Contacts of the helix formed by residues 473 - 483 (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 ASP 473 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471C LYS 3.5 1.7 + - - -
472C LEU* 1.3 75.8 - - - +
474C ARG* 1.3 75.0 + - - +
475C SER* 2.5 27.5 + - - +
476C LEU* 3.0 22.4 + - + +
477C ALA* 2.9 17.8 + - - +
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Residues in contact with ARG 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463C VAL* 5.6 2.9 - - + -
464C GLU* 6.0 4.0 - - - +
467C VAL* 3.5 39.3 - - + +
472C LEU 3.6 1.6 + - - -
473C ASP* 1.3 75.8 + - - +
475C SER* 1.3 68.8 + - - +
477C ALA* 2.6 14.7 + - - -
478C GLN* 2.8 20.4 + - + +
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Residues in contact with SER 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473C ASP* 2.5 28.5 + - - -
474C ARG* 1.3 75.9 - - - +
476C LEU* 1.3 66.0 + - - +
478C GLN* 4.2 4.2 - - - +
479C THR* 2.9 34.1 + - - -
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Residues in contact with LEU 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472C LEU* 3.9 5.4 - - + -
473C ASP* 3.0 31.3 + - + +
474C ARG 2.8 1.4 + - - -
475C SER* 1.3 83.6 + - - +
477C ALA* 1.3 62.6 + - - +
479C THR* 4.1 2.9 - - - -
480C LEU* 2.8 33.4 + - - +
501C LEU* 4.5 9.9 - - + +
504C SER* 3.3 33.4 - - - +
505C ILE* 3.7 30.7 - - + +
508C VAL* 4.1 11.8 - - + +
509C VAL* 5.2 5.4 - - + +
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Residues in contact with ALA 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463C VAL* 3.5 31.9 - - + +
466C TYR* 3.9 19.3 - - + -
467C VAL* 3.9 9.0 - - + -
472C LEU* 3.5 12.0 - - + +
473C ASP 2.9 10.8 + - - +
474C ARG 2.6 12.7 + - - +
476C LEU* 1.3 74.3 - - - +
478C GLN* 1.3 65.0 + - - +
480C LEU* 3.3 13.4 + - - +
481C VAL* 3.3 12.0 + - - +
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Residues in contact with GLN 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460C GLN* 2.4 32.5 + - - +
463C VAL* 2.8 39.7 - - + +
474C ARG* 2.8 20.2 + - + +
475C SER* 4.2 4.0 - - - +
477C ALA* 1.3 70.4 - - - +
479C THR* 1.3 54.7 + - - +
481C VAL* 2.6 9.9 + - - +
482C ASP* 2.5 73.8 + - - +
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Residues in contact with THR 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475C SER* 2.9 23.8 + - - -
476C LEU 4.1 0.2 - - - -
478C GLN* 1.3 76.9 - - - +
480C LEU* 1.3 61.3 + - - +
482C ASP* 4.4 7.2 - - - +
483C ASP* 3.1 43.4 + - + +
485C ARG* 5.0 0.9 - - - +
508C VAL* 3.5 35.4 - - + +
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Residues in contact with LEU 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466C TYR* 4.4 4.9 - - + -
472C LEU* 3.9 12.6 - - + -
476C LEU 2.8 26.9 + - - +
477C ALA* 3.3 8.5 - - - +
478C GLN 3.0 0.6 - - - -
479C THR* 1.3 76.2 - - - +
481C VAL* 1.3 55.6 + - - +
485C ARG* 2.9 16.5 + - - +
486C ASP* 2.6 37.7 + - - +
489C PHE* 3.4 56.3 - - + -
504C SER* 4.1 11.2 - - - +
507C VAL* 4.0 32.5 - - + -
508C VAL* 4.4 5.2 - - + +
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Residues in contact with VAL 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C ARG* 2.6 44.0 + - - +
459C PRO* 3.7 30.1 - - + +
460C GLN* 4.8 3.1 - - - +
462C LYS* 4.5 3.1 - - + -
463C VAL* 3.3 32.3 - - + +
466C TYR* 4.4 9.6 - - + -
477C ALA 3.7 5.4 - - - +
478C GLN* 2.6 11.6 + - - +
480C LEU* 1.3 70.0 - - - +
482C ASP* 1.3 60.6 + - - +
483C ASP 3.0 4.3 - - - -
484C GLU* 3.0 16.3 + - - -
486C ASP* 3.7 20.9 - - + +
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Residues in contact with ASP 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C LYS* 5.5 4.9 + - - -
214C ARG* 4.4 13.2 + - - +
460C GLN* 5.2 2.3 + - - -
478C GLN* 2.5 52.9 + - - +
479C THR* 4.2 4.6 + - - -
481C VAL* 1.3 73.2 - - - +
483C ASP* 1.3 66.9 + - - +
484C GLU 3.4 1.8 + - - -
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Residues in contact with ASP 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479C THR* 3.1 38.4 + - + +
481C VAL 3.0 1.2 - - - -
482C ASP* 1.3 86.1 - - - +
484C GLU* 1.3 57.9 + - - +
485C ARG* 2.5 25.9 + - + +
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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