Contacts of the helix formed by residues 352 - 378 (chain D) in PDB entry 5WJ9
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 352 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D PHE* 5.6 12.3 - - + -
49D PHE* 5.7 11.2 - - + -
320D LEU* 5.3 0.9 - - - +
350D PHE 3.6 3.5 + - - -
351D VAL* 1.3 82.2 - - + +
353D GLY* 1.3 63.7 + - - +
354D TRP* 3.3 27.2 + - - +
355D TYR* 3.5 35.5 + - + +
356D ILE* 4.0 7.3 + - - +
403D ARG* 3.0 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 353 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351D VAL 3.5 4.5 + - - -
352D ASN* 1.3 72.0 + - - +
354D TRP* 1.3 62.8 + - - +
355D TYR 3.2 2.5 - - - -
356D ILE* 2.8 18.4 + - - +
357D LEU* 2.8 28.3 + - - +
419D ARG* 5.5 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 354 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352D ASN* 3.3 18.0 + - - +
353D GLY* 1.3 76.4 - - - +
355D TYR* 1.3 58.8 + - - +
357D LEU* 3.5 22.3 + - + +
358D LEU* 2.8 31.0 + - - +
399D VAL* 3.6 26.9 - - + -
400D GLY* 5.2 3.1 - - - -
402D ILE* 3.5 30.5 - - + -
403D ARG* 3.5 49.4 - - + +
415D ILE* 4.7 11.7 - - + -
419D ARG* 3.4 33.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 355 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D PHE* 5.5 9.0 - + - -
65D LYS* 3.4 36.6 + - - -
316D CYS* 3.5 22.1 - - + -
319D SER* 3.6 28.4 - - - +
320D LEU* 5.1 9.6 - - + -
352D ASN* 3.5 34.1 - - + +
353D GLY 3.2 0.2 - - - -
354D TRP* 1.3 75.5 - - - +
356D ILE* 1.3 56.2 + - - +
358D LEU* 3.2 15.6 + - + +
359D VAL* 2.8 39.0 + - - +
403D ARG* 2.9 38.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 356 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D LEU* 4.8 17.3 - - + -
351D VAL* 5.3 10.3 - - + +
352D ASN 4.1 13.2 - - - +
353D GLY* 2.8 21.2 + - - +
355D TYR* 1.3 71.7 - - - +
357D LEU* 1.3 52.1 + - - +
359D VAL* 3.5 8.9 + - - +
360D THR* 2.7 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 357 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353D GLY 2.8 14.6 + - - +
354D TRP* 3.6 26.0 - - + +
356D ILE* 1.3 71.8 - - - +
358D LEU* 1.3 57.0 + - - +
360D THR* 3.3 7.7 + - - -
361D SER* 2.8 35.5 + - - +
396D LEU* 3.6 50.4 - - + +
399D VAL* 4.3 10.1 - - + -
400D GLY* 5.4 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 358 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D LYS* 5.8 3.4 - - - -
69D GLN* 3.5 44.2 - - + +
72D LYS* 4.3 15.2 + - - +
312D SER* 4.7 11.0 - - - +
313D PHE* 5.7 0.7 - - - +
316D CYS* 5.1 7.9 - - + -
354D TRP 2.8 22.3 + - - +
355D TYR* 3.4 23.1 - - + +
357D LEU* 1.3 76.2 - - - +
359D VAL* 1.3 56.4 + - - +
361D SER* 2.6 20.0 + - - +
362D ASP* 2.8 16.6 + - + +
397D VAL* 6.6 0.2 - - + -
400D GLY* 6.2 5.6 - - - -
403D ARG* 6.0 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 359 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313D PHE* 3.6 35.2 - - + -
316D CYS* 3.5 23.6 - - + -
317D ALA 5.8 0.4 - - - +
320D LEU* 4.7 13.0 - - + -
355D TYR 2.8 23.7 + - - +
356D ILE* 3.7 7.4 - - - +
358D LEU* 1.3 70.3 - - - +
360D THR* 1.3 63.0 + - - +
362D ASP* 3.2 7.5 + - - +
363D VAL* 2.9 36.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 360 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356D ILE* 2.7 27.7 + - - +
357D LEU* 3.3 11.0 + - - -
359D VAL* 1.3 77.8 - - - +
361D SER* 1.3 63.3 + - - +
363D VAL* 3.4 6.7 + - + +
