Contacts of the helix formed by residues 479 - 484 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F HIS* 3.4 18.6 + - + -
142G LYS* 3.4 31.8 + - - -
131H TYR* 3.8 4.8 + - - -
135H TRP* 3.3 44.1 - - + +
139H TYR* 4.0 24.2 - - + -
462H GLN 4.5 1.0 + - - -
478H GLY* 1.3 72.1 - - - -
480H TYR* 1.3 59.5 + - - +
482H LEU* 2.9 30.5 + - + +
483H GLN* 4.0 6.4 + - - +
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Residues in contact with TYR 480 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142G LYS* 3.5 37.8 - - + +
144G ILE* 4.9 1.3 - - + -
154G THR* 2.6 27.8 + - + -
156G HIS* 3.0 32.7 + + - -
488G VAL* 3.3 25.8 - - + -
464H PRO* 3.0 33.4 - - + -
475H ARG* 4.2 25.7 + - + +
477H LEU 4.1 5.4 - - - +
478H GLY 3.2 0.2 - - - -
479H GLU* 1.3 81.6 - - - +
481H GLY* 1.3 62.1 + - - +
482H LEU 3.2 1.0 + - - -
483H GLN* 3.3 46.4 + - - +
484H ALA* 4.2 2.1 + - - +
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Residues in contact with GLY 481 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132H TYR* 4.3 3.1 - - - -
181H PRO* 4.0 9.2 - - - +
475H ARG 3.7 16.0 + - - +
476H GLU* 4.6 0.7 - - - -
477H LEU 3.1 25.7 + - - -
478H GLY 3.4 3.6 + - - -
479H GLU 3.1 1.2 + - - -
480H TYR* 1.3 76.2 - - - +
482H LEU* 1.3 61.2 + - - +
483H GLN 3.4 0.6 + - - -
484H ALA* 3.8 6.5 + - - +
485H TYR* 3.4 24.4 - - - -
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Residues in contact with LEU 482 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H TYR* 3.9 24.5 - - + -
135H TRP* 3.6 38.1 - - + +
139H TYR* 3.5 43.1 - - + -
181H PRO* 4.1 11.9 - - + +
184H ALA* 4.7 2.5 - - + -
185H THR* 3.7 20.6 - - + -
478H GLY 4.4 4.5 - - - +
479H GLU* 2.9 17.1 + - - +
481H GLY* 1.3 77.8 - - - +
483H GLN* 1.3 62.2 + - - +
485H TYR* 3.0 14.0 + - - +
486H THR* 3.2 18.3 + - - +
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Residues in contact with GLN 483 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139G TYR* 5.5 2.0 + - - -
142G LYS* 6.2 1.0 - - - +
483G GLN* 3.4 41.6 + - - +
139H TYR* 3.4 20.8 + - - +
264H ARG* 3.5 4.0 + - - -
479H GLU* 4.6 5.1 + - + +
480H TYR* 3.3 46.0 + - - +
482H LEU* 1.3 78.2 - - - +
484H ALA* 1.3 60.5 + - - +
485H TYR 3.1 1.1 + - - -
486H THR* 3.4 21.5 + - - +
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Residues in contact with ALA 484 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159H VAL* 4.0 0.3 - - - +
240H LYS* 3.2 32.1 - - - +
264H ARG* 2.8 26.7 + - - +
266H THR* 6.1 2.2 - - + -
475H ARG 5.1 11.2 - - - +
480H TYR 4.2 1.9 + - - +
481H GLY 3.8 10.3 + - - +
482H LEU 3.3 1.0 - - - -
483H GLN* 1.3 78.8 - - - +
485H TYR* 1.3 62.2 + - + +
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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