Contacts of the helix formed by residues 352 - 373 (chain A) in PDB entry 5AM8
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 352 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A THR* 3.6 20.4 - - + -
283A MET* 3.5 16.0 - - - +
293A MET* 3.7 0.5 - - - +
350A ARG* 3.0 25.6 + - + +
351A VAL* 1.3 81.7 - - - +
353A MET* 1.3 64.0 + - - +
354A ASP* 2.7 26.8 + - - +
355A GLN* 3.1 17.5 + - - +
356A LEU 3.2 16.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LEU* 3.2 25.4 - - + +
278A ASP* 3.8 15.9 - - - +
279A VAL* 3.7 28.7 - - + -
280A THR* 3.2 7.0 + - - +
283A MET* 3.6 9.1 - - - -
352A THR* 1.3 73.8 - - - +
354A ASP* 1.3 63.2 + - - +
356A LEU* 3.1 18.9 + - + +
357A SER* 3.3 14.5 + - - +
400A SER* 4.5 20.0 - - - +
405A LEU* 3.9 24.0 - - + -
424A TYR* 6.1 1.3 - - + -
427A LYS* 3.3 29.2 - - + +
428A MET* 6.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A GLU* 3.8 30.0 - - + +
263A ASN* 4.2 17.2 + - - +
350A ARG* 4.3 16.6 + - - -
352A THR* 2.7 23.7 + - - +
353A MET* 1.3 78.5 - - - +
355A GLN* 1.3 66.5 + - - +
357A SER* 3.4 10.1 + - - +
358A THR* 3.1 23.9 + - - -
431A GLU* 6.5 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A MET* 3.7 5.2 - - + -
347A GLN* 3.1 27.1 + - - +
348A CYS 3.8 4.0 - - - +
349A THR* 3.2 4.2 - - - -
350A ARG* 2.9 77.6 + - - +
352A THR* 3.1 19.4 + - - +
353A MET 3.2 0.2 - - - -
354A ASP* 1.3 76.7 + - - +
356A LEU* 1.3 59.8 + - - +
358A THR* 3.1 17.3 + - - +
359A VAL* 2.8 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A VAL* 5.8 0.2 - - + -
283A MET* 4.4 14.6 - - + -
288A TRP* 4.6 9.9 - - + -
293A MET* 3.5 41.5 - - + +
296A VAL* 4.9 4.3 - - + -
352A THR 3.2 11.3 + - - +
353A MET* 3.1 16.7 + - + +
355A GLN* 1.3 73.3 - - - +
357A SER* 1.3 60.4 + - - +
359A VAL* 3.3 5.6 + - + +
360A HIS* 2.7 53.6 + - + -
399A VAL* 4.6 16.8 - - + -
405A LEU* 5.6 2.5 - - + -
408A ILE* 5.0 3.1 - - + -
410A LEU* 4.4 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A MET* 3.3 10.7 + - - +
354A ASP* 3.6 11.6 - - - -
355A GLN 3.2 0.6 - - - -
356A LEU* 1.3 80.6 - - - +
358A THR* 1.3 63.4 + - - +
360A HIS* 3.2 11.2 + - - +
361A HIS* 2.9 21.8 + - - +
393A ASP* 5.2 0.9 - - - +
396A ALA* 4.3 19.7 + - - +
400A SER* 5.5 5.9 - - - -
431A GLU* 4.2 21.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ALA* 3.9 22.9 - - + -
347A GLN* 3.7 15.7 - - - +
354A ASP* 3.1 14.7 + - - -
355A GLN* 3.1 23.7 + - - +
357A SER* 1.3 76.9 - - - +
359A VAL* 1.3 62.7 + - - +
361A HIS* 3.0 10.7 + - + +
362A GLU* 3.0 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A MET* 3.9 13.0 - - + +
294A PHE* 3.6 57.0 - - + -
297A ALA* 3.9 19.7 - - + -
345A ILE* 4.7 1.2 - - - +
347A GLN* 3.8 15.7 - - - +
