Contacts of the helix formed by residues 417 - 434 (chain B) in PDB entry 2BAP
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 ALA 417 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B TYR* 3.2 32.7 - - + +
416B GLU* 1.3 73.9 - - + +
418B ARG* 1.3 52.9 + - - +
419B PRO 3.3 1.1 - - - -
420B GLN* 2.7 26.8 + - + +
421B TYR* 2.7 33.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B VAL* 4.0 13.5 + - + -
412B ARG 3.4 14.0 + - - -
413B ASN* 3.2 40.8 + - - +
415B TYR* 3.1 25.9 + - + +
417B ALA* 1.3 75.5 - - - +
419B PRO* 1.4 68.2 - - + +
421B TYR* 3.1 6.9 + - - +
422B TYR* 2.9 65.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B TYR 4.4 0.7 - - - +
416B GLU 3.6 11.7 - - - +
417B ALA 3.4 0.7 - - - -
418B ARG* 1.4 100.0 - - + +
420B GLN* 1.3 81.6 + - - +
422B TYR* 3.4 6.7 + - + +
423B LYS* 3.3 18.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
416B GLU 3.6 3.4 + - - +
417B ALA* 2.7 42.9 + - + +
419B PRO* 1.3 90.9 - - - +
421B TYR* 1.3 66.2 + - - +
423B LYS* 3.2 21.9 + - - +
424B LEU* 3.0 30.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B VAL* 3.5 38.3 - - + +
415B TYR* 4.4 17.5 - + + -
417B ALA* 2.7 18.5 + - + +
418B ARG* 3.2 12.8 - - - +
420B GLN* 1.3 72.8 - - - +
422B TYR* 1.3 65.0 + + - +
424B LEU* 3.0 18.9 - - + +
425B ILE* 3.0 57.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B LEU* 2.6 39.9 + - + -
409B LEU* 4.0 12.1 - - + +
411B VAL* 3.7 26.1 + - + +
418B ARG* 2.9 60.5 + - + +
419B PRO* 3.9 6.5 - - + +
420B GLN 3.2 0.2 - - - -
421B TYR* 1.3 81.7 - + - +
423B LYS* 1.3 59.8 + - - +
424B LEU 3.0 1.1 - - - -
425B ILE* 3.9 11.2 - - + +
426B GLU* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B PRO 3.3 10.3 + - - +
420B GLN* 3.2 26.3 + - - +
422B TYR* 1.3 76.2 - - - +
424B LEU* 1.3 69.5 + - + +
426B GLU* 3.4 13.4 - - - +
427B GLU* 3.0 44.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 424 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B GLN* 3.0 23.8 + - + +
421B TYR* 3.0 21.8 - - + +
422B TYR 3.0 0.4 - - - -
423B LYS* 1.3 97.2 - - + +
425B ILE* 1.3 63.1 + - + +
427B GLU* 3.5 12.3 + - - +
428B CYS* 3.3 25.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 425 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B LEU* 4.4 23.3 - - + -
421B TYR* 3.0 53.6 + - + +
422B TYR* 4.2 12.8 - - + +
423B LYS 3.5 0.2 - - - -
424B LEU* 1.3 74.2 - - + +
426B GLU* 1.3 60.0 + - - +
427B GLU 3.2 0.2 - - - -
428B CYS* 3.1 12.0 + - + +
429B VAL* 2.9 34.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 426 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ARG* 4.8 10.7 + - - -
422B TYR 2.9 20.0 + - - +
423B LYS* 3.4 16.1 - - + +
425B ILE* 1.3 76.5 - - - +
427B GLU* 1.3 66.3 + - - +
429B VAL* 3.2 12.3 - - + +
430B SER* 3.0 39.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B LYS* 3.0 33.4 + - - +
424B LEU* 3.8 12.8 - - - +
425B ILE 3.2 0.2 - - - -
426B GLU* 1.3 81.6 - - - +
428B CYS* 1.3 64.8 + - - +
430B SER* 3.5 6.5 + - - -
431B GLN* 3.4 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B LEU 3.3 15.3 + - - +
425B ILE* 3.1 19.4 + - + +
427B GLU* 1.3 81.4 - - - +
429B VAL* 1.3 62.7 + - - +
431B GLN* 3.5 16.2 + - - +
432B ILE* 3.3 23.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B ILE* 6.5 0.9 - - + -
408B LEU* 6.1 6.5 - - + -
425B ILE* 2.9 23.9 + - + +
426B GLU* 3.2 19.7 - - + +
428B CYS* 1.3 70.6 - - - +
430B SER* 1.3 70.0 + - - +
432B ILE* 3.1 24.8 + - + +
433B VAL* 3.2 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B GLU* 3.0 29.9 + - - -
427B GLU* 3.7 9.4 - - - -
428B CYS 3.3 0.2 - - - -
429B VAL* 1.3 78.9 - - - +
431B GLN* 1.3 63.7 + - - +
433B VAL* 3.1 7.5 + - - +
434B LEU* 3.0 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B GLU* 3.4 20.1 + - + +
428B CYS* 3.7 12.3 - - - +
429B VAL 3.3 0.4 - - - -
430B SER* 1.3 77.5 - - - +
432B ILE* 1.3 66.3 + - + +
433B VAL 3.1 1.0 + - - -
434B LEU 3.2 9.5 + - - -
435B HIS* 3.2 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B SER* 3.5 26.2 + - - -
331B ARG* 5.6 11.4 - - + +
428B CYS* 3.3 21.1 - - + +
429B VAL* 3.1 19.5 + - + +
431B GLN* 1.3 78.2 - - + +
433B VAL* 1.3 63.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B VAL* 3.6 15.7 - - + +
327B SER* 5.3 0.2 - - - -
367B LEU* 3.3 26.3 - - + +
429B VAL* 3.3 26.5 - - + +
430B SER* 3.1 7.0 + - - +
431B GLN 3.1 0.6 - - - -
432B ILE* 1.3 85.2 - - + +
434B LEU* 1.3 63.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B VAL* 5.2 4.9 - - - +
326B ARG* 5.5 5.9 - - - -
360B GLY 5.6 1.0 - - - +
364B PHE* 3.7 43.1 - - + +
367B LEU* 4.0 19.7 - - + +
368B LYS* 4.0 35.0 - - + +
371B LEU* 4.3 22.9 - - + -
430B SER* 3.0 30.0 + - - +
431B GLN* 3.2 1.9 + - - -
433B VAL* 1.3 84.7 - - + +
435B HIS* 1.3 62.6 + - + +
----------------------------------------------------------
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