Contacts of the helix formed by residues 353 - 375 (chain A) in PDB entry 6DWW
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 ASN 353 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A PRO* 5.5 9.3 - - + +
351A HIS 3.6 5.5 + - - +
352A ILE* 1.3 69.5 - - - +
354A LYS* 1.3 68.8 + - - +
355A SER* 3.1 26.7 + - - -
356A ILE* 3.2 33.9 + - + +
357A ILE* 3.3 14.0 + - - +
403A VAL* 6.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU* 4.4 15.0 - - + -
333A TRP* 3.2 68.6 - - + +
352A ILE 3.1 7.1 + - - +
353A ASN* 1.3 73.3 + - - +
355A SER* 1.3 59.3 + - - +
357A ILE* 3.1 7.1 + - - +
358A GLN* 2.9 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ASN* 3.1 23.7 + - - -
354A LYS* 1.3 79.2 - - - +
356A ILE* 1.3 64.6 + - - +
358A GLN* 3.3 8.4 + - - +
359A THR* 2.8 32.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A LEU* 3.8 29.4 - - + -
287A PRO* 5.0 10.5 - - + -
353A ASN* 3.2 30.3 + - + +
354A LYS 3.3 0.4 - - - -
355A SER* 1.3 85.8 + - - +
357A ILE* 1.3 67.5 + - + +
359A THR* 3.2 8.5 + - - +
360A MET* 3.0 28.5 + - - +
403A VAL* 3.5 39.0 - - + -
405A ASP* 5.7 2.0 - - + -
406A ILE* 4.0 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A PRO* 3.9 26.9 - - + +
288A ILE 5.0 0.2 - - - +
291A CYS* 3.8 25.8 - - - -
326A LEU* 4.1 27.0 - - + +
329A ILE* 5.1 4.5 - - + -
330A LEU* 3.9 24.9 - - + -
333A TRP* 5.1 2.0 - - + -
352A ILE* 3.9 16.2 - - + -
353A ASN 3.3 14.1 + - - +
354A LYS* 3.1 9.8 + - - +
356A ILE* 1.3 78.9 - - - +
358A GLN* 1.3 61.0 + - - +
360A MET* 3.4 11.4 + - - +
361A VAL* 3.2 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU* 3.3 32.2 - - + +
354A LYS* 2.9 18.7 + - + +
355A SER* 3.6 10.5 - - - +
357A ILE* 1.3 74.0 - - - +
359A THR* 1.3 65.4 + - - +
361A VAL* 3.3 5.7 + - - +
362A ASN* 2.8 57.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A SER* 2.8 22.5 + - - -
356A ILE* 3.2 13.6 + - - +
358A GLN* 1.3 78.4 - - - +
360A MET* 1.3 59.7 + - - +
362A ASN* 3.4 6.8 + - - +
363A ILE* 3.0 38.6 + - + +
402A ASP* 5.5 2.9 - - - +
406A ILE* 3.9 35.0 - - + -
410A LYS* 5.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A PHE* 3.4 34.3 - - + -
284A LEU* 3.7 19.5 - - + -
287A PRO* 5.4 1.6 - - - -
288A ILE* 3.6 24.7 - - + -
326A LEU* 4.2 21.1 - - + -
356A ILE* 3.0 30.1 + - - +
357A ILE* 3.9 12.1 - - - +
359A THR* 1.3 75.9 - - - +
361A VAL* 1.3 57.6 + - - +
363A ILE* 3.8 6.6 - - - +
364A LEU* 3.0 39.7 + - + +
406A ILE* 4.1 17.0 - - + -
409A LEU* 5.0 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A TYR* 3.6 24.5 - - + +
326A LEU* 3.6 30.1 - - + -
