Contacts of the helix formed by residues 342 - 364 (chain C) in PDB entry 2UZ1
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 342 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C LEU 3.1 13.7 + - - -
202C ARG* 3.1 22.2 + - - +
204C ALA 2.8 30.0 + - - -
205C GLU* 3.5 10.5 + - - +
207C PRO* 3.4 33.8 - - - +
231C THR 4.0 13.9 + - - +
232C GLY* 3.6 19.9 - - - +
233C VAL* 4.1 11.2 - - - +
339C TRP* 5.3 2.2 - - - -
340C PRO* 3.4 27.8 + - + +
341C ASP* 1.3 79.9 + - - +
343C GLY* 1.3 58.2 + - - +
344C ASP 3.3 2.9 - - - -
345C TRP* 3.2 14.3 + - + +
346C CYS* 2.9 33.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 343 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C ASP* 2.9 16.7 + - - -
342C ARG* 1.3 75.6 - - - +
344C ASP* 1.3 57.9 + - - +
346C CYS* 3.4 6.8 + - - +
347C ALA* 2.8 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 344 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C ASP* 4.6 2.3 + - - -
342C ARG 3.3 0.6 - - - -
343C GLY* 1.3 75.4 - - - +
345C TRP* 1.3 57.9 + - - +
347C ALA* 3.3 7.7 + - - +
348C LYS* 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 345 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C GLU 4.5 8.3 - - - +
206C ARG* 3.4 47.0 - - + -
207C PRO* 2.7 38.3 + - + -
208C VAL* 3.6 17.9 - - + -
234C PRO* 3.5 21.6 - - + +
263C PHE* 3.6 23.6 - + - -
268C ALA* 3.3 35.0 - - + -
270C PRO* 4.3 4.3 - - + -
342C ARG* 3.2 18.2 + - + +
344C ASP* 1.3 76.4 - - - +
346C CYS* 1.3 64.6 + - - +
348C LYS* 3.0 16.2 + - + +
349C VAL* 2.9 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 346 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C GLY 3.3 26.5 - - - -
234C PRO* 4.0 15.3 - - - -
251C ALA* 3.2 38.1 - - + +
252C MET* 4.3 8.1 - - - -
342C ARG 2.9 19.8 + - - +
343C GLY* 3.7 7.9 - - - +
345C TRP* 1.3 75.4 - - - +
347C ALA* 1.3 56.4 + - - +
349C VAL* 3.3 10.5 + - - +
350C THR* 3.0 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 347 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C GLY 2.8 18.5 + - - +
344C ASP* 3.5 9.0 - - - +
346C CYS* 1.3 77.2 - - - +
348C LYS* 1.3 56.5 + - - +
350C THR* 3.3 7.6 + - - -
351C ASP* 2.8 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 348 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C ALA* 4.4 15.5 + - - +
268C ALA* 4.2 20.6 - - + -
344C ASP 2.9 14.4 + - - +
345C TRP* 3.3 21.1 - - + +
347C ALA* 1.3 73.4 - - - +
349C VAL* 1.3 65.6 + - - +
351C ASP* 3.2 11.8 + - + +
352C LEU* 2.9 54.3 + - + +
355C GLU* 5.8 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 349 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C PRO* 4.0 26.2 - - + -
236C PHE* 3.7 25.4 - - + -
251C ALA 5.6 2.2 - - - +
253C ARG 4.7 3.6 - - - +
254C GLY* 3.8 18.4 - - - +
263C PHE* 3.9 28.2 - - + -
345C TRP* 2.9 27.3 + - + +
346C CYS* 3.4 9.9 - - - +
348C LYS* 1.3 76.3 - - - +
350C THR* 1.3 64.0 + - - +
352C LEU* 3.4 2.3 + - - +
353C ALA* 3.1 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 350 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C ASP 4.6 11.6 + - - -
251C ALA* 4.6 6.4 + - - -
253C ARG 5.4 2.4 + - - -
346C CYS 3.0 16.0 + - - -
347C ALA* 3.5 10.9 - - - +
349C VAL* 1.3 78.1 - - - +
351C ASP* 1.3 69.2 + - - +
353C ALA* 3.4 6.0 + - - +
354C GLN* 3.0 25.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 351 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C ALA* 2.8 27.8 + - - +
348C LYS* 3.6 15.5 - - + +
350C THR* 1.3 80.0 - - - +
352C LEU* 1.3 58.4 + - + +
354C GLN* 3.2 8.3 + - - +
355C GLU* 2.9 41.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 352 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C ASN 6.0 0.9 - - - -
262C SER* 4.3 19.6 + - - +
263C PHE* 3.7 46.9 - - + -
266C ALA* 3.7 26.9 - - + -
268C ALA* 4.3 1.1 - - + -
348C LYS* 2.9 45.7 + - + +
349C VAL 3.9 3.8 - - - +
351C ASP* 1.3 77.1 - - + +
353C ALA* 1.3 60.7 + - - +
355C GLU* 3.4 24.4 + - - +
356C ARG* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 353 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C GLY 5.3 4.0 - - - +
