Contacts of the helix formed by residues 479 - 484 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B HIS* 3.6 18.7 + - + -
142C LYS* 3.5 30.5 + - - -
131D TYR* 3.8 4.4 + - - -
135D TRP* 3.5 43.7 - - + +
139D TYR* 4.0 25.6 - - + -
462D GLN 4.6 0.8 + - - -
478D GLY* 1.3 72.6 - - - -
480D TYR* 1.3 60.6 + - + +
482D LEU* 3.0 27.8 + - + +
483D GLN* 3.9 6.5 + - + +
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Residues in contact with TYR 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C TYR* 6.0 0.2 - - - -
142C LYS* 3.5 37.4 + - + +
144C ILE* 5.1 1.1 - - + -
154C THR* 2.8 24.4 + - + -
156C HIS* 2.8 37.1 + + - -
488C VAL* 3.6 25.8 - - + -
464D PRO* 3.0 39.5 - - + -
477D LEU 4.2 4.3 - - - +
478D GLY 3.2 0.4 - - - -
479D GLU* 1.3 75.1 - - - +
481D GLY* 1.3 63.4 + - - +
482D LEU 3.0 3.5 + - - -
483D GLN* 3.2 46.9 + - - +
484D ALA* 4.1 3.1 + - - +
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Residues in contact with GLY 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D TYR* 4.3 3.6 - - - -
181D PRO* 4.1 10.1 - - - +
477D LEU 3.1 28.2 + - - -
478D GLY 3.4 3.3 + - - -
479D GLU 3.2 1.2 - - - -
480D TYR* 1.3 76.3 - - - +
482D LEU* 1.3 60.9 + - - +
483D GLN 3.7 0.2 + - - -
484D ALA* 3.8 7.9 + - - +
485D TYR* 3.4 24.9 - - - -
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Residues in contact with LEU 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D TYR* 4.0 29.4 - - + -
135D TRP* 3.8 38.1 - - + +
139D TYR* 3.7 42.6 - - + -
181D PRO* 4.2 8.5 - - + +
184D ALA* 4.6 2.9 - - + -
185D THR* 3.6 23.0 - - + +
478D GLY 4.3 0.2 + - - -
479D GLU* 3.0 19.2 + - + +
481D GLY* 1.3 76.5 - - - +
483D GLN* 1.3 64.2 + - - +
484D ALA 3.2 0.4 - - - -
485D TYR* 3.0 14.3 + - - +
486D THR* 3.4 15.6 + - - -
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Residues in contact with GLN 483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C TYR* 5.2 3.0 + - - -
483C GLN* 3.1 42.4 + - - +
139D TYR* 3.3 23.4 + - + +
264D ARG* 3.4 5.3 + - - -
479D GLU* 4.4 3.8 - - + +
480D TYR* 3.2 43.4 + - - +
482D LEU* 1.3 76.3 - - - +
484D ALA* 1.3 61.0 + - - +
485D TYR 3.2 1.0 + - - -
486D THR* 3.3 20.9 + - - +
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Residues in contact with ALA 484 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D VAL* 4.2 0.9 - - - +
240D LYS* 3.1 35.8 - - - +
264D ARG* 3.1 23.2 + - - +
266D THR* 5.6 6.5 - - + -
480D TYR 4.1 2.6 + - - +
481D GLY* 3.8 11.3 + - - +
482D LEU 3.2 0.8 - - - -
483D GLN* 1.3 77.9 - - - +
485D TYR* 1.3 64.3 + - + +
486D THR 3.4 0.4 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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