Contacts of the helix formed by residues 353 - 376 (chain E) in PDB entry 6DWZ
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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287E PRO* 6.2 0.9 - - + -
352E ILE* 1.3 83.2 - - - +
354E LYS* 1.3 53.4 + - - +
355E SER* 2.8 29.6 + - - +
356E ILE* 2.6 51.4 + - + +
357E ILE 2.9 9.2 + - - -
403E VAL* 6.1 0.4 - - - +
405E ASP* 5.3 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 354 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330E LEU* 4.1 20.2 + - - +
333E TRP* 3.3 73.7 - - + +
334E GLU* 4.8 3.2 + - - -
352E ILE* 3.4 3.7 - - - +
353E ASN* 1.3 73.0 - - - +
355E SER* 1.3 64.3 + - - +
357E ILE* 3.7 10.3 - - - +
358E GLN* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 355 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353E ASN* 2.8 24.2 + - - +
354E LYS* 1.3 85.9 - - - +
356E ILE* 1.3 78.0 + - - +
357E ILE 3.0 1.0 + - - -
358E GLN* 3.2 6.2 + - - +
359E THR* 2.8 23.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 356 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283E GLU 5.6 0.4 - - - +
284E LEU* 3.5 29.7 - - + +
287E PRO* 4.9 6.3 - - + -
353E ASN* 2.6 39.2 + - + +
355E SER* 1.3 87.2 + - - +
357E ILE* 1.3 67.7 + - + +
359E THR* 3.2 18.9 - - - +
360E MET* 2.9 20.4 - - - +
403E VAL* 3.6 45.1 - - + -
405E ASP* 4.9 5.4 - - + +
406E ILE* 4.2 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 357 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287E PRO* 4.4 18.2 - - + -
288E ILE 5.2 1.6 - - - +
291E CYS* 4.9 13.5 - - - -
326E LEU* 4.6 18.4 - - + +
329E ILE* 5.2 5.8 - - + -
330E LEU* 3.4 27.4 - - + -
333E TRP* 5.6 7.0 - - + -
352E ILE 4.1 13.5 - - - +
353E ASN 2.9 7.2 + - - +
354E LYS* 3.8 10.3 - - - +
355E SER 3.1 0.2 - - - -
356E ILE* 1.3 83.5 - - + +
358E GLN* 1.3 70.1 + - - +
359E THR 3.0 1.3 - - - -
360E MET* 2.7 40.2 + - + +
361E VAL* 3.0 20.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 358 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330E LEU* 3.6 32.4 - - + +
354E LYS* 3.1 17.2 + - - +
355E SER* 3.6 9.2 - - - +
357E ILE* 1.3 76.4 - - - +
359E THR* 1.3 63.4 + - - +
361E VAL* 3.4 3.7 + - - +
362E ASN* 2.7 47.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 359 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355E SER 2.8 16.6 + - - -
356E ILE* 3.2 19.5 + - - +
357E ILE 3.0 0.2 - - - -
358E GLN* 1.3 78.6 - - - +
360E MET* 1.3 62.9 + - - +
362E ASN* 3.2 5.5 + - - +
363E ILE* 2.9 36.6 + - + +
406E ILE* 3.5 41.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 360 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278E PHE* 3.2 37.7 - - + -
284E LEU* 3.6 35.7 - - + +
288E ILE* 4.1 19.1 - - - -
326E LEU* 3.7 12.6 - - + -
356E ILE* 2.9 18.6 - - + +
357E ILE* 2.7 34.4 + - + +
359E THR* 1.3 72.4 - - - +
361E VAL* 1.3 52.4 + - - +
362E ASN 3.0 0.3 + - - -
363E ILE* 3.1 6.8 + - - +
364E LEU* 2.5 42.7 + - + +
409E LEU* 5.0 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 361 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323E TYR* 4.0 13.3 - - + +
326E LEU* 4.0 20.2 - - + -
