Contacts of the helix formed by residues 435 - 446 (chain E) 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 ASP 435 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280E ASP* 3.4 19.6 + - - +
433E THR* 3.1 8.0 + - - +
434E LYS* 1.3 78.7 - - - +
436E LEU* 1.3 65.3 + - - +
437E ASP* 3.3 12.3 + - - +
438E LYS* 2.8 41.6 + - + +
439E ALA* 3.0 23.0 + - - +
434H LYS* 3.4 26.1 - - - +
436H LEU* 4.3 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 436 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434E LYS 3.7 2.2 + - - -
435E ASP* 1.3 72.6 - - - +
437E ASP* 1.3 69.3 + - - +
439E ALA* 3.2 2.4 + - - +
440E ASN* 3.0 43.7 + - - +
493G VAL* 4.2 14.8 - - + -
494G LYS 4.9 0.4 - - - +
433H THR 4.3 4.0 - - - +
434H LYS* 2.9 21.7 + - - +
436H LEU* 3.7 33.4 - - + +
439H ALA* 4.1 18.6 - - + -
440H ASN* 5.7 2.2 - - - +
453H VAL* 3.9 17.3 - - + -
454H ASN* 3.5 28.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 437 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435E ASP* 3.3 10.7 + - - +
436E LEU* 1.3 88.3 - - - +
438E LYS* 1.3 57.9 + - - +
440E ASN* 4.8 1.0 + - - -
441E TYR* 2.8 31.8 + - - +
494G LYS* 4.0 17.8 - - - +
495G VAL 5.5 0.6 - - - -
496G PRO* 3.5 28.8 - - + +
434H LYS 4.7 0.2 + - - -
454H ASN* 4.8 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 438 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278E MET* 4.2 24.4 - - + +
279E SER* 4.8 8.3 + - - -
280E ASP* 3.1 25.3 + - - +
311E GLN* 5.2 1.0 + - - +
413E ILE* 3.9 20.0 - - + -
433E THR* 3.8 22.7 - - + +
435E ASP* 2.8 31.2 + - + +
436E LEU 3.4 0.2 - - - -
437E ASP* 1.3 70.6 - - + +
439E ALA* 1.3 60.9 + - - +
441E TYR* 3.6 4.9 - - - +
442E LEU* 2.9 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 439 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431E VAL* 4.8 6.0 - - - +
433E THR* 3.8 16.7 - - + +
435E ASP 3.0 17.6 + - - +
436E LEU 3.5 4.3 - - - +
438E LYS* 1.3 77.5 - - - +
440E ASN* 1.3 59.0 + - - +
442E LEU* 3.9 0.9 - - - +
443E SER* 3.0 33.2 + - - -
453E VAL* 4.1 24.7 - - + +
436H LEU* 4.3 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 440 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436E LEU* 3.0 42.6 + - - +
437E ASP* 4.1 3.7 + - - +
439E ALA* 1.3 75.6 - - - +
441E TYR* 1.3 65.8 + - - +
443E SER* 3.4 8.1 + - - -
444E GLN* 3.3 23.9 + - - +
153F TYR* 4.4 9.9 + - - -
3120F EDO 4.3 7.7 - - - -
151G PHE* 4.7 9.6 - - - -
493G VAL* 4.0 10.1 - - - +
494G LYS 4.8 1.2 + - - -
495G VAL* 3.9 31.3 - - + +
496G PRO* 4.4 6.7 - - + -
436H LEU* 5.8 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 441 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413E ILE* 3.6 35.0 - - + -
414E GLU* 3.8 25.8 - - + +
417E VAL* 3.9 24.3 - - + +
437E ASP 2.8 19.0 + - - +
438E LYS* 3.6 7.2 - - - +
440E ASN* 1.3 78.5 - - - +
442E LEU* 1.3 62.6 + - + +
444E GLN* 3.8 6.1 + - - +
445E ALA* 3.0 35.7 + - + +
496G PRO* 4.1 25.7 - - + +
497G GLN* 5.6 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 442 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276E ILE* 4.6 10.3 - - + -
278E MET* 4.0 17.9 - - + -
413E ILE* 3.8 26.7 - - + -
416E VAL* 4.6 7.2 - - + -
417E VAL* 3.4 32.1 - - + -
431E VAL* 3.4 42.2 - - + -
438E LYS 2.9 17.7 + - - +
439E ALA 4.0 0.7 - - - +
441E TYR* 1.3 75.3 - - + +
443E SER* 1.3 61.5 + - - +
444E GLN 3.1 2.0 + - - -
445E ALA* 3.1 1.1 + - - +
446E LEU* 2.8 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 443 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431E VAL* 4.7 0.8 - - - +
439E ALA 3.0 19.9 + - - -
440E ASN* 3.4 8.0 + - - -
442E LEU* 1.3 76.5 - - - +
444E GLN* 1.3 57.5 + - - +
451E VAL* 3.9 23.2 - - - +
453E VAL* 4.6 5.6 - - - -
153F TYR* 4.0 2.9 + - - -
489F LYS* 2.8 30.7 + - - +
491F VAL* 4.0 24.7 - - - -
3120F EDO 3.0 21.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 444 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440E ASN 3.3 15.5 + - - +
441E TYR* 3.8 5.1 + - - +
442E LEU 3.1 0.6 - - - -
443E SER* 1.3 82.1 + - - +
445E ALA* 1.3 62.1 + - - +
72F LEU* 5.2 9.0 - - + +
155F ARG* 3.8 23.2 + - - +
157F GLU* 4.5 1.9 - - - +
489F LYS* 2.9 18.5 + - - +
3120F EDO 4.2 14.2 - - - -
495G VAL* 6.0 1.2 - - - +
497G GLN 2.6 29.5 + - - -
498G LYS* 3.8 6.2 - - - +
499G ASN* 3.0 45.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 445 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417E VAL* 3.8 31.3 - - + +
421E ASN* 3.1 18.3 + - - -
441E TYR* 3.0 26.9 + - + +
442E LEU 3.1 1.8 + - - +
444E GLN* 1.3 77.3 - - - +
446E LEU* 1.3 64.4 + - - +
447E GLN* 3.3 6.2 + - - +
72F LEU* 4.3 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 446 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E PRO* 5.4 0.7 - - + -
276E ILE* 4.0 15.5 - - + -
417E VAL* 4.8 9.2 - - + -
420E ALA* 3.8 29.4 - - + -
421E ASN* 3.6 7.4 - - - +
429E ALA* 4.0 26.2 - - + -
430E ALA 4.8 0.7 - - - +
431E VAL* 3.7 28.5 - - + -
442E LEU* 2.8 30.6 + - + +
444E GLN 3.4 0.6 - - - -
445E ALA* 1.3 71.6 - - - +
447E GLN* 1.3 59.9 + - - +
448E ALA* 3.1 5.5 + - + +
451E VAL* 4.1 18.6 - - + +
489F LYS* 2.8 29.1 + - - -
----------------------------------------------------------
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