Contacts of the helix formed by residues 412 - 422 (chain F) in PDB entry 3SZ9
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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410F PHE* 3.4 12.5 - - - -
411F LYS* 1.3 99.5 - - + +
413F ILE* 1.3 60.1 + - - +
414F GLU* 3.5 12.9 + - - +
415F GLU* 3.2 25.5 + - - +
416F VAL 3.0 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 413 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278F MET* 3.9 18.5 - - + +
412F THR* 1.3 73.5 - - - +
414F GLU* 1.3 84.6 + - - +
416F VAL* 3.3 6.0 - - - +
417F VAL* 3.2 28.3 + - - +
438F LYS* 3.7 33.2 - - + -
441F TYR* 3.7 33.0 - - + -
442F LEU* 3.7 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 414 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412F THR* 3.5 16.0 + - - +
413F ILE* 1.3 89.7 + - - +
415F GLU* 1.3 64.7 + - - +
417F VAL* 3.5 5.0 + - - +
418F GLY* 3.5 14.4 + - - -
441F TYR* 3.7 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 415 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410F PHE* 3.6 9.3 - - - +
411F LYS* 2.8 34.6 + - - +
412F THR* 3.2 22.5 + - - +
414F GLU* 1.3 77.7 - - - +
416F VAL* 1.3 61.3 + - - +
418F GLY* 3.3 4.3 + - - -
419F ARG* 2.9 58.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 416 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276F ILE* 3.9 24.7 - - + -
278F MET* 5.1 0.2 - - - -
309F PHE* 3.9 40.8 - - + -
410F PHE* 3.7 28.7 - - + -
412F THR 3.0 9.8 + - - +
413F ILE* 3.3 18.6 - - + +
415F GLU* 1.3 74.9 - - - +
417F VAL* 1.3 63.0 + - - +
419F ARG* 4.4 4.7 - - - +
420F ALA* 2.8 30.7 + - - +
442F LEU* 4.2 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 417 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E LEU* 5.5 4.0 - - + -
413F ILE 3.2 14.3 + - - +
414F GLU* 3.7 8.7 - - - +
415F GLU 3.3 0.2 - - - -
416F VAL* 1.3 78.3 - - - +
418F GLY* 1.3 65.4 + - - +
420F ALA* 3.8 3.4 - - - +
421F ASN* 3.0 43.5 + - - +
441F TYR* 3.7 20.4 - - + +
442F LEU* 3.4 24.7 - - + -
445F ALA* 4.0 21.8 - - + +
446F LEU* 5.2 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 418 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414F GLU 3.5 5.5 + - - -
415F GLU 3.3 6.4 + - - -
417F VAL* 1.3 82.8 - - - +
419F ARG* 1.3 57.0 + - - +
421F ASN* 3.8 4.3 - - - +
422F ASN* 3.1 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 419 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307F ARG* 3.1 16.0 + - - -
309F PHE* 3.9 19.4 - - + -
389F VAL 4.6 3.8 + - - -
390F GLN* 4.8 7.3 + - - -
391F ASP* 2.8 47.0 + - - +
408F LEU* 3.8 17.8 - - - +
409F LYS 2.7 30.4 + - - +
410F PHE* 3.6 5.6 - - - +
415F GLU* 2.9 49.3 + - + +
416F VAL* 3.9 4.3 - - - +
418F GLY* 1.3 73.9 - - - +
420F ALA* 1.3 66.4 + - - +
422F ASN* 3.2 16.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 420 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274F PRO* 3.8 22.5 - - + +
276F ILE* 4.1 7.0 - - + -
307F ARG* 2.8 32.0 + - - +
309F PHE* 4.2 5.9 - - + -
416F VAL 2.8 21.9 + - - +
417F VAL 3.8 1.3 - - - +
419F ARG* 1.3 73.5 - - - +
421F ASN* 1.3 60.5 + - - +
423F SER* 4.4 1.4 - - - -
446F LEU* 3.6 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 421 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417F VAL* 3.0 31.6 + - - +
418F GLY* 4.0 4.5 - - - +
420F ALA* 1.3 74.3 - - - +
422F ASN* 1.3 60.1 + - - +
423F SER* 2.8 5.4 + - - +
445F ALA 3.0 22.6 + - - -
446F LEU* 3.6 9.8 - - - +
447F GLN* 3.0 50.6 + - - +
469F LYS* 2.8 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 422 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307F ARG* 4.5 3.6 + - - -
391F ASP* 5.9 5.9 + - + +
418F GLY 3.1 18.1 + - - +
419F ARG* 3.2 16.5 + - - +
420F ALA 3.3 0.2 - - - -
421F ASN* 1.3 72.5 - - - +
423F SER* 1.3 60.2 + - - +
----------------------------------------------------------
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