Contacts of the helix formed by residues 504 - 515 (chain C) in PDB entry 3PQZ
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 504 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493C PHE* 3.9 16.4 - - + -
502C PHE* 3.3 10.2 - - - +
503C THR* 1.3 91.5 + - - +
505C LEU* 1.3 66.2 + - - +
506C LEU* 3.4 14.9 + - - +
507C GLN* 3.3 29.9 + - - +
508C LEU* 3.5 8.1 + - - +
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Residues in contact with LEU 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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431C TRP* 4.0 15.9 - - + -
432C PHE* 4.3 10.8 - - + -
457C VAL* 4.1 14.6 - - + -
467C PHE* 3.7 44.0 - - + -
482C ILE* 3.9 41.1 - - + -
493C PHE* 4.4 13.8 - - + -
504C ASP* 1.3 73.4 - - - +
506C LEU* 1.3 67.1 + - - +
508C LEU* 3.1 10.5 + - + +
509C VAL* 3.0 25.3 + - + +
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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
----------------------------------------------------------
431C TRP* 3.8 35.4 - - + +
504C ASP* 3.4 11.7 + - - +
505C LEU* 1.3 77.3 - - - +
507C GLN* 1.3 58.2 + - - +
509C VAL* 3.3 3.0 + - + +
510C GLU* 2.9 57.4 + - + +
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Residues in contact with GLN 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501C ARG 4.9 2.6 + - - -
502C PHE* 3.3 18.7 - - + -
503C THR* 2.9 40.2 + - - +
504C ASP* 3.3 16.0 + - - +
505C LEU 3.2 0.8 - - - -
506C LEU* 1.3 78.8 - - - +
508C LEU* 1.3 57.5 + - - +
510C GLU* 4.0 8.5 - - + +
511C PHE* 2.9 31.6 + - + +
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Residues in contact with LEU 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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457C VAL* 5.7 1.3 - - + -
469C LEU* 4.6 11.0 - - + -
482C ILE* 4.0 41.1 - - + -
493C PHE* 4.9 4.9 - - + +
495C MET* 4.2 26.7 - - + +
502C PHE* 3.5 43.9 - - + -
504C ASP 3.5 5.1 + - - +
505C LEU* 3.1 13.1 + - + +
507C GLN* 1.3 79.6 - - - +
509C VAL* 1.3 72.5 + - + +
511C PHE* 3.4 0.3 + - - +
512C HIS* 2.7 40.1 + - + +
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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
----------------------------------------------------------
431C TRP* 4.1 38.1 - - + +
455C PHE* 3.9 26.5 - - + -
457C VAL* 4.2 14.6 - - + -
469C LEU* 6.0 0.2 - - + -
505C LEU 3.0 17.4 + - - +
506C LEU* 3.6 8.7 - - + +
508C LEU* 1.3 81.8 - - + +
510C GLU* 1.3 66.1 + - + +
512C HIS 2.9 13.3 + - - -
513C GLN* 3.0 25.1 + - - +
523C LEU* 3.8 14.7 - - + +
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Residues in contact with GLU 510 (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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506C LEU* 2.9 50.3 + - + +
507C GLN* 4.0 8.8 - - + +
509C VAL* 1.3 72.6 - - + +
511C PHE* 1.3 63.9 + - - +
513C GLN* 3.2 34.8 + - - +
514C LEU* 3.9 8.8 + - - +
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Residues in contact with PHE 511 (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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500C THR* 4.6 13.0 - - + -
502C PHE* 3.5 33.0 - + + -
507C GLN* 2.9 20.0 + - + +
508C LEU 3.6 1.3 - - - +
510C GLU* 1.3 75.7 - - - +
512C HIS* 1.3 74.7 + + - +
513C GLN 3.3 1.7 + - - -
514C LEU* 3.3 3.2 + - - +
515C ASN* 3.1 66.8 + - + +
517C GLY* 5.1 7.4 - - - -
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Residues in contact with HIS 512 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495C MET* 3.4 27.4 - - + +
500C THR* 5.4 2.5 - - + +
502C PHE* 3.6 28.5 - + - -
508C LEU* 2.7 29.9 + - + +
509C VAL 2.9 7.9 + - - +
511C PHE* 1.3 84.8 - + - +
513C GLN* 1.3 58.9 + - - +
514C LEU 3.3 0.2 - - - -
515C ASN 3.3 16.3 - - - +
516C ARG 3.4 17.3 - - - -
517C GLY* 4.1 10.9 - - - -
518C ILE 4.7 0.8 + - - -
519C LEU* 3.4 33.9 - - + +
522C LEU* 3.7 3.5 - - - -
523C LEU* 3.0 31.5 + - + -
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Residues in contact with GLN 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C TRP* 6.0 0.8 - - - -
455C PHE* 5.1 8.3 - - - -
509C VAL* 3.0 28.7 + - - +
510C GLU* 3.2 30.4 + - - +
512C HIS* 1.3 77.8 - - - +
514C LEU* 1.3 71.4 + - + +
522C LEU* 3.2 22.5 - - - +
523C LEU* 3.2 24.9 - - + +
524C ARG* 5.0 3.9 + - - +
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Residues in contact with LEU 514 (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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510C GLU 3.9 6.5 + - - +
511C PHE* 3.3 3.8 + - - +
513C GLN* 1.3 93.8 - - + +
515C ASN* 1.3 73.7 + - - +
522C LEU* 3.2 20.1 - - - +
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Residues in contact with ASN 515 (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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511C PHE* 3.1 59.3 + - + +
512C HIS* 3.3 22.5 - - - +
514C LEU* 1.3 92.6 - - - +
516C ARG* 1.3 63.2 + - - +
517C GLY 3.4 3.1 + - - +
519C LEU* 5.3 0.2 - - - +
522C LEU* 3.3 8.0 - - - +
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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