Contacts of the helix formed by residues 350 - 354 (chain E) in PDB entry 1ZMC
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 350 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348E HIS* 4.6 13.2 - - + -
349E ILE* 1.3 81.3 - - - +
351E TYR* 1.3 60.4 + - - +
352E ASN* 2.8 34.7 + - - +
353E CYS* 2.8 39.5 + - + +
354E VAL* 3.8 4.9 + - - +
437E GLU* 5.8 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 351 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308E PHE* 3.5 15.6 - - - -
322E VAL* 5.4 0.2 - - - +
323E ALA* 4.3 7.1 + - + -
324E GLY* 4.6 12.1 - - - -
325E PRO* 3.9 28.7 - - + +
330E LYS* 3.9 14.6 - - + -
334E GLU* 2.6 29.8 + - + -
349E ILE* 3.5 30.3 - - + +
350E ASP* 1.3 71.6 + - - +
352E ASN* 1.3 59.9 + - - +
353E CYS 3.2 0.7 - - - -
354E VAL* 3.4 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 352 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350E ASP* 2.8 20.6 + - - +
351E TYR* 1.3 78.5 - - - +
353E CYS* 1.3 61.0 + - - +
354E VAL 3.2 3.1 + - - +
367E VAL* 3.7 0.5 - - - +
368E GLY* 3.3 39.7 + - - +
369E LYS* 3.4 35.1 - - - +
373E GLN* 5.3 1.0 + - - -
416E LEU 4.9 3.6 + - - -
436E LEU* 4.3 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 353 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350E ASP* 2.8 31.3 + - + +
352E ASN* 1.3 82.1 - - - +
354E VAL* 1.3 60.4 + - - +
355E PRO* 3.1 13.7 - - - +
367E VAL* 3.6 13.1 - - - +
433E ALA* 4.5 7.2 - - - +
436E LEU* 4.3 29.6 - - + -
437E GLU* 3.6 31.0 - - + +
449F CYS* 4.1 9.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 354 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325E PRO* 4.4 14.7 - - + +
327E LEU* 4.4 4.7 - - + -
329E HIS* 4.0 16.2 - - + +
330E LYS* 4.3 19.1 - - + -
349E ILE* 5.2 7.4 - - + -
350E ASP 3.9 4.5 - - - +
351E TYR* 3.4 43.6 - - + +
352E ASN 3.2 2.7 - - - +
353E CYS* 1.3 78.9 - - - +
355E PRO* 1.3 75.0 - - - +
356E SER* 4.7 1.9 + - - -
366E TRP* 4.5 0.7 - - - +
367E VAL* 4.1 8.5 - - - +
368E GLY 5.1 0.2 + - - -
449F CYS* 4.4 12.1 - - + -
----------------------------------------------------------
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