Contacts of the helix formed by residues 408 - 421 (chain B) in PDB entry 4BEJ
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 VAL 408 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B ALA* 4.2 20.8 + - - +
400B THR* 5.5 9.3 - - - +
409B PRO* 1.3 70.5 - - + +
410B GLU* 3.3 31.8 + - + +
411B VAL* 3.5 33.7 + - + +
412B SER* 4.0 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B ILE* 6.0 1.3 - - + -
408B VAL* 1.3 83.9 - - + +
410B GLU* 1.3 74.5 + - - +
412B SER* 2.2 31.3 + - - +
413B PHE* 2.9 14.5 + - - +
617B ASP* 5.9 3.4 - - + +
620B VAL* 5.7 6.1 - - + -
621B ILE* 4.1 21.1 - - + +
624B LEU* 5.4 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 410 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B VAL* 3.3 21.6 - - + +
409B PRO* 1.3 86.9 - - - +
411B VAL* 1.3 62.0 + - + +
413B PHE* 3.1 14.4 + - + +
414B GLU* 2.9 41.6 + - + +
496B THR* 6.1 4.7 - - + -
504B ALA* 4.2 26.5 - - - +
624B LEU* 5.4 5.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 411 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B ALA* 4.2 19.7 - - + +
408B VAL* 3.5 33.7 + - + +
409B PRO 3.3 0.4 - - - -
410B GLU* 1.3 75.4 - - + +
412B SER* 1.3 66.5 + - - +
413B PHE 3.4 0.2 + - - -
414B GLU* 3.6 14.4 + - - +
415B LEU* 3.6 14.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B ALA* 4.0 23.0 - - - +
396B ILE* 4.0 27.4 - - - +
399B ALA* 4.4 3.5 - - - +
408B VAL 4.0 1.0 + - - -
409B PRO* 2.2 33.7 + - - +
411B VAL* 1.3 80.5 - - - +
413B PHE* 1.3 62.3 + - - +
415B LEU* 3.5 4.2 + - - +
416B LEU* 3.1 30.5 + - - +
621B ILE* 3.2 17.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B PRO 2.9 13.7 + - - +
410B GLU* 3.2 18.6 - - + +
412B SER* 1.3 75.7 + - - +
414B GLU* 1.3 71.7 + - + +
416B LEU* 3.7 6.7 - - - +
417B VAL* 3.1 41.4 + - + +
494B ILE* 3.5 26.0 - - + -
496B THR* 5.4 8.5 - - + -
501B PHE* 3.9 16.8 - + - -
621B ILE* 4.4 4.7 - - + -
624B LEU* 3.1 44.9 - - + -
625B ILE* 3.2 20.4 - - + -
628B TYR* 3.8 19.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 414 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B GLU* 2.9 24.9 + - - +
411B VAL* 3.6 8.3 + - - +
412B SER 3.5 0.4 - - - -
413B PHE* 1.3 76.7 - - + +
415B LEU* 1.3 58.0 + - - +
417B VAL* 4.1 0.2 - - - +
418B LYS* 2.8 41.8 + - + +
494B ILE* 3.8 42.2 - - + +
496B THR* 5.3 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B ALA* 4.4 19.3 - - + -
411B VAL* 3.6 11.2 + - + +
412B SER* 3.5 8.2 + - - +
413B PHE 3.3 0.2 - - - -
414B GLU* 1.3 78.9 - - - +
416B LEU* 1.3 61.1 + - + +
418B LYS* 3.7 7.8 - - - +
419B ARG* 3.2 62.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B LEU* 3.8 23.1 - - + -
391B ASP 4.3 8.3 - - - +
392B ILE* 3.6 26.2 - - + +
395B ALA* 4.0 18.8 - - + -
412B SER* 3.1 22.6 + - - +
413B PHE 3.7 3.4 - - - +
414B GLU 3.3 0.2 - - - -
415B LEU* 1.3 78.8 - - + +
417B VAL* 1.3 65.8 + - - +
419B ARG* 3.0 30.9 + - - +
420B GLN* 3.4 14.2 + - - +
621B ILE* 3.7 14.6 - - + -
625B ILE* 3.5 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B PHE* 3.1 47.2 + - + +
416B LEU* 1.3 68.3 - - - +
418B LYS* 1.3 55.5 + - - +
419B ARG 2.7 6.0 + - - -
420B GLN* 2.6 32.1 + - + +
421B ILE* 2.9 39.1 + - + +
494B ILE* 3.9 8.7 - - + -
625B ILE* 3.6 19.7 - - + -
628B TYR* 3.7 23.6 - - + -
629B PHE* 4.5 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B GLU* 2.8 26.3 + - + +
415B LEU* 3.7 9.6 - - - +
417B VAL* 1.3 75.8 - - - +
419B ARG* 1.3 58.8 + - + +
421B ILE* 4.4 8.3 - - + +
422B LYS* 3.9 4.9 + - - +
490B GLU 2.4 32.9 + - - -
491B LEU* 3.1 59.3 - - + +
492B ALA 3.3 2.6 - - - +
493B TYR 3.4 2.5 - - - +
494B ILE* 3.2 44.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B LEU* 5.3 2.6 - - - +
391B ASP* 4.5 25.7 + - - +
394B THR* 5.9 4.8 - - - +
395B ALA* 5.4 2.4 - - - +
415B LEU* 3.2 45.4 + - + +
416B LEU* 3.0 18.9 + - - +
417B VAL 2.7 3.0 + - - -
418B LYS* 1.3 75.5 - - + +
420B GLN* 1.3 72.0 + - - +
421B ILE 3.5 0.2 - - - -
422B LYS* 3.5 17.2 - - - +
423B ARG* 4.1 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B PRO 3.2 18.4 - - - +
384B LEU* 3.9 0.2 - - - -
385B GLY 3.6 7.5 + - - +
387B LEU* 3.3 38.1 - - - +
416B LEU 3.5 15.1 + - - +
417B VAL* 2.6 14.7 + - - +
419B ARG* 1.3 75.3 + - - +
421B ILE* 1.3 64.1 + - - +
422B LYS 3.1 0.9 + - - -
423B ARG* 2.3 49.3 + - - +
424B LEU 4.5 0.2 + - - -
625B ILE* 3.7 22.9 - - + -
629B PHE* 3.2 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B VAL* 2.9 35.4 + - + +
418B LYS* 4.5 7.0 - - + +
420B GLN* 1.3 75.7 - - - +
422B LYS* 1.3 58.7 - - - +
424B LEU* 3.3 23.3 + - + +
487B VAL* 3.7 9.4 - - + +
490B GLU* 3.6 22.7 - - + +
491B LEU* 4.2 15.9 - - + -
628B TYR* 5.4 1.8 - - + -
629B PHE* 3.5 26.2 - - + -
632B VAL* 3.6 45.8 - - + -
636B ILE* 5.9 0.2 - - + -
----------------------------------------------------------
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