Contacts of the helix formed by residues 387 - 408 (chain B) in PDB entry 2A19
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 ASP 387 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B TRP* 5.5 5.6 - - + -
381B ARG* 5.5 6.0 + - - +
385B LYS 3.3 5.0 + - - +
386B LEU* 1.3 74.3 - - - +
388B LYS* 1.3 60.9 + - - +
389B VAL* 3.4 10.0 + - - +
390B LEU* 2.9 42.4 + - + +
391B ALA* 3.0 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B LEU* 3.5 33.4 + - + +
387B ASP* 1.3 69.5 + - - +
389B VAL* 1.3 69.5 + - + +
391B ALA* 3.2 1.7 + - - +
392B LEU* 2.8 47.4 + - + +
482B LEU* 4.0 17.3 - - + -
508B ASP* 4.2 9.7 + - - -
511B GLU* 3.0 33.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B ASP* 3.3 7.2 - - - +
388B LYS* 1.3 80.6 - - + +
390B LEU* 1.3 62.4 + - - +
392B LEU* 3.5 6.9 + - - +
393B GLU* 3.1 22.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B TRP* 3.7 30.7 - - + +
387B ASP* 2.9 36.8 + - + +
389B VAL* 1.3 74.5 - - - +
391B ALA* 1.3 57.8 + - - +
393B GLU* 3.3 12.8 - - + +
394B LEU* 2.8 43.2 + - + +
425B THR* 3.8 25.1 - - - +
426B LYS* 4.3 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B TRP* 4.9 5.3 - - + -
381B ARG* 4.4 6.7 - - - +
386B LEU* 4.4 1.1 - - + -
387B ASP 3.0 17.8 + - - +
388B LYS* 3.2 7.4 + - - +
390B LEU* 1.3 74.5 - - - +
392B LEU* 1.3 59.1 + - - +
394B LEU* 3.2 7.6 + - - +
395B PHE* 2.9 29.5 + - - +
481B LEU* 3.5 43.1 - - + +
482B LEU* 4.6 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B LYS* 2.8 48.3 + - + +
389B VAL* 3.8 5.6 - - - +
391B ALA* 1.3 72.6 - - - +
393B GLU* 1.3 61.2 + - - +
395B PHE* 3.3 4.9 + - + +
396B GLU* 3.0 25.8 + - - +
478B LEU* 4.4 12.3 - - + -
482B LEU* 3.5 23.8 - - + -
511B GLU* 5.5 0.2 - - - +
536B LEU* 4.8 9.2 - - + +
539B TRP* 4.3 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 393 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B VAL* 3.1 15.0 + - + +
390B LEU* 3.3 19.3 - - + +
392B LEU* 1.3 73.1 - - - +
394B LEU* 1.3 65.8 + - - +
396B GLU* 3.1 29.6 + - - +
397B GLN* 3.1 41.3 + - - +
426B LYS* 4.5 9.2 - - + +
540B LYS* 5.8 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B LEU* 3.9 26.2 - - + -
377B TRP* 4.2 28.5 - - + +
390B LEU* 2.8 34.9 + - + +
391B ALA* 3.8 4.5 - - - +
393B GLU* 1.3 74.2 - - + +
395B PHE* 1.3 61.9 - - - +
397B GLN* 3.4 9.1 + - - +
398B ILE* 3.1 30.1 + - + +
422B LEU* 5.1 5.2 - - + -
425B THR 4.9 2.5 - - - +
426B LYS* 4.0 29.6 - - - +
427B GLN 4.2 0.4 - - - +
428B VAL* 4.0 23.9 - - + +
481B LEU* 4.6 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ALA 2.9 16.7 + - - +
392B LEU* 3.7 5.6 - - + +
393B GLU 3.1 0.2 - - - -
394B LEU* 1.3 77.5 - - - +
396B GLU* 1.3 53.6 + - - +
398B ILE* 3.2 5.2 + - + +
399B THR* 2.8 54.7 + - - -
474B LEU* 3.2 44.0 - - + -
477B ILE* 4.3 10.1 - - + -
478B LEU* 3.7 50.0 - - + -
481B LEU* 3.8 11.4 - - + +
514B LEU* 5.1 0.2 - - + -
518B LEU* 4.9 3.4 - - + -
532B ILE* 3.7 24.9 - - + -
536B LEU* 3.8 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LEU 3.0 13.6 + - - +
393B GLU* 3.4 24.2 - - - +
395B PHE* 1.3 78.1 - - - +
397B GLN* 1.3 56.1 + - + +
399B THR* 3.3 3.2 + - - -
400B LYS* 2.9 55.7 + - + +
533B LEU* 4.2 6.0 - - + +
536B LEU* 3.7 29.0 - - + +
537B THR* 5.3 2.8 + - - -
540B LYS* 2.9 41.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B ASN* 3.2 41.5 + - - +
393B GLU* 3.1 36.2 + - - +
394B LEU* 3.7 9.7 - - - +
396B GLU* 1.3 74.4 - - + +
398B ILE* 1.3 65.6 + - - +
400B LYS* 3.4 6.2 + - + -
401B GLY 3.0 18.2 + - - -
426B LYS 3.0 18.7 - - - +
427B GLN* 3.2 13.8 - - - +
428B VAL* 2.9 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B ASN* 5.4 0.4 - - - -