327A ARG* 4.0 18.8 - - + +
330A LEU* 3.8 22.0 - - + -
357A ILE 3.2 18.2 + - - +
358A GLN* 3.8 9.4 - - - +
359A THR 3.2 0.2 - - - -
360A MET* 1.3 75.0 - - - +
362A ASN* 1.3 61.2 + - - +
364A LEU* 5.2 0.4 - - - -
365A ASP* 2.9 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A GLN* 2.8 48.7 + - - +
359A THR* 3.4 7.2 + - - +
361A VAL* 1.3 77.9 - - - +
363A ILE* 1.3 69.4 + - + +
365A ASP* 3.5 15.1 + - - +
366A GLY 4.2 2.1 + - - -
395A ILE* 5.3 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A THR* 3.0 29.9 + - + +
360A MET* 3.8 7.0 - - - +
361A VAL 3.2 0.2 - - - -
362A ASN* 1.3 84.3 - - + +
364A LEU* 1.3 65.0 + - + +
365A ASP 3.3 1.0 + - - -
366A GLY* 3.6 6.1 + - - -
367A PHE* 3.2 27.0 - - + -
395A ILE* 3.8 34.1 - - + +
396A CYS* 4.5 10.3 - - - -
406A ILE* 5.2 3.8 - - + -
409A LEU* 5.2 10.1 - - + -
410A LYS* 4.2 28.3 - - + +
413A ILE* 4.9 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LEU* 3.9 29.4 - - + -
278A PHE* 4.2 26.2 - - + -
320A ASN* 3.5 15.3 + - - +
322A THR* 4.5 8.5 - - + -
323A TYR* 3.7 44.2 - - + +
326A LEU* 4.7 2.0 - - + -
360A MET* 3.0 29.7 + - + +
363A ILE* 1.3 77.1 - - + +
365A ASP* 1.3 64.8 + - - +
366A GLY 3.3 0.4 - - - -
367A PHE* 3.2 24.4 + - + +
368A GLU* 3.3 8.7 + - - +
409A LEU* 6.2 0.7 - - + -
413A ILE* 5.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A TYR* 3.4 25.5 + - + -
327A ARG* 5.5 1.6 + - - -
361A VAL* 2.9 19.1 + - + +
362A ASN* 3.6 12.8 - - - +
363A ILE 3.2 0.4 - - - -
364A LEU* 1.3 77.0 - - - +
366A GLY* 1.3 63.9 + - - +
368A GLU* 3.2 14.9 + - - +
369A ARG* 3.4 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ASN 4.2 2.4 + - - -
363A ILE 3.6 4.6 + - - -
364A LEU 3.3 0.4 - - - -
365A ASP* 1.3 79.6 + - - +
367A PHE* 1.3 65.3 + - - +
369A ARG* 3.3 16.9 + - - +
370A ILE* 3.2 27.4 + - - +
391A LYS* 5.7 5.8 - - - -
395A ILE* 4.2 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LEU* 3.8 31.5 - - + +
273A VAL* 5.6 1.3 - - + -
274A LEU* 3.7 30.1 - - + -
320A ASN* 3.6 14.4 - - - +
363A ILE* 3.2 42.6 - - + -
364A LEU* 3.2 21.8 + - + +
366A GLY* 1.3 77.4 - - - +
368A GLU* 1.3 57.1 + - - +
370A ILE* 3.3 7.9 + - - +
371A PHE* 2.9 32.4 + - + -
392A VAL* 3.9 32.1 - - + -
395A ILE* 4.6 12.3 - - + -
396A CYS* 4.5 1.8 - - - -
413A ILE* 4.2 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A TRP 4.8 1.1 - - - +
320A ASN* 3.0 36.7 + - - +
323A TYR* 3.5 28.0 - - + +
324A THR* 4.7 6.1 + - - -
364A LEU 3.3 0.8 + - - +
365A ASP 3.2 11.5 + - - +
367A PHE* 1.3 77.4 - - - +
369A ARG* 1.3 63.7 + - - +
371A PHE* 3.9 6.8 - - - +