327E ARG* 4.0 23.8 - - + +
330E LEU* 3.5 35.2 - - + -
357E ILE* 3.0 20.8 + - + +
358E GLN* 3.7 4.5 - - - +
360E MET* 1.3 73.6 - - - +
362E ASN* 1.3 70.9 + - - +
364E LEU* 3.7 10.2 - - - +
365E ASP* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 362 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323E TYR* 5.8 0.2 + - - -
358E GLN* 2.7 41.3 + - - +
359E THR* 3.6 5.6 - - - +
360E MET 3.0 1.0 - - - -
361E VAL* 1.3 83.1 + - - +
363E ILE* 1.3 68.7 + - + +
365E ASP* 2.9 22.3 + - - +
366E GLY 3.8 2.6 + - - -
395E ILE* 5.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 363 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359E THR* 2.9 32.9 + - + +
360E MET* 3.6 7.4 - - - +
362E ASN* 1.3 76.5 - - + +
364E LEU* 1.3 68.6 + - + +
365E ASP 3.1 1.0 + - - -
366E GLY* 3.7 4.0 + - - -
367E PHE* 3.0 36.5 - - + -
395E ILE* 4.4 20.9 - - + +
396E CYS* 5.7 1.1 - - - -
406E ILE* 5.3 6.5 - - + -
409E LEU* 5.4 7.4 - - + -
410E LYS* 4.4 27.6 - - + -
413E ILE* 5.2 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 364 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E LEU* 4.0 26.7 - - + -
278E PHE* 4.2 24.0 - - + -
320E ASN* 4.3 6.7 - - + +
322E THR* 4.7 5.4 - - + -
323E TYR* 4.0 30.7 - - + +
326E LEU* 3.8 22.2 - - + -
360E MET* 2.5 37.2 + - + +
361E VAL* 3.7 8.5 - - - +
363E ILE* 1.3 78.5 - - + +
365E ASP* 1.3 62.7 + - - +
367E PHE* 3.1 26.5 + - + +
368E GLU 3.7 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 365 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323E TYR* 2.7 36.4 + - - +
361E VAL 2.9 17.9 + - - +
362E ASN* 2.9 15.4 + - - +
364E LEU* 1.3 78.8 - - - +
366E GLY* 1.3 58.6 + - - +
368E GLU* 3.0 22.7 - - - +
369E ARG* 3.0 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 366 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362E ASN 3.8 2.6 + - - -
363E ILE 3.7 6.1 + - - -
364E LEU 3.3 0.4 - - - -
365E ASP* 1.3 80.2 + - - +
367E PHE* 1.3 63.1 + - - +
368E GLU 3.2 0.7 - - - -
369E ARG* 3.8 23.9 + - - +
370E ILE* 3.1 24.1 + - - +
391E LYS* 4.8 2.4 + - - -
395E ILE* 5.1 13.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 367 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270E LEU* 3.9 11.8 - - + +
274E LEU* 3.5 35.4 - - + -
363E ILE* 3.0 38.4 - - + -
364E LEU* 3.1 16.9 + - + +
366E GLY* 1.3 77.3 - - - +
368E GLU* 1.3 55.5 + - - +
369E ARG 3.3 0.2 - - - -
370E ILE* 3.1 11.2 + - + +
371E PHE* 2.7 48.8 + - + +
392E VAL* 4.3 25.8 - - + -
395E ILE* 3.6 31.9 - - + -
396E CYS* 4.6 2.0 - - - -
413E ILE* 4.0 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 368 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319E TRP 5.3 4.3 - - - +
320E ASN 5.4 1.2 - - - +
323E TYR* 4.2 27.6 - - + +
324E THR* 5.4 7.4 - - - +
364E LEU 3.7 3.0 + - - -
365E ASP* 3.0 20.6 + - - +
367E PHE* 1.3 75.2 - - - +
369E ARG* 1.3 66.8 + - + +
371E PHE* 2.9 13.3 + - - +
372E LYS* 2.8 52.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 369 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365E ASP* 3.0 31.9 + - - +
366E GLY* 3.9 21.9 - - - +
367E PHE 3.3 0.2 - - - -
368E GLU* 1.3 73.5 - - + +
370E ILE* 1.3 64.5 + - - +
