Contacts of the helix formed by residues 432 - 440 (chain C) in PDB entry 1Z5S
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 ALA 432 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433C ASP* 1.3 65.3 + - - +
434C VAL* 3.7 12.5 - - - +
435C SER* 3.7 19.9 - - - -
436C THR* 3.2 19.6 + - - +
456C LEU* 5.5 3.2 - - - +
460C GLN* 6.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 433 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C ALA* 1.3 77.4 - - - +
434C VAL* 1.3 68.8 + - - +
435C SER 3.0 1.3 - - - -
436C THR* 2.9 9.9 + - - -
437C PHE* 2.9 21.7 + - - +
448C ARG 5.2 3.8 - - - +
449C LEU* 3.4 28.5 - - + +
456C LEU* 5.0 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 434 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C ALA 4.4 9.6 - - - +
433C ASP* 1.3 74.8 - - - +
435C SER* 1.3 74.7 + - - +
437C PHE* 2.9 10.7 + - - +
438C LEU* 2.9 25.4 + - + +
449C LEU* 4.3 6.7 - - + -
456C LEU* 3.3 45.5 - - + +
457C ILE* 3.5 35.0 - - + -
460C GLN* 3.4 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 435 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C ALA* 3.7 21.1 - - - -
434C VAL* 1.3 87.6 - - - +
436C THR* 1.3 64.6 + - - +
438C LEU* 2.9 15.9 + - - +
439C ALA* 3.2 9.6 + - - +
460C GLN* 4.3 17.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 436 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C ALA 3.2 14.0 + - - +
433C ASP* 2.9 18.2 + - - -
435C SER* 1.3 82.5 - - - +
437C PHE* 1.3 59.3 + - - +
439C ALA* 3.3 10.2 + - + +
440C PHE* 3.3 23.2 + - - +
445C LYS* 5.3 3.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 437 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433C ASP 2.9 12.8 + - - +
434C VAL* 2.9 11.2 + - - +
436C THR* 1.3 77.9 + - - +
438C LEU* 1.3 70.7 + - + +
440C PHE 4.4 2.2 - - - -
441C PRO* 3.1 30.9 - - + +
442C SER 3.4 32.1 - - - -
445C LYS* 4.0 26.0 - - + +
446C LEU* 3.4 38.1 - - + -
449C LEU* 4.6 9.0 - - + -
457C ILE* 3.7 20.9 - - + -
475C LYS 4.9 2.7 - - - -
476C VAL* 4.3 19.3 - - + -
479C VAL* 4.6 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 438 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434C VAL 2.9 17.0 + - - +
435C SER* 2.9 9.2 + - - +
437C PHE* 1.3 91.1 - - + +
439C ALA* 1.3 66.5 + - - +
441C PRO* 3.9 2.5 - - - +
457C ILE* 4.4 16.2 - - + -
460C GLN* 3.8 25.4 - - - +
461C THR* 4.4 14.6 - - + +
472C ALA* 5.0 9.0 - - + -
475C LYS* 3.1 57.9 + - + +
476C VAL* 5.3 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 439 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C SER 3.2 10.5 + - - +
436C THR* 3.5 13.7 - - + +
437C PHE 3.3 0.2 - - - -
438C LEU* 1.3 80.7 - - - +
440C PHE* 1.3 88.4 + - + +
441C PRO* 3.6 4.2 - - - +
475C LYS* 4.3 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 440 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C THR 3.3 7.8 + - - +
437C PHE 3.3 6.3 - - - +
439C ALA* 1.3 99.8 - - + +
441C PRO* 1.3 72.6 - - - +
445C LYS* 3.8 26.9 + - - +
----------------------------------------------------------
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