Contacts of the helix formed by residues 412 - 422 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311D GLN* 4.5 1.3 - - - +
410D PHE* 3.4 11.3 - - - -
411D LYS* 1.3 105.6 - - + +
413D ILE* 1.3 64.1 + - - +
414D GLU* 3.3 18.1 + - - +
415D GLU* 3.0 27.6 + - - +
416D VAL 3.1 18.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 413 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278D MET* 3.8 25.6 - - + -
311D GLN* 4.6 3.8 - - - +
410D PHE* 4.6 0.4 - - - -
412D THR* 1.3 71.0 - - - +
414D GLU* 1.3 90.3 + - + +
416D VAL* 3.2 22.3 - - + +
417D VAL* 3.2 11.1 + - - +
438D LYS* 4.2 21.8 - - + +
441D TYR* 3.3 36.3 - - + -
442D LEU* 3.9 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 414 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412D THR* 3.3 22.0 - - - +
413D ILE* 1.3 92.7 - - - +
415D GLU* 1.3 62.3 + - - +
417D VAL* 3.7 4.4 + - - +
418D GLY* 3.6 13.3 + - - -
441D TYR* 3.9 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 415 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410D PHE* 4.2 9.4 - - - -
411D LYS* 2.8 37.1 + - - +
412D THR* 3.0 25.6 + - - +
413D ILE 3.2 0.2 - - - -
414D GLU* 1.3 77.2 - - - +
416D VAL* 1.3 63.6 + - - +
418D GLY* 3.2 4.7 + - - -
419D ARG* 3.0 50.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 416 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276D ILE* 3.9 31.2 - - + -
278D MET* 5.0 0.4 - - - -
309D PHE* 3.8 38.4 - - + -
410D PHE* 3.5 33.4 - - + -
412D THR 3.1 3.6 + - - +
413D ILE* 3.2 17.0 - - + +
415D GLU* 1.3 77.0 - - - +
417D VAL* 1.3 61.1 + - - +
419D ARG* 3.1 5.3 + - - -
420D ALA* 2.7 38.8 + - + +
442D LEU* 4.5 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 417 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C LEU* 5.6 4.7 - - + -
413D ILE 3.2 14.8 + - - +
414D GLU* 3.7 9.4 - - - +
416D VAL* 1.3 77.1 - - - +
418D GLY* 1.3 60.1 + - - +
420D ALA* 3.8 4.0 - - - +
421D ASN* 3.0 44.0 + - - +
441D TYR* 3.7 19.7 - - + +
442D LEU* 3.4 26.9 - - + -
445D ALA* 3.8 24.2 - - + +
446D LEU* 4.7 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 418 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414D GLU 3.6 6.0 + - - -
415D GLU 3.2 6.5 + - - -
416D VAL 3.2 0.2 - - - -
417D VAL* 1.3 83.0 - - - +
419D ARG* 1.3 56.2 + - - +
421D ASN* 3.9 3.6 - - - +
422D ASN* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 419 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D ARG* 3.1 18.3 + - - -
309D PHE* 3.9 25.8 - - + -
389D VAL 5.7 0.2 + - - -
390D GLN* 5.0 9.1 + - - -
391D ASP* 2.6 61.4 + - - +
408D LEU* 4.5 4.2 - - - +
409D LYS 2.5 34.8 + - - +
410D PHE* 4.0 8.7 - - - +
415D GLU* 3.0 40.6 + - + +
416D VAL* 3.1 4.4 + - - +
418D GLY* 1.3 73.9 - - - +
420D ALA* 1.3 67.0 + - - +
422D ASN* 3.4 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 420 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D PRO* 3.8 29.4 - - + +
276D ILE* 4.1 7.4 - - + -
307D ARG* 2.9 29.0 + - - +
309D PHE* 4.3 6.0 - - + -
416D VAL* 2.7 22.2 + - + +
417D VAL 3.8 0.4 - - - +
419D ARG* 1.3 74.4 - - - +
421D ASN* 1.3 61.6 + - - +
422D ASN 3.5 0.2 + - - -
423D SER* 4.1 2.9 - - - -
446D LEU* 3.8 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 421 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C LEU* 5.1 1.6 - - - +
274D PRO* 6.1 0.2 - - - +
417D VAL* 3.0 30.2 + - - +
418D GLY* 4.2 3.8 - - - +
420D ALA* 1.3 75.3 - - - +
422D ASN* 1.3 52.2 + - - +
423D SER* 2.6 26.9 + - - +
445D ALA 2.9 26.1 + - - -
446D LEU* 3.5 9.2 - - - +
447D GLN* 2.9 57.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 422 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D ARG* 4.2 4.3 + - - -
391D ASP* 5.8 4.8 + - - +
418D GLY 3.0 19.4 + - - +
419D ARG* 3.7 15.2 - - - +
420D ALA 3.3 1.2 - - - -
421D ASN* 1.3 72.0 - - - +
423D SER* 1.3 61.5 + - - +
----------------------------------------------------------
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