Contacts of the helix formed by residues 396 - 409 (chain B) in PDB entry 2WFD
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 SER 396 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A MSE 4.3 20.9 - - - +
392B VAL 2.9 10.1 + - - -
393B PRO* 3.9 0.2 - - - +
395B ASP* 1.3 77.3 - - - +
397B PRO* 1.3 63.6 - - - +
398B ASP* 3.5 9.2 + - - +
399B ASP* 2.9 48.1 + - - +
400B ILE* 3.0 14.0 - - - +
442B ALA* 3.4 0.4 - - - +
468B TYR* 4.1 9.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B ASP 4.0 5.8 - - - +
396B SER* 1.3 83.7 - - - +
398B ASP* 1.3 64.9 + - - +
399B ASP 3.2 0.2 - - - -
400B ILE* 3.6 15.1 - - + +
401B ALA* 3.4 15.6 + - - +
442B ALA* 3.9 3.7 - - + -
445B ILE* 4.8 4.0 - - + -
446B CYS* 4.3 12.2 - - - -
460B LEU* 3.4 20.5 - - + +
463B ALA* 4.0 18.6 - - + -
464B LYS* 3.7 34.8 - - + +
467B ILE* 4.3 6.5 - - + -
468B TYR* 3.8 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B MSE 3.8 9.8 - - + +
396B SER* 3.3 5.8 + - - +
397B PRO* 1.3 77.5 - - - +
399B ASP* 1.3 63.0 + - - +
401B ALA* 3.7 6.2 - - - +
402B ALA* 3.1 27.9 + - - +
454B GLN* 5.3 1.0 - - - +
460B LEU* 3.2 24.4 - - - +
464B LYS* 2.8 42.4 + - - +
468B TYR* 4.1 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A MSE 4.6 2.8 - - - +
306B TRP* 3.1 18.8 + - - +
377B MSE 4.1 3.5 - - - +
389B VAL* 5.2 2.3 - - - +
390B THR* 3.5 7.8 - - - +
391B SER* 3.3 24.6 - - - +
392B VAL 3.1 19.4 + - - -
393B PRO* 3.6 15.5 - - + -
396B SER* 2.9 28.8 + - - +
398B ASP* 1.3 81.7 - - - +
400B ILE* 1.3 61.0 + - - +
402B ALA* 3.4 3.9 + - - +
403B LEU* 2.8 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B PRO* 2.8 49.5 - - + +
396B SER 3.0 23.6 - - - +
397B PRO* 3.6 10.5 - - + +
399B ASP* 1.3 72.5 - - - +
401B ALA* 1.3 61.5 + - - +
403B LEU* 4.3 5.4 - - + -
404B ARG* 2.7 55.4 + - + +
428B PRO* 4.9 6.5 - - + -
442B ALA* 3.3 19.1 - - + -
443B VAL* 3.4 25.1 - - + +
446B CYS* 3.8 17.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B PRO 3.4 16.3 + - - +
398B ASP* 3.7 6.5 - - - +
400B ILE* 1.3 82.3 - - - +
402B ALA* 1.3 62.7 + - - +
404B ARG* 3.8 6.4 - - - +
405B ASP* 3.0 29.5 + - - +
446B CYS* 6.3 1.3 - - + -
451B ILE* 4.9 4.7 - - + -
452B GLN 4.8 2.5 - - - +
453B SER 3.9 20.4 - - - +
454B GLN* 4.2 9.6 - - - -
460B LEU* 4.4 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B TRP* 3.4 17.9 - - + -
377B MSE 3.3 34.5 - - + -
398B ASP 3.1 7.9 + - - +
401B ALA* 1.3 74.4 - - - +
403B LEU* 1.3 58.4 + - - +
405B ASP* 2.6 32.2 + - - +
406B LEU* 3.2 7.0 + - - +
454B GLN* 3.6 23.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B THR* 3.7 17.9 - - + +
304B ASN* 4.3 7.0 - - - +
306B TRP* 3.5 15.5 - - + -
375B LEU* 5.7 4.7 - - + -
391B SER* 5.3 0.2 - - - +
393B PRO* 3.7 29.6 - - + -
399B ASP 2.8 20.1 + - - +
400B ILE* 4.0 4.3 - - + +
402B ALA* 1.3 71.4 - - - +
404B ARG* 1.3 65.9 + - + +
406B LEU* 3.2 16.1 + - - +
407B LYS* 3.2 46.7 + - + +
423B VAL* 4.8 4.6 - - + +
426B PHE* 4.4 11.4 - - + +
428B PRO* 5.2 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B ILE* 2.7 45.3 + - + +
401B ALA* 3.8 5.8 - - - +
403B LEU* 1.3 78.6 - - + +
405B ASP* 1.3 63.0 + - - +
406B LEU 3.2 0.2 + - - -
407B LYS* 3.2 9.2 + - + +
408B LYS* 3.2 60.2 + - + +
443B VAL* 3.4 29.4 + - - +
446B CYS* 5.4 6.5 + - - +
447B ASP* 3.3 28.4 + - - -
451B ILE 5.0 10.0 + - - -
452B GLN 5.7 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B ALA 3.0 18.5 + - - +
402B ALA 2.6 18.3 + - - +
404B ARG* 1.3 75.0 - - - +
406B LEU* 1.3 59.5 + - - +
408B LYS* 4.3 4.0 - - - -
409B LYS* 2.7 66.6 + - + +
452B GLN 3.2 7.6 - - - +
453B SER* 3.1 32.2 - - - -
454B GLN* 3.4 20.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B TRP* 4.6 8.3 - - + -
375B LEU* 3.1 37.0 - - + -
376B PRO* 3.8 33.7 - - + +
402B ALA 3.2 7.6 + - - +
403B LEU 3.2 9.0 + - - +
404B ARG 3.2 0.6 - - - -
405B ASP* 1.3 77.1 - - - +
407B LYS* 1.3 66.9 + - - +
408B LYS 3.1 1.2 + - - -
409B LYS* 3.1 22.7 + - + +
412B LEU 5.1 2.2 - - - +
413B ARG* 3.4 40.9 + - + +
416B TYR* 6.3 0.2 - - + -
418B ILE* 5.1 2.7 - - + -
423B VAL* 4.2 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B LEU* 3.2 31.3 + - + +
404B ARG* 3.6 11.7 - - + +
406B LEU* 1.3 78.2 - - - +
408B LYS* 1.3 62.4 + - + +
410B GLN* 4.0 5.7 - - - +
413B ARG* 3.1 21.1 + - - +
423B VAL* 3.4 37.2 - - + -
424B LEU* 3.9 26.9 + - + +
426B PHE 3.0 19.6 + - - -
427B GLU* 3.9 19.2 + - - -
428B PRO* 5.1 2.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
404B ARG* 3.2 51.4 + - - +
405B ASP* 4.7 4.3 - - - +
406B LEU 3.2 0.6 - - - -
407B LYS* 1.3 80.7 - - + +
409B LYS* 1.3 62.8 + - + +
410B GLN* 3.2 12.7 + - - +
452B GLN* 5.4 7.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B ASP* 2.7 45.3 + - + +
406B LEU* 3.1 13.5 + - + +
408B LYS* 1.3 76.9 - - + +
410B GLN* 1.3 64.1 + - - +
411B ALA 3.3 3.4 - - - -
412B LEU* 3.9 37.8 - - + +
413B ARG* 3.1 17.3 + - - +
453B SER* 5.2 4.8 - - - -
454B GLN* 5.6 2.6 - - - +
----------------------------------------------------------
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