Contacts of the helix formed by residues 410 - 422 (chain B) in PDB entry 2BEX
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 GLY 410 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B ASP* 2.6 19.1 + - - -
409B LEU* 1.3 74.2 - - - +
411B ASP* 1.3 67.7 + - - -
412B ALA 3.2 3.9 + - - -
413B GLY 3.2 1.0 + - - -
414B ILE* 3.0 23.7 + - - +
442B MET* 3.8 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 411 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B GLY* 1.3 72.1 - - - -
412B ALA* 1.3 56.4 + - - +
414B ILE* 4.2 0.6 - - - +
415B LEU* 2.9 33.6 + - - +
439B SER* 2.5 34.1 + - - -
441B GLU* 3.1 23.4 - - + +
442B MET* 3.3 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B ASP* 3.0 17.9 - - + +
410B GLY 3.2 0.6 - - - -
411B ASP* 1.3 80.2 - - - +
413B GLY* 1.3 58.6 + - - +
415B LEU* 3.6 8.8 - - - +
416B GLN* 3.2 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B ASP* 2.7 25.3 + - - -
386B CYS* 3.4 35.3 - - - +
409B LEU* 5.8 0.2 - - - -
410B GLY 3.2 1.0 + - - -
412B ALA* 1.3 71.7 - - - +
414B ILE* 1.3 64.8 + - - +
416B GLN* 3.0 18.2 + - - +
417B LEU* 3.1 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 414 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B CYS* 4.5 0.2 - - - -
409B LEU* 4.6 16.3 - - + +
410B GLY 3.0 17.4 + - - +
411B ASP 4.2 2.0 - - - +
413B GLY* 1.3 73.2 - - - +
415B LEU* 1.3 63.2 + - - +
417B LEU* 3.1 15.5 + - + +
418B VAL* 2.9 43.0 + - + +
431B LEU* 6.3 0.9 - - + -
433B LEU* 4.6 14.8 - - + -
436B ILE* 5.3 2.9 - - + -
438B TRP* 4.5 2.7 - - + -
442B MET* 3.1 47.8 - - + +
445B ARG* 5.8 2.9 - - + -
446B LEU* 3.9 30.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
411B ASP 2.9 21.0 + - - +
412B ALA* 3.6 9.6 - - - +
414B ILE* 1.3 77.3 - - - +
416B GLN* 1.3 62.6 + - + +
418B VAL* 3.2 13.0 + - + +
419B GLU* 3.0 42.7 + - + +
422B ARG* 6.3 0.2 - - - +
445B ARG* 5.6 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B ASP* 3.5 24.0 + - - +
386B CYS* 3.8 15.4 - - - +
387B SER* 3.2 30.8 - - - +
390B ALA* 3.5 14.2 - - + +
412B ALA* 3.2 21.6 + - - +
413B GLY* 3.0 8.2 + - - +
415B LEU* 1.3 79.1 - - + +
417B LEU* 1.3 62.1 + - - +
419B GLU* 3.2 30.1 + - - +
420B SER 3.5 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B CYS* 3.9 24.0 - - + +
389B LEU* 3.7 31.2 - - + -
390B ALA* 4.1 7.0 - - - +
393B LEU* 4.3 13.5 - - + -
402B LEU* 5.5 0.9 - - + -
404B LEU* 3.9 24.9 - - + -
409B LEU* 4.9 7.2 - - + -
413B GLY 3.1 12.1 + - - +
414B ILE* 3.1 17.2 + - + +
416B GLN* 1.3 76.0 - - - +
418B VAL* 1.3 59.1 + - + +
420B SER* 2.9 20.6 + - - -
421B VAL* 3.0 18.5 + - + +
431B LEU* 4.7 21.5 - - + -
433B LEU* 5.3 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B ILE* 2.9 26.6 + - + +
415B LEU* 3.2 14.1 + - + +
417B LEU* 1.3 75.1 - - + +
419B GLU* 1.3 62.7 + - - +
421B VAL* 3.6 7.9 - - + -
422B ARG* 3.0 33.6 + - + +
431B LEU* 6.2 1.1 - - + -
445B ARG* 5.0 12.1 - - + +
446B LEU* 3.5 31.0 - - + -
449B LEU* 3.9 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B LEU* 5.5 1.1 - - - +
415B LEU* 3.0 41.3 + - + +
416B GLN* 3.3 19.5 - - - +
418B VAL* 1.3 76.6 - - - +
420B SER* 1.3 56.8 + - - +
422B ARG* 3.2 49.2 + - - +
423B GLN* 3.4 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ALA* 2.7 45.9 + - - +
393B LEU* 4.1 9.2 - - - -
394B LEU* 3.6 24.7 - - - +
416B GLN 3.5 0.8 + - - -
417B LEU 2.9 9.5 + - - -
419B GLU* 1.3 78.3 - - - +
421B VAL* 1.3 65.1 + - - -
422B ARG 3.1 1.6 - - - -
423B GLN* 3.0 23.6 + - - +
426B CYS* 3.7 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B LEU* 3.9 21.8 - - + -
417B LEU* 3.0 19.6 + - + +
418B VAL* 3.6 7.0 - - + -
420B SER* 1.3 73.9 - - - +
422B ARG* 1.3 59.6 + - - +
423B GLN 3.1 1.5 + - - +
426B CYS* 3.9 14.1 - - - +
428B LEU* 3.9 22.0 - - + -
431B LEU* 5.1 11.7 - - + -
449B LEU* 3.5 30.3 - - + -
453B LYS* 2.9 35.6 + - - -
456B LEU* 3.9 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B LEU* 6.3 0.6 - - - +
418B VAL* 3.0 26.4 + - + +
419B GLU* 3.2 47.4 + - - +
421B VAL* 1.3 75.0 - - - +
423B GLN* 1.3 82.3 + - - +
424B PRO* 3.5 5.0 - - - +
449B LEU* 4.0 21.1 - - + -
453B LYS* 4.1 8.3 + - - +
----------------------------------------------------------
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