Contacts of the helix formed by residues 458 - 468 (chain C) in PDB entry 1ZQ1
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 LEU 458 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C LEU* 3.5 35.0 - - + +
208C PHE* 3.2 37.2 - - + -
211C ASP* 5.0 4.0 - - + -
212C ALA* 4.9 9.2 - - - +
215C ALA* 4.5 6.5 - - + -
456C PRO 4.1 2.0 - - - +
457C GLU* 1.3 77.6 - - - +
459C PRO* 1.3 76.7 - - + +
460C GLN* 3.3 4.0 - - + +
461C ALA* 3.3 17.6 + - + +
462C LYS* 3.2 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 459 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C ASP* 3.7 39.0 - - + +
214C ARG* 3.6 34.5 - - + +
215C ALA* 4.5 5.4 - - - +
457C GLU 4.3 2.2 - - - +
458C LEU* 1.3 87.8 - - + +
460C GLN* 1.3 65.6 + - - +
462C LYS* 3.1 26.8 - - + +
463C VAL* 3.1 10.9 + - - +
481C VAL* 3.7 23.7 - - + +
486C ASP* 5.7 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 460 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C LYS* 5.1 12.1 - - - +
211C ASP* 5.1 11.4 + - - +
214C ARG* 5.9 1.0 - - - +
458C LEU* 3.3 3.3 - - + +
459C PRO* 1.3 82.6 - - - +
461C ALA* 1.3 68.7 + - - +
462C LYS 2.9 3.1 + - - -
463C VAL* 3.0 4.5 + - - +
464C GLU* 2.9 40.7 + - + +
478C GLN* 2.4 40.0 + - - +
481C VAL* 4.8 2.6 - - - +
482C ASP* 5.2 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 461 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C GLU* 3.9 11.2 - - + +
458C LEU* 3.3 29.2 + - + +
460C GLN* 1.3 78.7 - - - +
462C LYS* 1.3 60.1 + - - +
464C GLU* 3.2 16.1 + - - +
465C ARG* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 462 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C LYS* 5.1 12.9 - - - +
457C GLU* 2.9 53.6 - - + +
458C LEU 3.2 6.4 + - - +
459C PRO* 3.1 14.9 + - + +
460C GLN 2.9 0.4 - - - -
461C ALA* 1.3 75.5 - - - +
463C VAL* 1.3 67.8 + - - +
464C GLU 3.0 1.1 - - - -
465C ARG* 2.7 15.6 + - - -
466C TYR* 2.8 41.9 + - + +
481C VAL* 4.5 3.4 - - + -
486C ASP* 3.6 26.2 + - + +
487C GLU* 5.7 0.8 - - - +
490C GLU* 3.4 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 463 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459C PRO 3.4 8.1 - - - +
460C GLN* 3.0 8.0 + - + +
462C LYS* 1.3 76.6 - - - +
464C GLU* 1.3 63.7 + - + +
466C TYR* 3.5 7.6 + - - +
467C VAL* 3.2 24.6 + - + +
474C ARG* 4.8 3.4 - - + +
477C ALA* 3.5 10.5 - - + +
478C GLN* 2.8 60.8 - - + +
481C VAL* 3.3 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 464 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460C GLN* 2.9 24.8 + - + +
461C ALA* 3.2 27.5 + - - +
463C VAL* 1.3 76.2 - - + +
465C ARG* 1.3 64.2 + - - +
467C VAL* 3.2 9.0 + - - +
468C LYS* 3.1 23.8 + - - +
474C ARG* 6.0 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 465 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C GLU* 3.3 28.1 + - - -
461C ALA 3.1 14.8 + - - +
462C LYS* 2.7 13.4 + - - +
464C GLU* 1.3 68.7 - - - +
466C TYR* 1.3 82.7 + - - +
468C LYS* 2.8 17.7 + - + +
469C GLU* 2.9 54.7 + - + +
470C TYR* 3.7 14.8 + - + -
490C GLU* 3.1 27.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 466 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462C LYS* 2.8 32.3 + - + +
463C VAL* 3.5 9.2 - - - +
465C ARG* 1.3 92.1 - - - +
467C VAL* 1.3 57.8 + - - +
470C TYR* 3.3 15.0 - + - -
471C LYS 2.9 24.3 + - - -
472C LEU* 3.1 31.9 + - + +
477C ALA* 3.9 22.7 - - + -
480C LEU* 4.4 5.8 - - + -
481C VAL* 4.4 16.8 - - + -
486C ASP* 4.0 5.9 + - + +
489C PHE* 3.7 32.3 - + - -
490C GLU* 2.7 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 467 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463C VAL* 3.2 18.1 + - + +
464C GLU* 3.2 9.8 + - - +
465C ARG 3.0 0.6 - - - -
466C TYR* 1.3 78.1 - - - +
468C LYS* 1.3 63.9 + - + +
471C LYS* 3.4 16.0 - - - +
472C LEU 3.8 10.8 - - - +
474C ARG* 3.5 46.4 - - + +
477C ALA* 3.9 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 468 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464C GLU 3.1 13.6 + - - +
465C ARG* 2.8 14.1 + - - +
467C VAL* 1.3 73.9 - - + +
469C GLU* 1.3 72.3 + - + +
471C LYS* 3.1 29.7 + - - +
----------------------------------------------------------
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