +
345C ILE* 1.3 64.3 + - - +
347C GLY* 3.2 11.6 + - - -
349C PHE* 3.8 20.9 - - + -
350C ARG* 5.9 1.9 - - - +
379C LEU* 4.5 13.5 - - + -
383C THR* 6.0 1.1 - - + -
384C LEU* 4.3 20.6 - - + -
387C ALA* 4.6 13.5 - - + -
1U G 3.9 47.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 345 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C CYS 3.2 14.1 + - - +
342C SER* 3.6 9.9 - - - +
344C ILE* 1.3 82.1 - - - +
346C ASP* 1.3 65.0 + - + +
347C GLY 3.2 1.1 + - - -
378C SER* 3.7 27.6 - - - +
379C LEU* 4.1 23.3 - - + -
1U G 4.2 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 346 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C SER* 3.1 17.2 - - - +
343C SER 3.1 15.4 - - - +
345C ILE* 1.3 81.9 - - + +
347C GLY* 1.3 59.2 + - - +
348C ARG* 3.2 34.7 + - - +
----------------------------------------------------------
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