364D LEU* 3.3 33.6 + - + +
396D LEU* 4.8 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 361 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D LYS* 5.4 0.5 + - - -
357D LEU 2.8 17.4 + - - -
358D LEU* 2.6 27.0 + - - +
360D THR* 1.3 71.5 - - - +
362D ASP* 1.3 55.3 + - - -
364D LEU* 3.5 5.6 + - - +
365D THR* 2.6 32.3 + - - -
393D SER* 3.6 13.4 + - - +
396D LEU* 3.5 38.2 + - - +
397D VAL* 4.1 12.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 362 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D LYS* 3.9 17.9 - - - +
309D CYS* 3.3 27.0 - - - +
310D SER 4.3 0.2 + - - -
312D SER* 5.0 0.9 - - - +
313D PHE* 3.2 40.9 - - + +
358D LEU* 2.8 19.5 + - + +
359D VAL* 3.2 11.6 + - - +
361D SER* 1.3 69.6 - - - +
363D VAL* 1.3 64.4 + - - +
365D THR* 2.8 12.5 + - - -
366D ILE* 2.8 43.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 363 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313D PHE* 5.3 4.0 - - + -
359D VAL* 2.9 29.9 + - + +
360D THR* 3.6 10.3 - - - +
362D ASP* 1.3 81.5 - - - +
364D LEU* 1.3 59.6 + - + +
366D ILE* 3.5 9.7 - - + +
367D SER* 2.6 46.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 364 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360D THR* 3.3 20.6 + - + +
361D SER 3.6 8.1 - - - +
362D ASP 3.2 0.8 - - - -
363D VAL* 1.3 86.3 - - + +
365D THR* 1.3 58.7 + - - +
367D SER* 2.9 5.4 + - - +
368D GLY* 2.8 26.3 + - - -
389D LEU* 3.7 38.4 - - + +
392D THR* 3.5 37.9 - - + -
393D SER* 3.8 8.1 - - - +
396D LEU* 4.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 365 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D LYS* 4.6 0.5 + - - -
76D VAL* 3.5 21.3 - - + -
305D VAL* 3.8 10.1 - - + -
309D CYS* 3.4 28.8 - - - -
361D SER 2.6 25.0 + - - -
362D ASP* 2.8 14.0 + - - -
364D LEU* 1.3 71.2 - - - +
366D ILE* 1.3 51.6 + - - -
368D GLY* 3.2 1.7 + - - -
369D THR* 2.8 38.7 + - - +
390D LEU* 4.4 10.5 - - + +
393D SER* 2.6 21.6 + - - +
397D VAL* 4.5 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 366 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D ILE* 3.9 42.6 - - + +
309D CYS* 4.7 4.7 - - + -
310D SER* 4.6 11.9 - - - +
362D ASP* 2.8 32.0 + - - +
363D VAL* 3.5 18.2 - - + +
365D THR* 1.3 70.6 - - - +
367D SER* 1.3 66.4 + - - +
369D THR* 3.0 16.6 + - - -
370D ILE* 3.3 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 367 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363D VAL* 2.6 35.2 + - - +
364D LEU* 2.9 12.8 + - - +
366D ILE* 1.3 71.7 - - - +
368D GLY* 1.3 66.7 + - - +
370D ILE* 3.2 12.6 - - - +
371D MET* 3.2 23.1 + - - +
389D LEU* 3.8 18.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 368 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364D LEU 2.8 20.5 + - - -
365D THR 3.2 1.8 + - - -
367D SER* 1.3 75.8 + - - +
369D THR* 1.3 50.5 + - - +
371D MET* 2.8 12.4 + - - +
372D LYS* 2.8 31.7 + - - +
386D CYS* 3.8 3.8 - - - -
389D LEU* 4.3 11.9 - - - -
390D LEU* 4.2 19.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 369 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D GLN* 3.5 26.2 - - + +
302D ASP* 4.2 6.9 - - - +
305D VAL* 3.6 30.7 - - + -
306D ILE* 3.2 25.5 - - - +
365D THR 2.8 20.6 + - - +
366D ILE* 3.0 18.7 + - - -
368D GLY* 1.3 71.0 - - - +
370D ILE* 1.3 55.4 + - - +
372D LYS* 3.3 8.2 + - - +
373D ILE* 2.8 36.0 + - - +