349A THR* 4.2 8.5 - - + -
355A GLN 2.8 19.3 + - - +
356A LEU* 3.5 9.2 - - + +
358A THR* 1.3 75.3 - - - +
360A HIS* 1.3 57.4 + - - +
362A GLU* 3.4 2.8 + - - +
363A MET* 3.0 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A VAL* 4.7 5.0 + - + +
297A ALA* 3.4 35.0 - - + +
300A PHE* 4.7 4.8 - - + +
301A PHE* 4.4 6.8 - + + -
356A LEU* 2.7 52.7 + - + +
357A SER* 3.2 8.8 + - - +
359A VAL* 1.3 76.2 - - - +
361A HIS* 1.3 57.0 + - - +
363A MET* 3.3 6.1 + - - +
364A GLY 2.9 25.8 + - - -
392A GLY* 3.3 23.0 - - - +
395A LEU* 4.5 14.1 - - + -
396A ALA* 4.2 9.8 - - + +
399A VAL* 3.5 35.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A SER 2.9 11.6 + - - +
358A THR* 3.3 13.9 - - + +
360A HIS* 1.3 75.3 - - - +
362A GLU* 1.3 87.7 + - - +
364A GLY* 3.3 10.6 + - - -
365A HIS* 3.3 22.3 + + - -
388A HIS 5.4 0.7 - - - +
389A GLU* 2.9 47.8 + - + +
392A GLY* 3.9 12.4 + - - -
393A ASP* 2.8 27.7 + - - +
501A TYR* 4.4 12.1 - + - -
505A PHE* 6.4 0.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ALA* 3.3 35.8 - - + +
333A SER* 3.6 2.1 - - - -
334A ALA* 3.5 24.6 + - + +
345A ILE* 3.5 28.9 - - + -
347A GLN* 3.9 15.7 - - - +
358A THR* 3.0 21.0 + - - +
359A VAL 3.9 2.0 - - - +
361A HIS* 1.3 92.8 - - - +
363A MET* 1.3 62.1 + - - +
365A HIS* 3.1 28.3 + - - +
366A ILE* 3.2 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A PHE* 3.4 44.9 - - + +
297A ALA* 3.8 6.1 - - + -
298A GLU* 3.4 32.5 - - - +
301A PHE* 3.5 21.8 - - + -
309A MET* 3.9 39.0 - - + -
313A PHE* 4.5 4.3 - - + -
314A TRP* 5.1 0.2 - - + -
345A ILE* 3.6 7.5 - - + +
359A VAL* 3.0 16.5 + - + +
360A HIS* 3.3 4.9 + - - +
362A GLU* 1.3 73.2 - - - +
364A GLY* 1.3 59.6 + - - +
366A ILE* 3.2 2.8 + - - +
367A GLN* 2.8 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A PHE* 3.7 15.8 - - - -
360A HIS 2.9 10.9 + - - -
361A HIS 3.3 5.6 + - - -
362A GLU 3.2 0.6 - - - -
363A MET* 1.3 73.1 - - - +
365A HIS* 1.3 63.8 + - - +
367A GLN* 3.4 2.6 + - - +
368A TYR* 3.1 21.8 + - - +
388A HIS 5.1 0.4 - - - -
391A ILE* 3.8 16.8 - - - +
392A GLY 3.8 17.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ALA* 3.3 17.9 - - + -
361A HIS* 3.3 22.7 + + - -
362A GLU* 3.1 30.1 + - - +
364A GLY* 1.3 74.6 - - - +
366A ILE* 1.3 63.3 + - - +
368A TYR* 3.3 3.5 + - - +
369A TYR* 3.0 35.3 + - - +
388A HIS* 2.9 52.0 + + + +
389A GLU* 3.1 40.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A MET* 3.5 28.9 - - + -
310A PRO* 5.5 0.4 - - + -
313A PHE* 4.3 5.2 - - + -
334A ALA* 3.9 3.1 - - + -
335A TRP 3.9 5.4 - - - +
343A PHE* 4.2 12.8 - - + -
344A ARG 3.5 39.0 - - - +
345A ILE* 3.8 17.0 - - + -
362A GLU 3.2 12.5 + - - +
363A MET 3.2 7.7 + - - +
365A HIS* 1.3 76.5 - - - +
367A GLN* 1.3 57.1 + - - +
