Contacts of the helix formed by residues 326 - 339 (chain C) in PDB entry 3KDO
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 GLU 326 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C ALA 4.3 0.2 - - - -
319C GLY* 4.6 2.0 - - - +
324C GLU* 4.2 16.1 + - - +
325C GLY* 1.3 75.0 - - - +
327C ARG* 1.3 63.0 + - - +
328C ASP* 3.7 1.3 - - + +
329C ILE* 3.5 34.6 + - + +
330C THR* 2.7 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 327 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C ALA* 3.8 25.8 + - - +
319C GLY* 4.4 1.0 - - - +
325C GLY 4.0 0.2 + - - -
326C GLU* 1.3 71.5 - - - +
328C ASP* 1.3 69.9 + - - +
330C THR* 2.9 15.4 + - - -
331C LEU* 3.1 28.7 + - + +
380C GLU* 4.8 3.8 + - - +
381C ALA* 3.9 38.5 - - + +
382C LEU* 5.2 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 328 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C GLU* 5.0 1.7 - - + +
327C ARG* 1.3 83.6 - - - +
329C ILE* 1.3 67.0 + - + +
331C LEU* 3.0 20.4 + - - +
332C GLY* 3.0 10.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 329 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C ARG* 5.6 9.4 - - - +
324C GLU* 5.8 2.2 - - - +
325C GLY* 6.3 0.7 - - - -
326C GLU* 3.5 41.8 + - + +
327C ARG 3.2 0.6 - - - -
328C ASP* 1.3 78.0 - - + +
330C THR* 1.3 63.1 + - - +
332C GLY* 3.1 11.5 + - - +
333C PHE* 3.2 43.8 + - + -
351C HIS* 6.5 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 330 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C VAL* 3.8 24.9 + - + +
316C GLY 4.2 4.2 - - - +
317C THR 4.8 0.2 + - - -
318C ALA* 3.2 33.0 + - - +
325C GLY* 4.0 8.0 - - - -
326C GLU 2.7 19.9 + - - -
327C ARG 2.9 8.3 + - - -
329C ILE* 1.3 75.8 - - - +
331C LEU* 1.3 63.1 + - - +
333C PHE* 3.0 13.6 + - - +
334C VAL* 3.0 21.1 + - - +
382C LEU* 3.8 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 331 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C ARG* 3.1 25.0 + - + +
328C ASP* 3.0 13.6 + - - +
330C THR* 1.3 76.4 - - - +
332C GLY* 1.3 62.9 + - - +
334C VAL* 3.1 11.3 + - + -
335C ASP* 3.0 48.9 + - - +
338C ARG* 5.4 1.8 - - - +
381C ALA* 4.0 22.2 - - + +
382C LEU* 4.1 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 332 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C PHE* 4.1 13.0 - - - -
328C ASP 3.0 11.9 + - - -
329C ILE* 3.1 6.8 + - - -
331C LEU* 1.3 77.0 - - - +
333C PHE* 1.3 63.2 + - - +
335C ASP* 3.5 6.3 + - - +
336C LEU* 3.0 24.1 + - - +
342C TYR* 4.3 8.1 - - - -
351C HIS* 6.0 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 333 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C ARG* 5.0 0.9 - - - -
297C SER* 4.7 2.9 - - - -
298C MET* 3.5 35.0 - - + -
299C PHE* 3.5 41.3 - + + -
302C ALA* 4.8 6.1 - - + -
315C VAL* 3.5 42.0 - - + -
329C ILE* 3.2 41.3 + - + -
330C THR* 3.0 9.5 + - - +
332C GLY* 1.3 76.2 - - - +
334C VAL* 1.3 63.2 + - - +
336C LEU* 3.2 7.1 + - - +
337C LEU* 3.0 29.0 + - - +
351C HIS* 5.8 1.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 334 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C VAL* 4.3 6.3 - - + -
330C THR 3.0 14.8 + - - +
331C LEU* 3.1 11.4 + - + +
333C PHE* 1.3 76.1 - - - +
335C ASP* 1.3 64.2 + - - +
337C LEU* 3.2 2.1 + - - +
338C ARG* 3.0 71.8 + - - +
364C PRO* 4.1 22.7 - - + -
382C LEU* 3.8 36.1 - - + +
386C ILE* 5.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 335 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C LEU* 3.0 43.6 + - - +
332C GLY* 3.9 5.0 - - - +
334C VAL* 1.3 78.0 - - - +
336C LEU* 1.3 58.4 + - - +
338C ARG* 4.5 7.0 + - - -
339C GLU* 2.8 68.1 + - - +
342C TYR* 4.1 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 336 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C PHE* 3.1 62.8 - - + +
302C ALA* 3.9 7.9 - - + -
303C LYS* 3.8 28.7 - - + +
306C ARG* 2.7 27.9 + - - -
332C GLY 3.0 17.4 + - - +
333C PHE* 3.5 6.3 - - - +
335C ASP* 1.3 77.4 - - - +
337C LEU* 1.3 51.7 + - - +
342C TYR* 4.0 19.7 - - + -
354C GLN* 5.2 0.2 - - + -
356C PHE* 3.6 31.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
302C ALA* 3.3 38.4 - - + +
306C ARG* 3.2 29.9 + - + +
313C LEU* 4.1 20.2 - - + -
315C VAL* 3.5 32.3 - - + -
333C PHE 3.0 14.9 + - - +
334C VAL 3.2 3.8 + - - +
335C ASP 3.2 0.2 - - - -
336C LEU* 1.3 77.7 - - - +
338C ARG* 1.3 58.7 + - - +
361C ALA* 3.4 0.2 - - - -
362C ALA* 2.9 42.4 + - + +
364C PRO* 4.2 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 338 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C ILE* 3.6 24.0 - - + -
306C ARG* 4.1 1.1 + - - -
331C LEU* 5.4 2.0 - - - +
334C VAL* 3.0 35.6 + - - +
335C ASP* 4.4 9.9 + - - +
337C LEU* 1.3 78.9 - - - +
339C GLU* 1.3 64.7 + - + +
340C SER 3.7 1.2 + - - -
361C ALA* 3.4 18.3 - - - +
362C ALA 3.8 1.1 - - - +
364C PRO* 3.7 14.6 - - + -
382C LEU 2.8 28.5 + - - -
383C GLY* 4.5 2.6 - - - -
385C ASP* 2.8 60.6 + - - +
386C ILE* 3.7 1.6 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
306C ARG* 2.8 24.2 + - - -
335C ASP* 2.8 53.0 + - - +
338C ARG* 1.3 75.6 - - + +
340C SER* 1.3 63.0 + - - +
341C HIS 3.4 15.2 + - - +
342C TYR* 3.5 23.5 - - - +
343C LYS 4.1 4.0 + - - +
356C PHE* 3.5 8.1 - - - -
----------------------------------------------------------
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