Contacts of the helix formed by residues 479 - 484 (chain G) 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 GLU 479 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E HIS* 3.6 19.4 + - + -
131G TYR* 3.9 4.2 + - - -
135G TRP* 3.5 43.9 - - + +
139G TYR* 4.2 22.3 - - + -
462G GLN 4.7 0.6 + - - -
478G GLY* 1.3 72.3 - - - -
480G TYR* 1.3 60.3 + - - +
482G LEU* 2.9 30.9 + - + +
483G GLN* 4.0 4.3 + - + +
142H LYS* 3.5 31.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 480 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464G PRO* 3.0 36.1 - - + -
475G ARG* 3.9 26.7 + - + +
477G LEU 4.2 2.5 - - - +
479G GLU* 1.3 81.8 - - - +
481G GLY* 1.3 60.8 + - - +
482G LEU 3.0 1.5 + - - -
483G GLN* 3.2 45.4 + - - +
484G ALA* 4.2 2.3 + - - +
142H LYS* 3.4 37.6 - - + +
144H ILE* 5.0 1.3 - - + -
154H THR* 2.7 27.7 + - + -
156H HIS* 2.9 30.3 + + - -
488H VAL* 3.5 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 481 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G TYR* 4.3 6.1 - - - -
181G PRO* 3.9 7.0 - - - +
475G ARG 3.5 20.2 + - - +
476G GLU* 4.5 0.4 - - - -
477G LEU 3.2 19.6 + - - -
478G GLY 4.0 3.4 - - - -
479G GLU 3.1 2.0 - - - -
480G TYR* 1.3 77.3 - - - +
482G LEU* 1.3 61.7 + - - +
484G ALA* 4.1 4.8 + - - +
485G TYR* 3.3 27.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 482 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G TYR* 3.8 30.3 - - + -
135G TRP* 3.7 39.3 - - + -
139G TYR* 3.8 42.4 - - + -
181G PRO* 4.1 9.9 - - + +
184G ALA* 4.7 2.2 - - + -
185G THR* 3.7 21.1 - - + -
478G GLY 4.4 0.2 - - - +
479G GLU* 2.9 17.7 + - - +
481G GLY* 1.3 78.0 - - - +
483G GLN* 1.3 64.2 + - - +
484G ALA 3.3 0.4 - - - -
485G TYR* 2.9 14.7 + - - +
486G THR* 3.3 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 483 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139G TYR* 3.5 21.0 + - + +
264G ARG* 3.5 3.3 + - - -
475G ARG* 6.1 0.3 - - - +
479G GLU* 4.6 1.6 - - + +
480G TYR* 3.2 40.5 + - - +
482G LEU* 1.3 76.6 - - - +
484G ALA* 1.3 61.3 + - - +
485G TYR 3.1 1.0 + - - -
486G THR* 3.3 21.8 + - - +
139H TYR* 4.8 3.4 + - - -
483H GLN* 3.4 47.1 - - - +
488H VAL* 5.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 484 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159G VAL* 4.0 0.5 - - - +
240G LYS* 3.0 37.1 - - - +
264G ARG* 2.7 25.7 + - - +
266G THR* 5.4 7.0 - - + -
475G ARG 5.0 15.7 - - - +
480G TYR 4.2 2.3 + - - +
481G GLY 4.1 8.6 + - - +
482G LEU 3.3 0.8 - - - -
483G GLN* 1.3 77.9 - - - +
485G TYR* 1.3 62.0 + - + +
----------------------------------------------------------
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