Contacts of the helix formed by residues 336 - 346 (chain C) in PDB entry 3WTW
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 GLN 336 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C PRO 3.7 5.3 + - - +
335C ILE* 1.3 75.7 - - - +
337C LEU* 1.3 67.5 + - - +
338C TRP* 2.8 35.7 + - + -
339C GLN* 2.8 36.1 + - - +
340C PHE* 2.9 11.4 + - - +
375C TRP* 4.0 0.7 - - - -
396C TYR* 5.5 0.3 - - - -
7D A 3.4 37.4 + - - +
8D C 3.4 20.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
336C GLN* 1.3 70.7 - - - +
338C TRP* 1.3 57.4 + - - +
340C PHE* 3.4 2.5 + - + +
341C LEU* 2.9 42.1 + - + +
375C TRP* 3.5 34.0 - - + +
389C LEU* 3.6 50.7 - - + +
392C GLY* 3.9 9.6 - - - -
393C LEU* 3.7 26.9 - - + +
396C TYR* 3.3 11.4 + - + +
8D C 2.8 19.9 + - - +
9D A 5.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 338 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C ALA* 3.7 33.4 - - + -
336C GLN* 2.8 29.8 + - + -
337C LEU* 1.3 74.6 - - - +
339C GLN* 1.3 83.9 + - + +
341C LEU* 3.5 10.1 + - - +
342C LEU* 3.1 37.5 + - + +
396C TYR* 2.7 47.5 + + + +
401C ILE* 3.7 30.5 - - + +
402C ILE* 4.1 8.3 - - + -
414C PHE* 3.8 19.6 - + - -
416C CYS* 4.3 15.0 - - - -
418C LEU* 4.5 1.6 - - + -
421C LEU* 3.8 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 339 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C ALA* 4.7 6.2 - - - +
327C ALA* 3.4 34.3 + - + -
328C GLY* 4.2 1.6 - - - -
329C TYR* 3.5 35.5 - - + +
335C ILE* 3.8 11.6 - - + +
336C GLN* 2.8 34.5 + - - +
338C TRP* 1.3 109.4 - - + +
340C PHE* 1.3 58.9 + - - +
342C LEU* 3.3 7.7 + - - +
343C GLU* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 340 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C ILE* 3.6 13.6 - - + +
336C GLN 2.9 7.0 + - - +
337C LEU* 3.7 8.3 - - + +
339C GLN* 1.3 74.2 - - - +
341C LEU* 1.3 71.9 + - + +
343C GLU* 3.2 15.2 + - - +
344C LEU* 3.1 52.9 + - + +
371C VAL* 4.3 5.8 - - + -
374C ARG* 3.5 27.1 - - + -
375C TRP* 3.4 51.6 - + + -
378C ARG* 3.8 38.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
337C LEU* 2.9 34.4 + - + +
338C TRP* 3.7 4.3 - - - +
340C PHE* 1.3 81.6 - - + +
342C LEU* 1.3 55.6 + - - +
344C LEU* 2.8 28.0 + - + +
345C LEU* 3.0 15.3 + - + +
354C ILE* 3.5 28.2 - - + +
363C PHE* 4.2 19.7 - - + -
365C LEU* 4.9 4.7 - - + -
371C VAL* 3.7 22.0 - - + -
389C LEU* 5.2 1.6 - - + -
393C LEU* 3.5 34.5 - - + -
402C ILE* 4.4 5.2 - - + -
414C PHE* 4.7 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 342 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C ALA* 4.0 18.6 - - + -
327C ALA* 4.3 12.1 - - + -
338C TRP* 3.1 31.2 + - + +
339C GLN 3.4 5.8 - - - +
341C LEU* 1.3 75.9 - - - +
343C GLU* 1.3 62.0 + - - +
345C LEU* 3.1 13.0 + - - +
346C THR* 3.1 22.0 + - + +
356C TRP* 3.9 13.0 - - + -
414C PHE* 3.3 25.9 - - + -
418C LEU* 3.3 43.7 - - + -
422C LEU* 4.3 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 343 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C ALA* 4.2 6.5 - - - +
324C ALA* 3.0 33.2 - - + +
335C ILE* 3.9 3.8 - - - +
339C GLN 2.9 12.6 + - - +
340C PHE* 3.3 18.0 - - - +
342C LEU* 1.3 77.2 - - - +
344C LEU* 1.3 60.7 + - + +
346C THR* 2.9 20.0 + - - +
347C ASP* 3.5 12.8 + - - +
378C ARG* 2.9 33.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 344 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C PHE* 3.1 50.4 + - + +
341C LEU* 2.8 16.6 + - - +
343C GLU* 1.3 75.0 - - + +
345C LEU* 1.3 60.9 + - - +
346C THR 3.2 0.2 - - - -
347C ASP* 3.5 9.8 + - + +
350C CYS* 3.4 44.7 - - + +
353C PHE* 4.4 13.7 - - + -
354C ILE* 3.7 19.7 - - + +
371C VAL* 4.4 16.2 - - + -
374C ARG* 4.3 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 345 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C LEU 3.0 14.8 + - - +
342C LEU 3.1 7.1 + - - +
344C LEU* 1.3 78.0 - - - +
346C THR* 1.3 60.8 + - - +
347C ASP 3.4 1.4 - - - -
351C GLN* 5.3 3.5 + - - +
354C ILE* 3.8 15.3 - - + +
355C SER* 3.6 44.2 - - - +
356C TRP* 3.0 62.1 + - + +
363C PHE* 3.7 27.6 - - + -
414C PHE* 3.8 13.2 - - + -
433C LEU* 3.4 9.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 346 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C PRO* 3.6 1.3 - - - +
320C VAL* 3.1 23.9 + - - +
321C ILE* 3.4 39.7 + - + -
323C ALA* 3.4 21.2 + - + +
342C LEU* 3.1 16.2 + - + +
343C GLU* 2.9 16.6 + - - +
345C LEU* 1.3 81.5 - - + +
347C ASP* 1.3 59.8 + - - +
348C LYS 3.9 0.4 - - - -
356C TRP* 5.2 0.9 - - + -
422C LEU* 5.2 1.6 - - + -
429C LEU* 4.2 15.7 - - + -
433C LEU* 3.7 13.8 - - + +
----------------------------------------------------------
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