Contacts of the helix formed by residues 333 - 345 (chain C) in PDB entry 3J8B
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 ASP 333 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C GLU 3.8 10.9 + - - +
331C GLY 3.9 2.0 + - - -
332C GLU* 1.3 73.0 - - - +
334C SER* 1.3 62.6 + - - +
336C VAL* 4.1 2.9 - - - +
337C LEU* 3.3 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 334 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C ASP* 5.2 21.3 - - - -
308C ALA* 5.6 6.7 - - - -
309C HIS* 5.7 6.3 - - - -
332C GLU* 3.3 1.4 - - - +
333C ASP* 1.3 76.0 - - - +
335C ALA* 1.3 66.6 + - - +
336C VAL 3.1 1.8 - - - -
337C LEU* 2.9 17.9 + - - +
338C MET* 3.0 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 335 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C GLU* 4.1 20.2 + - + +
334C SER* 1.3 77.6 - - - +
336C VAL* 1.3 58.4 + - - +
338C MET* 3.4 6.0 + - - +
339C GLU* 2.9 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 336 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C ALA* 5.8 0.5 - - - +
328C GLU 5.3 4.0 - - - +
330C GLU* 3.7 21.5 - - + +
332C GLU 3.4 19.3 + - - +
333C ASP* 4.1 3.1 - - - +
334C SER 3.1 0.6 - - - -
335C ALA* 1.3 76.0 - - - +
337C LEU* 1.3 62.0 + - - +
339C GLU* 4.7 3.8 - - - -
340C ARG* 2.8 31.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
333C ASP 3.3 13.2 + - - +
334C SER* 2.9 12.2 + - - +
336C VAL* 1.3 76.1 - - - +
338C MET* 1.3 65.2 - - - +
340C ARG* 3.2 6.1 + - - +
341C LEU* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 338 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C SER 3.0 10.9 + - - +
335C ALA* 3.9 8.5 - - - +
337C LEU* 1.3 76.9 - - - +
339C GLU* 1.3 57.3 + - - +
341C LEU* 3.4 3.5 + - - +
342C CYS* 2.9 29.8 + - - +
362C HIS* 6.2 4.0 - - - -
365C HIS* 5.3 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 339 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C ALA 2.9 18.5 + - - +
336C VAL* 4.4 3.8 - - - +
338C MET* 1.3 76.6 - - - +
340C ARG* 1.3 57.3 + - - +
342C CYS* 3.4 8.3 - - - +
343C LYS* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 340 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C ALA* 4.8 17.5 - - + -
336C VAL 2.8 23.9 + - - +
337C LEU* 3.3 7.6 - - - +
339C GLU* 1.3 73.8 - - - +
341C LEU* 1.3 60.8 + - - +
343C LYS* 3.3 6.5 + - - +
344C TYR* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 341 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C TYR* 4.8 24.9 - - + +
297C ILE* 5.7 6.7 - - + -
337C LEU 3.0 15.1 + - - +
338C MET* 4.1 3.4 - - - +
340C ARG* 1.3 76.2 - - - +
342C CYS* 1.3 63.3 + - - +
344C TYR* 3.2 9.0 + - - +
345C ILE* 2.9 26.0 + - - +
358C ALA* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 342 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C MET 2.9 19.6 + - - +
339C GLU* 3.4 11.0 - - - +
341C LEU* 1.3 78.8 - - - +
343C LYS* 1.3 63.6 + - - +
345C ILE* 3.3 9.4 + - - +
346C TYR* 3.4 14.6 + - - +
358C ALA* 4.3 17.9 - - + +
359C ILE* 6.4 0.2 - - - -
362C HIS* 4.9 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 343 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C GLU 2.9 17.4 + - - +
340C ARG* 3.8 4.3 - - - +
342C CYS* 1.3 75.6 - - - +
344C TYR* 1.3 64.7 + - - +
346C TYR* 3.6 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 344 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C VAL* 6.4 1.8 - - + -
293C TYR* 6.2 2.9 - - + -
340C ARG 3.0 14.4 + - - +
341C LEU* 3.2 14.8 - - - +
342C CYS 3.1 0.2 - - - -
343C LYS* 1.3 80.6 - - - +
345C ILE* 1.3 64.0 + - - +
346C TYR 3.4 4.9 + - - +
347C ALA* 5.2 2.3 - - - +
----------------------------------------------------------
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 LEU 2.9 12.8 + - - +
342C CYS 3.3 0.6 + - - +
344C TYR* 1.3 76.5 - - - +
346C TYR* 1.3 61.9 + - - +
347C ALA* 4.5 0.2 - - - +
350C ARG* 3.2 21.7 - - - +
354C ILE* 4.4 12.6 - - + +
355C ARG* 4.5 5.4 + - - -
358C ALA* 3.5 29.2 - - + -
----------------------------------------------------------
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