369A TYR* 3.1 21.5 + - + +
370A LEU* 2.8 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A PHE* 3.5 37.4 - - + -
306A LEU* 3.6 7.6 - - + -
307A SER* 2.8 44.1 + - - +
309A MET* 4.0 9.1 - - - +
363A MET 2.8 19.8 + - - +
364A GLY 3.7 3.8 - - - +
366A ILE* 1.3 72.9 - - - +
368A TYR* 1.3 62.9 + - - +
370A LEU* 3.2 6.9 + - - +
371A GLN* 2.8 58.2 + - - +
391A ILE* 5.2 0.4 - - + -
544A LEU* 3.9 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A GLY 3.1 9.3 + - - +
365A HIS 3.3 9.6 - - - +
366A ILE 3.3 0.2 - - - -
367A GLN* 1.3 74.6 - - - +
369A TYR* 1.3 63.2 + - - +
371A GLN* 3.1 2.8 + - - +
372A TYR* 3.1 54.1 + + - -
381A ARG 4.4 0.7 - - - -
382A GLY* 3.6 11.2 - - - -
383A ALA* 3.2 21.5 + - - +
387A PHE* 3.6 15.7 - - - +
388A HIS* 3.4 43.1 - + + -
391A ILE* 3.6 30.5 - - + -
543A VAL* 4.0 10.1 + - + +
544A LEU* 3.4 44.9 - - + +
547A GLY* 4.4 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ALA* 2.9 24.2 + - + +
335A TRP 3.3 34.8 - - - -
336A ASP* 3.3 28.4 + - + +
343A PHE* 3.5 21.2 - + + -
365A HIS* 3.0 24.6 + - + +
366A ILE* 3.1 18.8 + - + +
368A TYR* 1.3 74.6 - - - +
370A LEU* 1.3 65.3 + - - +
372A TYR* 3.2 27.1 - - - -
373A LYS* 3.2 26.2 + - - +
388A HIS* 3.3 23.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A SER* 4.0 17.0 - - - +
308A PRO 3.7 23.8 - - - +
309A MET* 3.9 21.3 - - + -
310A PRO* 4.0 16.2 - - + -
343A PHE* 3.3 41.7 - - + -
366A ILE* 2.8 17.0 + - + +
367A GLN* 3.2 13.7 + - - +
369A TYR* 1.3 77.9 - - - +
371A GLN* 1.3 62.5 + - - +
373A LYS* 3.4 33.5 - - + +
545A ARG* 4.9 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A LEU* 4.0 12.3 - - - +
307A SER* 3.4 20.9 + - - +
367A GLN* 2.8 42.3 + - - +
368A TYR 3.7 1.6 - - - +
370A LEU* 1.3 78.8 - - - +
372A TYR* 1.3 58.9 + - - +
373A LYS* 3.5 0.9 + - - +
374A ASP* 5.1 1.0 + - - +
541A ARG* 3.6 18.6 - - - +
544A LEU* 3.7 34.3 - - + -
545A ARG* 3.1 64.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ASP* 3.9 7.6 + - - -
368A TYR* 3.1 44.7 + + - -
369A TYR* 3.2 29.5 - + - -
371A GLN* 1.3 74.9 - - - +
373A LYS* 1.3 64.1 + - - +
374A ASP 3.1 3.4 - - - -
375A LEU* 3.1 40.5 + - + +
380A ARG* 3.4 47.6 + - + +
381A ARG* 3.3 21.1 + - - -
388A HIS* 2.8 23.2 + - - -
544A LEU 3.7 8.7 - - - +
545A ARG 4.4 2.2 - - - +
547A GLY* 3.6 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ASP* 6.0 0.4 - - - -
340A ARG* 3.3 39.7 + - + +
343A PHE* 4.1 19.8 - - + -
369A TYR 3.2 15.0 + - - +
370A LEU* 3.4 21.0 - - - +
371A GLN 3.5 1.3 - - - +
372A TYR* 1.3 75.6 - - - +
374A ASP* 1.3 79.0 + - - +
375A LEU 3.4 0.2 - - - -
380A ARG* 3.2 35.1 + - - +
----------------------------------------------------------
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