Contacts of the helix formed by residues 412 - 422 (chain J) in PDB entry 1ZUM
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 J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311J GLN* 4.5 1.1 - - - +
410J PHE* 3.3 12.5 - - - -
411J LYS* 1.3 105.8 - - + +
413J ILE* 1.3 60.1 + - - +
414J GLU* 3.6 17.4 + - - +
415J GLU* 3.0 27.8 + - - +
416J VAL 3.1 23.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 413 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278J MET* 3.9 19.1 - - + -
311J GLN* 4.8 3.4 - - - +
410J PHE* 4.6 0.6 - - - -
412J THR* 1.3 71.4 - - - +
414J GLU* 1.3 91.6 + - - +
416J VAL* 3.2 22.3 - - + +
417J VAL* 3.2 15.3 - - - +
438J LYS* 3.9 33.4 - - + -
441J TYR* 3.6 33.9 - - + -
442J LEU* 3.9 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 414 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412J THR* 3.6 18.3 - - - +
413J ILE* 1.3 99.6 - - - +
415J GLU* 1.3 63.9 + - - +
417J VAL* 3.6 9.4 + - - +
418J GLY* 3.6 8.0 + - - -
441J TYR* 4.0 21.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 415 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410J PHE* 3.8 6.8 - - - -
411J LYS* 2.7 35.0 + - - +
412J THR* 3.0 23.8 + - - +
414J GLU* 1.3 75.9 - - - +
416J VAL* 1.3 64.2 + - - +
418J GLY* 3.2 5.2 + - - -
419J ARG* 2.9 59.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 416 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276J ILE* 3.9 31.6 - - + -
278J MET* 5.1 0.4 - - - -
309J PHE* 3.8 37.7 - - + -
410J PHE* 3.5 27.8 - - + -
412J THR 3.1 8.2 + - - +
413J ILE* 3.2 21.1 - - + +
415J GLU* 1.3 78.0 - - - +
417J VAL* 1.3 59.9 + - - +
419J ARG* 4.5 5.4 - - - +
420J ALA* 2.8 30.9 + - - +
442J LEU* 4.5 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 417 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I LEU* 6.1 1.6 - - + -
413J ILE 3.2 15.9 + - - +
414J GLU 3.7 7.4 - - - +
415J GLU 3.2 0.6 - - - -
416J VAL* 1.3 77.1 - - - +
418J GLY* 1.3 60.5 + - - +
420J ALA* 3.9 3.6 - - - +
421J ASN* 3.0 48.6 + - - +
441J TYR* 3.5 29.8 - - + +
442J LEU* 3.5 17.0 - - + -
445J ALA* 3.9 20.4 - - + +
446J LEU* 4.8 5.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 418 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414J GLU 3.6 5.0 + - - -
415J GLU 3.2 6.9 + - - -
417J VAL* 1.3 83.1 - - - +
419J ARG* 1.3 56.4 + - - +
421J ASN* 3.8 3.5 - - - +
422J ASN* 3.0 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 419 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307J ARG* 3.1 17.9 + - - -
309J PHE* 3.8 23.4 - - + -
389J VAL 4.8 3.4 + - - -
390J GLN* 5.3 3.8 + - - +
391J ASP* 2.8 48.8 + - - +
408J LEU* 4.0 9.5 - - - +
409J LYS 2.8 28.6 + - - -
410J PHE* 3.7 5.1 - - - +
415J GLU* 2.9 49.5 + - + +
416J VAL* 3.8 4.9 - - - +
418J GLY* 1.3 73.4 - - - +
420J ALA* 1.3 63.7 + - - +
422J ASN* 3.4 17.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 420 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274J PRO* 3.8 26.8 - - + +
276J ILE* 4.0 8.1 - - + -
307J ARG* 3.1 30.0 + - - +
309J PHE* 4.2 6.2 - - + -
416J VAL 2.8 21.7 + - - +
417J VAL 3.9 0.4 - - - +
419J ARG* 1.3 73.1 - - - +
421J ASN* 1.3 62.3 + - - +
423J SER* 4.1 2.8 - - - -
446J LEU* 3.8 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 421 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I LEU* 5.9 0.4 - - - +
417J VAL* 3.0 30.4 + - - +
418J GLY* 4.1 4.7 - - - +
420J ALA* 1.3 75.2 - - - +
422J ASN* 1.3 54.0 + - - +
423J SER* 2.6 24.6 + - - +
445J ALA 3.0 24.7 + - - -
446J LEU* 3.6 8.5 - - - +
447J GLN* 2.8 57.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 422 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307J ARG* 4.4 3.6 + - - -
391J ASP* 6.1 0.4 - - - +
418J GLY 3.0 19.0 + - - +
419J ARG* 3.6 15.8 - - - +
420J ALA 3.3 0.8 - - - -
421J ASN* 1.3 72.1 - - - +
423J SER* 1.3 61.3 + - - +
----------------------------------------------------------
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