374B LEU* 3.9 27.8 - - + -
394B LEU* 3.1 24.3 + - + +
395B PHE* 3.2 8.9 + - + +
397B GLN* 1.3 74.8 - - - +
399B THR* 1.3 56.9 + - - +
401B GLY* 3.3 2.9 + - - -
402B VAL* 3.0 31.1 + - + +
415B LEU* 5.1 2.5 - - + -
420B ILE* 4.0 30.3 - - + -
428B VAL* 3.9 15.0 - - + -
430B ILE* 3.7 13.9 - - + +
474B LEU* 3.6 24.0 - - + -
477B ILE* 4.2 17.0 - - + -
481B LEU* 4.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE* 2.8 45.2 + - - -
396B GLU* 3.6 6.3 - - - -
398B ILE* 1.3 73.7 - - - +
400B LYS* 1.3 60.0 + - - +
402B VAL* 3.3 1.5 + - - +
403B ASP* 2.8 31.1 + - - +
474B LEU* 4.3 10.0 - - + +
529B THR* 4.1 16.2 - - + -
532B ILE* 3.7 26.7 - - + -
533B LEU* 3.4 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B HIS* 3.9 20.4 + - + +
318B VAL* 6.1 0.9 - - + -
319B ASN* 4.0 12.6 - - - +
396B GLU* 2.9 48.9 + - + +
397B GLN* 3.6 9.4 - - + +
399B THR* 1.3 75.3 - - - +
401B GLY* 1.3 63.3 + - - +
403B ASP* 3.1 9.7 - - - +
404B TYR* 3.0 22.3 + - - +
533B LEU* 4.2 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B HIS* 3.9 15.8 - - - -
319B ASN* 4.2 4.5 - - - -
320B ILE* 3.8 5.8 - - - +
397B GLN 3.0 13.8 + - - -
398B ILE 3.6 3.4 - - - -
399B THR 3.2 0.2 - - - -
400B LYS* 1.3 77.2 - - - +
402B VAL* 1.3 61.2 + - - +
404B TYR* 3.0 5.8 + - - +
405B ILE* 3.0 24.8 + - - +
430B ILE* 3.9 17.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B ILE* 3.0 17.9 + - + +
399B THR 3.3 3.6 + - - +
401B GLY* 1.3 71.1 - - - +
403B ASP* 1.3 66.7 + - - +
404B TYR 3.1 0.2 + - - -
405B ILE* 3.2 10.5 + - + +
406B HIS* 3.0 53.6 + - + +
415B LEU* 3.5 24.7 - - + -
430B ILE* 3.9 10.5 - - + -
470B ASP* 4.0 13.5 - - + +
474B LEU* 3.9 20.9 - - + -
529B THR* 3.9 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B THR 2.8 14.5 + - - +
400B LYS* 3.1 15.5 - - - +
402B VAL* 1.3 77.8 - - - +
404B TYR* 1.3 56.9 + - - +
406B HIS* 3.5 3.6 + - - +
407B SER* 3.1 27.2 + - - -
529B THR* 2.3 36.5 + - - +
530B SER* 3.6 15.6 + - - -
533B LEU* 3.8 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B LYS 3.7 5.5 + - - -
315B LEU* 3.7 11.0 - - + -
316B ASP* 2.9 48.7 + - - +
317B HIS* 3.7 25.1 - + + -
320B ILE* 3.6 18.4 - - + -
400B LYS 3.0 12.4 + - - +
401B GLY 3.0 8.0 + - - +
403B ASP* 1.3 75.6 - - - +
405B ILE* 1.3 65.7 + - - +
407B SER* 2.6 29.6 + - - -
408B LYS* 3.0 48.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LEU* 4.5 6.7 - - + -
320B ILE* 3.8 14.1 - - + -
401B GLY 3.0 14.0 + - - +
402B VAL* 3.5 12.8 - - + +
404B TYR* 1.3 74.2 - - - +
406B HIS* 1.3 65.5 + - + +
408B LYS* 3.1 13.3 + - - +
410B LEU* 3.1 51.9 + - + +
411B ILE 4.3 0.7 - - - -
412B ASN* 4.1 27.1 - - + +
415B LEU* 5.2 0.2 - - + -
430B ILE* 4.0 19.5 - - + -
433B PHE* 3.7 33.7 - - + -
436B VAL* 5.3 0.9 - - + -
470B ASP* 4.8 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B VAL* 3.0 35.7 + - + +
403B ASP* 3.7 5.2 - - - +
405B ILE* 1.3 75.0 - - + +
407B SER* 1.3 59.6 + - - +
409B LYS* 2.9 21.5 + - - +
410B LEU 3.3 19.5 - - - -
411B ILE* 4.4 1.1 - - + +
439B LEU* 4.1 10.5 - - + +
467B LYS* 3.5 53.9 - - + +
470B ASP* 2.5 31.5 + - + +
471B LEU* 3.9 12.2 - - + +
529B THR* 4.5 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B ASP* 3.1 14.6 + - - -
404B TYR* 2.6 29.9 + - - -
406B HIS* 1.3 72.0 - - - +
408B LYS* 1.3 68.3 + - - +
409B LYS* 3.0 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B LYS* 3.8 24.3 + - + +
315B LEU* 3.6 28.7 - - + -
404B TYR* 3.0 44.8 + - + +
405B ILE 3.1 7.1 + - - +
407B SER* 1.3 88.9 - - - +
409B LYS* 1.3 70.2 + - - +
410B LEU* 3.2 14.3 + - + +
----------------------------------------------------------
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