Contacts of the helix formed by residues 485 - 495 (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 ARG 485 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C THR 5.0 0.2 - - - +
480C LEU* 2.9 15.3 + - - +
483C ASP* 2.5 18.6 + - + +
484C GLU* 1.3 71.4 - - - +
486C ASP* 1.3 63.0 + - - +
487C GLU 3.3 2.0 - - - -
488C LEU* 3.6 17.6 + - + +
489C PHE* 3.2 22.5 + - - +
507C VAL* 4.1 25.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 486 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C ARG* 3.4 29.1 + - - -
217C LYS* 5.5 3.6 - - - +
459C PRO* 5.7 1.5 - - - +
462C LYS* 3.6 22.7 + - + -
466C TYR* 4.0 8.2 + - + +
480C LEU* 2.6 18.6 + - + +
481C VAL* 3.7 24.9 - - + +
484C GLU* 3.0 7.8 - - - -
485C ARG* 1.3 74.5 - - - +
487C GLU* 1.3 74.2 + - - +
489C PHE* 3.7 6.6 + - - +
490C GLU* 3.1 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 487 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C LYS* 4.7 21.5 - - + +
462C LYS* 5.7 0.7 - - - +
484C GLU 3.9 8.7 + - - +
485C ARG 3.3 0.8 - - - -
486C ASP* 1.3 84.2 + - - +
488C LEU* 1.3 72.1 + - + +
490C GLU* 3.1 18.5 + - - +
491C GLU* 3.3 9.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 488 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C GLU 5.7 0.7 - - - +
485C ARG* 3.6 19.5 + - + +
486C ASP 3.5 0.2 - - - -
487C GLU* 1.3 82.2 - - + +
489C PHE* 1.3 54.8 + - - +
491C GLU* 2.7 39.0 + - + +
492C LEU* 3.2 5.7 + - - +
507C VAL* 6.2 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 489 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466C TYR* 3.7 36.3 - + - -
470C TYR* 4.8 9.4 - + - -
472C LEU* 4.2 17.7 - - + -
480C LEU* 3.4 39.9 - - + -
485C ARG 3.2 16.8 + - - +
486C ASP* 3.7 5.8 - - - +
487C GLU 3.3 0.2 - - - -
488C LEU* 1.3 76.5 - - - +
490C GLU* 1.3 67.1 + - - +
491C GLU 3.2 0.7 + - - -
492C LEU* 3.2 16.3 + - - +
493C VAL* 3.5 15.4 + - + +
500C SER* 3.8 11.9 - - - -
503C ALA* 3.6 16.6 - - + -
504C SER* 3.3 30.1 - - - -
507C VAL* 5.3 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 490 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C GLU* 4.7 1.4 - - - +
462C LYS* 3.4 25.5 + - - +
465C ARG* 3.1 25.8 + - - -
466C TYR* 2.7 25.5 + - - +
486C ASP 3.1 17.0 - - - +
487C GLU* 3.1 10.0 + - - +
489C PHE* 1.3 80.1 - - - +
491C GLU* 1.3 61.2 + - - +
493C VAL* 3.7 5.2 + - - +
494C SER* 3.2 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 491 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487C GLU 3.3 4.8 + - - +
488C LEU* 2.7 28.8 + - + +
490C GLU* 1.3 71.5 - - - +
492C LEU* 1.3 64.6 + - - +
494C SER* 3.3 18.4 + - - -
495C MET* 3.8 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 492 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488C LEU 3.2 5.5 + - - +
489C PHE* 3.2 10.3 + - - +
491C GLU* 1.3 80.7 - - - +
493C VAL* 1.3 63.5 + - - +
495C MET* 3.1 19.1 + - - +
497C VAL* 3.6 11.2 - - + +
498C LYS* 5.2 5.6 - - + -
503C ALA* 4.3 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 493 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C TYR* 4.3 26.2 - - + +
489C PHE* 3.5 13.2 + - + +
490C GLU* 4.1 7.9 - - - +
491C GLU 3.4 0.2 - - - -
492C LEU* 1.3 74.8 - - - +
494C SER* 1.3 52.9 + - - +
495C MET 2.7 5.3 + - - -
496C GLY* 2.5 34.0 + - - -
497C VAL 4.5 11.0 - - - +
498C LYS 5.1 4.2 + - - +
499C PRO 4.8 10.3 - - - +
500C SER* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 494 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490C GLU 3.2 15.0 + - - -
491C GLU* 3.3 15.0 + - - -
493C VAL* 1.3 73.1 - - - +
495C MET* 1.3 56.7 + - - +
496C GLY* 3.0 5.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 495 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491C GLU 3.8 3.1 + - - +
492C LEU 3.1 15.1 + - - +
493C VAL 2.7 1.8 + - - -
494C SER* 1.3 79.7 - - - +
496C GLY* 1.3 51.9 + - - -
497C VAL* 2.7 22.6 + - + +
----------------------------------------------------------
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