Contacts of the helix formed by residues 500 - 509 (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 SER 500 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470C TYR* 3.8 21.3 - - - -
472C LEU* 3.8 31.4 - - - -
489C PHE* 3.8 8.9 - - - -
493C VAL* 6.2 0.4 - - - -
498C LYS 2.5 9.5 + - - -
499C PRO* 1.3 79.6 - - - +
501C LEU* 1.3 58.8 + - - +
502C ALA 3.4 1.1 - - - +
503C ALA* 3.2 3.4 + - - +
504C SER* 2.6 40.4 + - - -
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Residues in contact with LEU 501 (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* 4.8 5.7 - - + +
476C LEU* 4.7 8.3 - - + -
499C PRO* 4.9 2.8 - - + +
500C SER* 1.3 75.2 - - - +
502C ALA* 1.3 68.2 + - - +
504C SER* 4.4 4.3 - - - -
505C ILE* 2.7 31.7 + - + +
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Residues in contact with ALA 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498C LYS* 3.8 22.7 - - + -
499C PRO* 5.2 3.5 - - + +
500C SER 3.4 1.0 - - - +
501C LEU* 1.3 79.2 - - - +
503C ALA* 1.3 64.6 + - - +
505C ILE* 3.9 2.0 - - - +
506C LEU* 2.8 38.6 + - + +
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Residues in contact with ALA 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489C PHE* 3.6 19.7 - - + +
492C LEU* 4.3 17.3 - - + -
493C VAL* 5.5 1.6 - - + +
498C LYS* 3.7 26.8 - - + +
500C SER 3.2 6.6 + - - +
502C ALA* 1.3 81.3 - - - +
504C SER* 1.3 66.4 + - - +
506C LEU* 3.6 6.7 - - - +
507C VAL* 3.1 27.0 + - + +
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Residues in contact with SER 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C LEU* 4.0 9.2 - - - -
476C LEU* 3.3 35.4 - - - -
480C LEU* 4.1 6.9 - - - +
489C PHE* 3.3 18.7 - - - -
500C SER 2.6 23.9 + - - -
503C ALA* 1.3 74.4 - - - +
505C ILE* 1.3 62.3 + - - +
507C VAL* 3.6 1.4 - - - +
508C VAL* 3.1 26.0 + - - +
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Residues in contact with ILE 505 (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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476C LEU* 3.7 18.8 - - + +
501C LEU* 2.7 23.7 + - + +
502C ALA* 3.9 2.5 - - - +
504C SER* 1.3 72.8 - - - +
506C LEU* 1.3 66.9 + - + +
509C VAL* 3.0 28.4 + - + +
510C LEU* 3.1 6.9 + - - -
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Residues in contact with LEU 506 (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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498C LYS* 6.1 1.1 - - + -
502C ALA* 2.8 42.4 + - + +
503C ALA* 3.6 6.5 - - - +
505C ILE* 1.3 73.2 - - + +
507C VAL* 1.3 61.2 + - + +
510C LEU* 2.8 35.1 - - + +
511C LYS* 3.0 13.0 + - - +
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Residues in contact with VAL 507 (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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480C LEU* 4.0 18.8 - - + -
485C ARG* 4.1 22.0 - - + +
488C LEU* 6.2 6.7 - - + -
489C PHE* 5.3 9.9 - - + +
503C ALA* 3.1 18.0 + - + +
504C SER 3.6 5.2 - - - +
505C ILE 3.1 0.6 + - - -
506C LEU* 1.3 80.9 - - + +
508C VAL* 1.3 70.5 + - - +
509C VAL 2.9 1.7 + - - -
511C LYS* 3.4 25.4 + - + +
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Residues in contact with VAL 508 (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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476C LEU* 4.1 15.7 - - + +
479C THR* 3.5 38.7 - - + +
480C LEU* 4.4 9.9 - - + -
504C SER 3.1 12.8 + - - +
507C VAL* 1.3 81.1 - - - +
509C VAL* 1.3 58.1 + - - +
511C LYS 5.0 0.5 - - - +
512C GLY* 5.0 6.4 - - - -
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Residues in contact with VAL 509 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476C LEU* 5.3 4.5 - - + -
505C ILE* 3.0 19.9 + - + +
507C VAL 2.9 2.8 + - - -
508C VAL* 1.3 76.9 - - + +
510C LEU* 1.3 68.0 + - - +
511C LYS 3.4 1.3 - - - -
512C GLY* 3.3 17.5 + - - -
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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