372A LYS* 3.1 47.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ASP* 3.4 26.9 + - - +
366A GLY* 3.3 14.6 + - - +
368A GLU* 1.3 78.2 - - + +
370A ILE* 1.3 63.4 + - + +
372A LYS* 4.0 2.8 - - - +
373A GLU* 3.1 38.5 + - - +
391A LYS* 5.3 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LEU* 3.8 18.2 - - + -
366A GLY 3.2 17.6 + - - +
367A PHE* 3.6 8.5 - - - +
368A GLU 3.3 0.2 - - - -
369A ARG* 1.3 76.2 - - + +
371A PHE* 1.3 60.2 + - - +
373A GLU* 3.3 10.5 + - - +
374A LEU* 2.9 46.6 + - + +
388A SER* 3.5 51.1 - - - +
391A LYS* 4.6 16.4 - - + -
392A VAL* 3.6 21.1 - - + +
395A ILE* 5.5 1.3 - - + -
421A TRP* 4.3 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A SER* 3.4 37.0 - - - -
270A LEU* 3.7 33.4 - - + -
271A SER* 3.9 13.7 - - - -
274A LEU* 4.0 16.4 - - + -
319A TRP* 4.1 24.7 - + + -
320A ASN* 3.7 37.5 - - + -
367A PHE* 2.9 22.5 + - + +
368A GLU* 3.9 9.4 - - + +
369A ARG 3.4 0.2 - - - -
370A ILE* 1.3 76.2 - - - +
372A LYS* 1.3 63.2 + - + +
374A LEU* 3.3 10.5 + - + +
375A GLN* 2.8 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A GLU* 3.1 41.3 + - + +
369A ARG* 4.3 3.1 - - - +
371A PHE* 1.3 73.4 - - + +
373A GLU* 1.3 67.0 + - - +
375A GLN* 3.6 12.5 + - - +
376A THR* 3.5 3.6 + - - -
1B A 2.5 90.3 + - + +
2B G 4.4 2.8 + - - -
15C C 5.6 0.2 - - - +
17C G 5.6 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ARG* 3.1 35.0 + - - +
370A ILE* 3.5 8.3 - - - +
372A LYS* 1.3 73.2 - - - +
374A LEU* 1.3 60.4 + - + +
375A GLN 2.9 10.6 + - - -
376A THR* 2.9 23.6 + - - -
381A SER* 4.4 5.5 - - - -
384A PHE* 4.6 20.7 - - + +
388A SER* 3.8 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A SER* 3.8 31.4 - - - +
267A SER* 3.7 17.0 - - - +
270A LEU* 4.5 7.9 - - + -
370A ILE* 2.9 40.1 + - + +
371A PHE* 3.3 4.9 + - - +
373A GLU* 1.3 76.8 - - + +
375A GLN* 1.3 55.9 + - - +
376A THR 3.3 4.6 + - - +
377A CYS* 6.1 0.2 - - - -
381A SER* 4.4 6.0 + - - +
384A PHE* 5.2 4.3 - - + +
385A VAL* 3.9 24.7 - - + +
388A SER* 5.3 1.3 - - - +
421A TRP* 4.6 4.5 - - + -
565A PRO* 5.9 0.2 - - - +
566A ALA* 3.7 30.3 + - + +
567A SER* 2.9 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A SER* 4.2 4.0 - - - +
319A TRP* 3.8 23.0 - - + -
371A PHE* 2.8 34.7 + - - +
372A LYS* 3.8 15.0 - - - +
373A GLU 2.9 2.0 + - - -
374A LEU* 1.3 78.3 - - - +
376A THR* 1.3 57.0 + - - +
377A CYS* 4.9 1.1 - - - -
567A SER* 4.0 0.2 - - - -
569A ALA* 3.8 22.4 - - + -
573A ARG* 2.5 28.3 + - - +
1B A 3.4 38.4 - - - +
17C G 2.9 35.2 + - - +
----------------------------------------------------------
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