Contacts of the helix formed by residues 328 - 345 (chain A) in PDB entry 3RC0
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 328 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A THR* 3.5 1.5 - - - -
327A LYS* 1.3 90.9 - - + +
329A GLU* 1.3 57.1 + - - +
330A ALA* 2.9 12.5 - - - +
331A GLU* 2.7 49.9 + - - +
332A ARG* 2.9 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A THR* 1.3 71.5 - - - +
330A ALA* 1.3 59.7 + - - +
332A ARG* 3.3 42.7 - - - +
333A HIS* 3.4 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A THR* 2.9 10.8 - - - +
329A GLU* 1.3 79.4 - - - +
331A GLU* 1.3 61.4 + - - +
333A HIS* 3.2 7.4 + - - +
334A LEU* 3.2 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A THR* 3.6 23.3 - - + -
327A LYS 4.4 1.1 - - - +
328A THR* 2.7 33.0 + - - +
330A ALA* 1.3 69.5 - - - +
332A ARG* 1.3 68.1 + - - +
334A LEU* 3.3 10.7 + - - +
335A VAL* 3.2 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LEU* 4.2 16.2 - - + +
326A THR* 3.6 23.6 + - - +
327A LYS 5.4 1.8 + - - -
328A THR* 2.9 9.5 + - - +
329A GLU* 3.3 48.4 - - - +
331A GLU* 1.3 75.6 - - - +
333A HIS* 1.3 62.1 + - + +
335A VAL* 2.8 27.4 + - - +
336A TYR* 3.1 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A GLU 3.4 12.4 + - - +
330A ALA* 3.2 10.0 + - - +
332A ARG* 1.3 80.9 - - + +
334A LEU* 1.3 61.2 + - - +
336A TYR* 3.5 26.3 + + - +
337A GLU* 3.3 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ALA 3.2 11.7 + - - +
331A GLU* 3.8 12.1 - - - +
332A ARG 3.2 0.4 - - - -
333A HIS* 1.3 74.3 - - - +
335A VAL* 1.3 64.0 + - + +
337A GLU* 3.4 10.8 + - + -
338A ARG* 3.2 43.7 + - - +
378A ALA* 3.9 28.9 - - + +
381A PHE* 4.4 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ARG* 4.5 11.7 - - + -
322A ALA* 4.1 25.8 - - + +
323A LEU* 3.4 26.2 - - + -
326A THR* 3.7 20.4 - - + -
331A GLU 3.2 16.0 + - - +
332A ARG 2.8 12.4 + - - +
334A LEU* 1.3 78.5 - - + +
336A TYR* 1.3 55.9 + - + +
338A ARG* 3.1 13.7 + - - +
339A TRP* 2.9 24.1 + - - +
374A LEU* 4.5 6.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ARG* 4.4 24.7 - - + -
323A LEU* 3.2 38.6 - - + +
332A ARG* 3.1 39.3 + - + +
333A HIS* 3.5 25.3 + + - +
334A LEU 3.4 0.4 - - - -
335A VAL* 1.3 73.8 - - - +
337A GLU* 1.3 60.3 + - - +
339A TRP* 3.6 8.8 - + + +
340A ASP* 3.0 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A HIS 3.3 12.4 + - - +
334A LEU* 3.6 15.5 - - + +
335A VAL 3.1 0.8 - - - -
336A TYR* 1.3 73.9 - - - +
338A ARG* 1.3 66.6 + - - +
340A ASP* 3.4 6.8 + - - +
341A PHE* 3.1 23.2 + - - +
381A PHE* 3.8 16.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A LEU* 3.2 31.5 + - - +
335A VAL* 3.1 11.6 + - - +
337A GLU* 1.3 74.1 - - - +
339A TRP* 1.3 65.3 + - - +
341A PHE* 3.4 3.5 + - - +
342A LEU* 3.2 25.5 + - - +
373A VAL* 2.6 41.4 + - + +
374A LEU* 3.5 37.5 + - + +
375A CYS 5.0 0.2 - - - -
376A MET* 2.7 35.3 + - - +
377A PRO 3.8 0.2 - - - -
378A ALA* 3.3 30.5 - - - +
381A PHE* 3.7 29.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A MET* 3.1 41.5 - - + -
316A VAL* 4.0 15.0 - - + -
318A VAL* 5.1 2.9 - - + -
319A ARG* 3.4 55.3 - - + +
335A VAL* 2.9 14.5 + - + +
336A TYR* 3.6 14.4 - + + +
337A GLU 3.3 0.2 - - - -
338A ARG* 1.3 75.9 - - - +
340A ASP* 1.3 66.8 + - - +
342A LEU* 3.0 14.2 + - + +
343A CYS* 2.9 45.3 + - - -
348A VAL* 3.7 32.1 - - + -
349A GLY 4.2 15.0 - - - -
350A GLU* 4.0 6.4 + - - -
354A PHE* 5.9 0.2 - + - -
370A THR* 5.2 1.6 - - + -
374A LEU* 4.3 12.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A TYR* 3.0 25.9 + - - +
337A GLU* 3.9 6.1 - - - +
338A ARG 3.3 0.4 - - - -
339A TRP* 1.3 86.8 - - - +
341A PHE* 1.3 57.2 + - - +
343A CYS* 3.1 11.6 + - - +
344A LYS* 2.9 41.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A GLU 3.1 17.3 + - - +
338A ARG 3.7 4.3 - - - +
339A TRP 3.3 0.2 - - - -
340A ASP* 1.3 75.3 - - - +
342A LEU* 1.3 58.4 + - - +
344A LYS* 3.2 15.6 + - + +
345A LEU* 3.0 58.5 + - + +
373A VAL* 4.2 19.7 - - + -
381A PHE* 3.9 26.2 - + + -
384A LEU* 4.1 31.2 - - + -
385A LYS* 4.5 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ARG 3.2 15.7 + - - +
339A TRP* 3.0 11.3 + - + +
341A PHE* 1.3 72.8 - - - +
343A CYS* 1.3 64.3 + - - +
345A LEU* 3.4 8.1 + - + +
346A GLU 3.1 3.3 + - - -
347A MET* 2.9 32.7 + - + -
348A VAL* 3.4 19.5 + - + +
369A THR* 3.7 23.6 - - + +
370A THR* 3.8 35.0 - - + +
373A VAL* 3.7 31.0 - - + -
374A LEU* 4.0 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A TRP* 2.9 46.7 + - - -
340A ASP* 3.1 15.7 + - - +
342A LEU* 1.3 77.7 - - - +
344A LYS* 1.3 61.6 + - + +
346A GLU* 3.2 15.8 + - - +
348A VAL* 3.6 23.4 - - - +
349A GLY* 4.8 4.9 - - - -
350A GLU 5.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A ASP* 2.9 29.3 + - - +
341A PHE* 3.4 17.3 - - + +
342A LEU 3.2 0.2 - - - -
343A CYS* 1.3 74.6 - - + +
345A LEU* 1.3 60.5 + - + +
346A GLU* 2.9 18.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A PHE* 3.0 52.0 + - + +
342A LEU* 3.4 9.6 + - + +
344A LYS* 1.3 74.4 - - + +
346A GLU* 1.3 71.7 + - - +
347A MET* 3.6 20.7 - - + +
369A THR* 4.0 26.0 - - + -
373A VAL* 5.1 1.1 - - + -
394A LYS 5.5 5.4 - - - +
395A ARG* 5.3 8.3 - - + -
----------------------------------------------------------
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