259C ASN* 4.1 27.3 - - + +
263C PHE* 5.6 0.8 - - - -
349C VAL* 3.1 14.5 + - + +
350C THR* 3.7 9.6 - - - +
351C ASP 3.3 0.2 - - - -
352C LEU* 1.3 74.6 - - - +
354C GLN* 1.3 64.2 + - - +
356C ARG* 3.2 8.7 + - - +
357C TYR* 3.0 23.3 + - - +
405C SER* 6.0 2.0 - - - -
406C ARG* 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 354 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C THR* 3.0 20.8 + - + +
351C ASP* 3.6 7.6 - - - +
353C ALA* 1.3 77.4 - - - +
355C GLU* 1.3 57.3 + - + +
357C TYR* 4.5 4.5 - - - -
358C ALA* 2.8 43.0 + - + +
406C ARG* 3.5 28.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 355 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C LYS* 5.8 1.4 + - - -
351C ASP* 2.9 26.5 + - - +
352C LEU* 3.6 27.1 - - + +
354C GLN* 1.3 76.0 - - + +
356C ARG* 1.3 60.7 + - - +
358C ALA* 4.0 4.9 - - - +
359C SER* 3.0 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 356 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C GLN* 3.2 30.8 + - - -
259C ASN* 3.5 25.5 + - - +
261C TYR* 4.0 16.2 - - - +
262C SER* 5.4 8.0 + - - +
352C LEU 3.1 13.7 + - - +
353C ALA* 3.2 10.1 + - - +
355C GLU* 1.3 76.6 - - - +
357C TYR* 1.3 62.5 - - - +
359C SER* 3.3 6.9 + - - -
360C ILE* 3.1 35.2 + - + +
402C GLU* 2.8 45.5 + - - -
551C PRO* 4.2 10.2 - - + +
552C GLU* 3.4 21.8 + - - -
555C ILE* 4.1 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 357 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C ALA 3.0 15.9 + - - +
354C GLN* 3.8 5.8 - - - +
356C ARG* 1.3 76.0 - - - +
358C ALA* 1.3 61.6 + - - +
360C ILE* 3.2 12.1 + - - +
361C ALA* 2.9 31.1 + - + +
373C PHE* 3.8 17.5 - + - -
377C GLN* 2.9 36.2 + - - +
402C GLU* 3.7 22.0 - - - +
403C VAL* 4.3 8.7 - - + +
406C ARG* 3.5 60.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 358 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C GLN* 2.8 29.9 + - + +
355C GLU* 4.0 5.4 - - - +
357C TYR* 1.3 76.1 - - - +
359C SER* 1.3 57.6 + - - +
361C ALA* 3.6 7.4 - - - +
362C ALA* 2.8 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 359 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C GLU 3.0 19.8 + - - -
356C ARG* 3.4 7.2 - - - -
357C TYR 3.3 0.2 - - - -
358C ALA* 1.3 76.2 - - - +
360C ILE* 1.3 62.5 + - - +
362C ALA* 3.4 6.9 + - - +
363C LYS* 3.3 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 360 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C ARG* 3.1 26.3 + - + +
357C TYR* 3.6 9.2 - - - +
359C SER* 1.3 73.9 - - - +
361C ALA* 1.3 62.5 - - - +
363C LYS* 3.1 6.6 + - - +
364C SER* 2.7 34.2 + - - +
373C PHE* 3.5 33.2 - - + -
399C TRP* 4.0 15.5 - - + -
402C GLU* 3.3 41.3 - - + +
551C PRO* 3.7 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 361 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C TYR* 2.9 25.5 + - + +
358C ALA* 3.3 9.4 + - - +
360C ILE* 1.3 76.7 - - - +
362C ALA* 1.3 62.1 + - - +
363C LYS 3.3 0.7 + - - -
364C SER* 3.4 16.8 + - - +
373C PHE* 3.8 22.4 - - + -
374C HIS* 4.9 4.9 - - + -
377C GLN* 4.9 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 362 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C ALA 2.8 18.1 + - - +
359C SER* 3.7 8.5 - - - +
360C ILE 3.2 0.2 - - - -
361C ALA* 1.3 76.1 - - - +
363C LYS* 1.3 61.3 + - + +
364C SER 3.8 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 363 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C SER* 3.3 19.9 + - - +
360C ILE* 3.1 7.6 + - - +
362C ALA* 1.3 79.8 - - + +
364C SER* 1.3 62.1 + - - +
365C SER* 3.6 4.6 + - - -
371C HIS* 4.9 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 364 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C ILE* 2.7 23.6 + - - +
361C ALA 3.4 9.7 + - - +
362C ALA 3.5 1.4 - - - +
363C LYS* 1.3 77.8 - - - +
365C SER* 1.3 60.2 + - - +
371C HIS* 3.3 34.6 + - - -
373C PHE* 3.5 15.3 - - - +
374C HIS* 3.3 26.8 + - - -
399C TRP* 4.7 0.7 - - - -
----------------------------------------------------------
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