372E LYS* 2.8 22.3 + - - +
373E GLU* 2.8 29.7 + - + +
391E LYS* 4.6 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 370 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270E LEU* 4.8 10.5 - - + -
366E GLY 3.1 21.5 - - - +
367E PHE* 3.1 15.7 + - + +
369E ARG* 1.3 74.4 - - - +
371E PHE* 1.3 63.5 + - - +
373E GLU* 3.3 9.8 + - - +
374E LEU* 2.9 35.6 + - + +
388E SER* 3.4 41.1 - - - +
391E LYS* 4.4 24.9 - - + +
392E VAL* 3.9 28.0 - - + +
395E ILE* 5.7 3.1 - - + -
421E TRP* 5.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 371 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267E SER* 3.3 39.9 - - - -
270E LEU* 3.6 34.1 - - + +
271E SER* 4.1 11.0 - - - -
274E LEU* 5.1 5.2 - - + -
319E TRP* 3.5 51.6 - + + -
320E ASN* 4.8 9.9 - - + -
367E PHE* 2.7 30.5 + - + +
368E GLU* 2.9 15.5 + - - +
370E ILE* 1.3 71.1 - - - +
372E LYS* 1.3 57.6 + - + +
374E LEU* 3.1 10.2 + - - +
375E GLN* 2.8 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 372 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368E GLU* 2.8 44.9 + - + +
369E ARG* 2.8 12.8 + - - +
371E PHE* 1.3 76.4 - - + +
373E GLU* 1.3 61.1 + - + +
374E LEU 3.1 1.0 + - - -
375E GLN* 3.2 8.8 + - - +
376E THR* 3.2 25.0 + - - -
2F G 5.2 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 373 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369E ARG* 2.8 35.0 + - + +
370E ILE* 3.8 7.8 + - - +
372E LYS* 1.3 72.5 - - + +
374E LEU* 1.3 66.3 + - + +
375E GLN 3.4 0.2 - - - -
376E THR* 4.0 15.3 + - - -
380E PRO 5.4 0.3 - - - +
381E SER* 4.5 13.2 - - - +
384E PHE* 4.0 31.5 - - + -
388E SER* 4.7 6.2 + - - -
391E LYS* 3.4 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 374 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266E SER* 3.7 32.3 - - - -
267E SER* 4.6 11.2 - - - +
270E LEU* 4.9 5.2 - - + -
370E ILE* 2.9 33.3 + - + +
371E PHE* 3.5 6.7 - - - +
372E LYS 3.1 0.6 - - - -
373E GLU* 1.3 88.6 - - + +
375E GLN* 1.3 60.1 + - - +
376E THR 3.4 0.6 + - - -
381E SER* 4.1 7.2 - - - +
384E PHE* 4.8 7.4 - - + +
385E VAL* 4.0 17.9 - - + -
388E SER* 3.4 26.2 - - - +
421E TRP* 4.3 12.3 - - + -
565E PRO 3.8 10.6 - - - +
566E ALA* 4.1 7.7 - - + +
567E SER* 3.4 14.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 375 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267E SER* 3.3 32.9 + - - -
318E ARG* 4.6 4.1 + - - -
319E TRP* 3.1 35.8 + - - +
371E PHE* 2.8 23.2 + - - +
372E LYS* 3.2 6.7 + - - +
374E LEU* 1.3 78.0 - - - +
376E THR* 1.3 55.9 + - - +
377E CYS* 2.9 6.3 + - - -
567E SER* 3.6 8.3 - - - +
569E ALA* 3.5 23.8 - - + +
573E ARG* 2.4 33.7 + - - +
2F G 4.9 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 376 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372E LYS 3.2 17.8 + - - -
373E GLU* 4.2 11.5 - - - -
374E LEU 3.4 1.8 - - - -
375E GLN* 1.3 74.0 - - - +
377E CYS* 1.3 61.4 + - - +
378E SER 3.3 31.4 - - - +
379E SER* 3.8 17.9 - - - +
380E PRO 5.4 0.9 - - - +
381E SER* 3.6 23.9 + - - -
573E ARG* 4.2 1.8 - - - +
----------------------------------------------------------
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