Contacts of the helix formed by residues 412 - 422 (chain B) in PDB entry 3KSA
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 THR 412 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B HIS* 3.1 34.3 + - + +
406B LYS* 4.9 4.7 - - - +
410B ASP 5.4 0.9 - - - +
411B PHE* 1.3 78.4 - - - +
413B GLU* 1.3 64.9 + - - +
414B GLU* 3.5 2.8 + - - +
415B GLN* 2.8 41.3 + - - +
416B ALA* 3.2 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B LYS* 4.9 13.8 - - - +
406B LYS* 6.1 0.9 - - - -
412B THR* 1.3 75.9 - - - +
414B GLU* 1.3 67.4 + - + +
416B ALA* 3.1 17.0 + - - +
417B GLU* 3.1 18.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
373B HIS* 5.3 6.1 - - + -
374B ILE* 4.2 19.3 - - + +
412B THR* 3.5 3.4 + - - +
413B GLU* 1.3 80.1 - - + +
415B GLN* 1.3 66.3 + - - +
417B GLU* 3.3 8.0 + - - +
418B ALA* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B HIS* 3.2 45.9 + - + +
374B ILE* 4.6 7.6 - - - +
376B GLU* 4.8 3.0 - - - +
377B GLY* 3.7 19.6 - - - +
378B LEU* 5.3 0.3 - - - +
380B ARG* 4.5 4.2 + - - +
411B PHE* 3.6 23.4 - - + -
412B THR* 2.8 54.1 + - - +
414B GLU* 1.3 77.5 - - - +
416B ALA* 1.3 52.1 + - - +
418B ALA* 3.3 6.0 + - - +
419B ILE* 2.8 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B LYS* 4.3 32.1 - - + +
405B LEU* 4.8 6.3 - - + -
406B LYS* 5.6 2.5 - - + +
411B PHE* 4.8 4.9 - - + +
412B THR 3.2 12.1 + - - +
413B GLU* 3.1 12.7 + - - +
415B GLN* 1.3 76.0 - - - +
417B GLU* 1.3 67.9 + - - +
419B ILE* 3.1 11.8 + - - +
420B VAL* 2.8 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B LYS* 5.5 4.9 - - - +
402B LYS* 4.5 14.9 - - + +
413B GLU* 3.1 15.2 + - - +
414B GLU* 4.0 9.0 - - - +
416B ALA* 1.3 76.8 - - - +
418B ALA* 1.3 53.2 + - - +
420B VAL* 4.5 4.5 - - - -
421B THR* 2.6 49.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ILE* 3.9 33.9 - - + -
378B LEU* 4.9 7.6 - - + -
414B GLU 3.0 17.2 + - - +
415B GLN 3.6 4.9 - - - +
417B GLU* 1.3 77.6 - - - +
419B ILE* 1.3 61.7 + - - +
421B THR* 3.6 5.8 + - - -
422B LEU* 3.0 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A LEU* 3.4 12.4 - - + +
377B GLY 5.8 0.7 - - - -
378B LEU* 4.1 11.4 - - + +
381B VAL* 3.6 41.5 - - + -
385B LEU* 6.4 0.4 - - + -
388B VAL* 4.5 13.5 - - + -
392B ILE* 5.6 2.5 - - + -
405B LEU* 4.3 10.8 - - + -
411B PHE* 3.9 28.0 - - + -
415B GLN* 2.8 24.4 + - + +
416B ALA* 3.1 7.4 + - - +
418B ALA* 1.3 73.6 - - - +
420B VAL* 1.3 64.0 + - - +
422B LEU* 3.0 39.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A LEU* 3.0 33.4 + - - +
425A TYR* 3.3 36.4 + - + +
392B ILE* 4.5 13.5 - - + -
398B LYS* 4.3 17.7 - - + +
401B ALA* 4.6 3.1 - - + -
402B LYS* 3.9 21.8 - - + +
405B LEU* 3.9 21.8 - - + -
416B ALA 2.8 22.9 + - - +
417B GLU* 3.8 2.0 - - - +
419B ILE* 1.3 75.9 - - + +
421B THR* 1.3 58.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A GLN* 3.3 34.4 + - - +
425A TYR* 4.5 7.6 - - + -
398B LYS* 4.0 25.8 - - - +
417B GLU* 2.6 36.2 + - + +
418B ALA* 3.6 5.9 + - - -
420B VAL* 1.3 70.1 - - - +
422B LEU* 1.3 71.5 + - - +
423B GLN* 3.1 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A LEU* 3.1 32.0 + - + +
378B LEU* 4.4 25.4 - - + -
381B VAL* 5.8 2.5 - - + -
385B LEU* 6.4 1.3 - - + -
418B ALA 3.0 20.6 + - - +
419B ILE* 3.0 37.5 - - + +
421B THR* 1.3 79.1 + - - +
423B GLN* 1.3 69.6 + - - +
426B ARG* 4.3 31.2 - - + +
427B LEU* 5.4 8.1 - - + -
----------------------------------------------------------
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