390D LEU* 4.7 3.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 370 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D ILE* 4.9 4.2 - - + +
366D ILE 3.3 11.8 + - - +
367D SER* 3.2 22.7 - - - +
369D THR* 1.3 80.4 + - - +
371D MET* 1.3 56.2 + - - +
373D ILE* 4.0 11.8 - - + +
374D GLY* 3.1 23.4 + - - -
380D LEU* 5.0 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 371 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367D SER 3.2 12.4 + - - +
368D GLY 2.8 12.2 + - - +
370D ILE* 1.3 76.6 - - + +
372D LYS* 1.3 52.4 + - - +
375D ILE* 2.8 38.9 + - + +
380D LEU* 3.7 24.6 - - + +
382D SER* 3.4 24.7 - - - +
385D VAL* 3.6 16.6 - - + -
386D CYS* 3.5 35.7 - - + -
389D LEU* 3.6 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 372 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D GLN* 3.1 42.5 - - - +
82D LEU* 5.7 0.6 - - - +
83D PHE* 3.8 25.8 - - + +
298D ARG* 3.2 46.7 - - - +
302D ASP* 3.9 17.5 - - - +
368D GLY 2.8 11.9 + - - +
369D THR* 3.5 9.9 - - - +
371D MET* 1.3 74.1 - - - +
373D ILE* 1.3 60.2 + - - +
375D ILE* 3.7 7.4 - - + -
376D GLU* 2.8 48.8 + - + +
386D CYS* 4.0 9.6 - - - -
390D LEU* 4.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 373 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D LEU* 5.9 8.1 - - + -
302D ASP* 3.1 39.5 - - - +
303D VAL* 5.1 4.0 - - + -
306D ILE* 3.8 23.6 - - + -
369D THR 2.8 25.3 + - - +
370D ILE* 4.0 10.5 - - + +
372D LYS* 1.3 70.0 - - - +
374D GLY* 1.3 56.0 + - - +
376D GLU* 4.8 3.4 - - - -
377D ALA* 2.8 42.8 + - + +
378D LYS* 4.5 3.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 374 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370D ILE 3.1 16.3 + - - -
371D MET 3.7 2.9 - - - -
373D ILE* 1.3 77.0 - - - +
375D ILE* 1.3 54.9 + - - +
378D LYS* 2.8 47.9 + - - +
380D LEU* 3.6 15.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 375 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D PHE* 4.3 15.9 - - + -
371D MET* 2.8 24.6 + - + +
372D LYS* 3.4 14.1 - - + +
374D GLY* 1.3 71.9 - - - +
376D GLU* 1.3 67.7 + - + +
378D LYS 3.9 3.3 - - - +
380D LEU* 3.5 32.0 - - + +
381D ALA* 4.0 3.6 - - - -
382D SER 3.5 22.9 - - - +
383D TYR* 3.4 61.0 + - + +
386D CYS* 5.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 376 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D SER* 6.1 1.1 - - - +
249D GLU* 3.0 54.7 - - + +
294D ASP* 5.2 4.1 - - - +
295D ASN* 5.1 10.8 - - - +
298D ARG* 4.0 45.8 - - - +
299D LEU* 5.3 2.8 + - - +
302D ASP* 5.7 1.0 - - - +
372D LYS* 2.8 34.2 + - + +
373D ILE* 4.2 3.1 - - - +
375D ILE* 1.3 79.9 - - + +
377D ALA* 1.3 72.1 + - - +
378D LYS 3.6 1.6 + - - +
383D TYR* 5.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 377 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D GLU* 4.4 3.6 - - - +
283D GLU* 5.5 3.8 - - - +
295D ASN* 4.8 11.4 - - - +
299D LEU* 6.4 2.2 - - + -
373D ILE* 2.8 25.4 + - + +
376D GLU* 1.3 90.0 - - - +
378D LYS* 1.3 76.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 378 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283D GLU* 5.4 8.0 + - - -
373D ILE* 4.9 3.8 - - + +
374D GLY* 2.8 34.6 + - - +
375D ILE 3.9 4.9 - - - +
376D GLU 3.6 1.7 + - - +
377D ALA* 1.3 83.5 - - + +
379D ASN* 1.3 68.1 + - - +
380D LEU* 3.0 9.5 + - + +
----------------------------------------------------------
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