Contacts of the helix formed by residues 452 - 466 (chain C) in PDB entry 4AY6
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 PHE 452 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419C ALA* 4.1 11.7 - - + -
420C ASP* 3.6 38.4 - - + -
423C SER* 3.8 28.5 - - - -
445C ALA* 4.6 5.8 - - + -
446C LEU* 3.6 9.6 - - + +
449C LYS* 3.7 29.6 - - - +
450C PRO 3.7 4.0 + - - -
451C ASP* 1.3 76.7 + - - +
453C PRO* 1.3 74.3 - - + +
454C ASP* 3.8 26.5 - - + -
455C ALA* 3.8 11.9 - - + -
456C TYR* 3.0 23.4 + - - +
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Residues in contact with PRO 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451C ASP* 3.6 15.9 - - - +
452C PHE* 1.3 87.8 - - + +
454C ASP* 1.3 69.3 + - - +
456C TYR* 2.8 18.0 + - + +
457C CYS* 2.8 14.9 + - - -
482C ILE* 3.9 27.4 - - + -
486C GLN* 3.7 19.7 - - + +
494C SER* 3.2 14.4 - - - +
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Residues in contact with ASP 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C SER* 5.0 3.4 - - - +
452C PHE* 3.6 21.4 - - + -
453C PRO* 1.3 74.9 - - - +
455C ALA* 1.3 62.8 + - - +
457C CYS* 3.9 1.0 - - - +
458C ASN* 3.0 40.1 + - - +
486C GLN* 5.1 1.3 + - - -
492C LEU 5.3 1.7 - - - +
493C PRO 5.2 0.5 - - - -
494C SER* 2.5 36.4 + - - +
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Residues in contact with ALA 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C SER* 4.1 9.6 + - - +
442C TYR* 3.9 27.3 - - + +
445C ALA* 4.5 5.2 - - + -
446C LEU* 3.8 17.7 - - + -
452C PHE* 3.6 28.3 + - + -
453C PRO 3.2 0.4 - - - -
454C ASP* 1.3 80.4 - - - +
456C TYR* 1.3 62.1 + - - +
459C LEU* 3.0 26.0 + - - +
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Residues in contact with TYR 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C LEU* 3.9 25.9 - - + +
450C PRO 6.1 0.7 - - - -
452C PHE 3.0 18.6 + - - +
453C PRO 2.8 10.7 + - - +
455C ALA* 1.3 73.2 - - - +
457C CYS* 1.3 57.9 + - - +
459C LEU* 3.5 5.7 - - + +
460C ALA* 2.9 25.8 + - + +
474C GLU* 4.8 4.0 + - - -
475C ARG* 3.3 44.0 - - + +
478C LYS* 3.7 40.9 - - + +
479C LEU* 3.8 18.6 - - + -
482C ILE* 3.7 20.2 - - + -
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Residues in contact with CYS 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453C PRO 2.8 15.2 + - - +
454C ASP 3.9 0.7 - - - +
456C TYR* 1.3 69.9 - - - +
458C ASN* 1.3 66.8 + - - +
460C ALA* 3.1 4.9 + - - +
461C HIS* 3.1 21.5 + - - +
479C LEU* 3.6 28.2 - - + +
482C ILE* 4.6 15.7 - - - -
483C VAL* 5.6 0.9 - - - -
494C SER* 3.2 46.2 - - - +
495C VAL* 4.0 15.3 - - + +
503C TYR* 4.5 2.8 + - - -
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Residues in contact with ASN 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C SER* 5.1 1.8 + - - -
427C SER* 4.2 6.7 + - - -
430C LYS* 3.7 13.2 - - - +
442C TYR* 3.3 33.6 + - + +
454C ASP* 3.0 31.3 + - - +
457C CYS* 1.3 79.1 - - - +
459C LEU* 1.3 61.5 + - - +
461C HIS* 3.2 15.2 + - - +
462C CYS* 3.2 20.6 + - - -
494C SER 4.7 9.3 + - - +
499C HIS* 5.9 3.3 - - - -
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Residues in contact with LEU 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C ILE* 3.8 35.4 - - + +
442C TYR* 4.0 24.5 - - + -
443C ARG* 4.5 19.5 - - + +
446C LEU* 3.7 27.4 - - + -
455C ALA 3.0 19.3 + - - +
456C TYR* 3.5 7.6 - - + +
458C ASN* 1.3 71.6 - - - +
460C ALA* 1.3 68.2 + - - +
462C CYS* 2.8 15.7 + - - +
463C LEU* 2.9 35.2 + - + +
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Residues in contact with ALA 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456C TYR* 2.9 16.4 + - + +
457C CYS* 3.1 13.9 + - - +
459C LEU* 1.3 75.2 - - - +
461C HIS* 1.3 57.4 + - - +
463C LEU* 3.6 6.9 + - - +
464C GLN* 3.0 26.3 + - - +
475C ARG* 3.8 30.8 + - + +
479C LEU* 4.2 23.6 - - + -
503C TYR* 4.3 6.7 + - + +
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Residues in contact with HIS 461 (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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430C LYS* 2.7 29.1 + - - +
457C CYS 3.1 9.6 + - - +
458C ASN* 3.4 11.4 - - - +
459C LEU 3.0 0.8 - - - -
460C ALA* 1.3 74.8 - - - +
462C CYS* 1.3 62.2 + - - +
464C GLN* 3.0 15.1 - - + +
465C ILE* 2.9 41.7 - - + +
499C HIS* 3.2 50.4 - + + +
502C LEU* 4.3 15.2 - - + +
503C TYR* 3.7 16.3 + - - +
841C TYR* 5.3 5.9 - - - -
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Residues in contact with CYS 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C LYS* 3.7 26.7 - - - -
435C ILE* 3.8 12.8 - - + -
438C ALA* 4.7 3.8 - - - -
439C ILE* 3.7 26.7 - - + -
442C TYR* 4.3 10.3 - - - -
458C ASN 3.2 18.2 - - - -
459C LEU* 2.8 12.6 + - - +
461C HIS* 1.3 67.5 - - - +
463C LEU* 1.3 60.4 + - - +
464C GLN 2.9 1.8 - - - -
465C ILE* 2.6 34.5 + - - +
466C VAL* 3.0 15.8 + - - +
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Residues in contact with LEU 463 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C ILE* 4.0 16.6 - - + -
443C ARG* 4.1 17.7 - - - +
459C LEU* 2.9 44.9 + - + +
460C ALA* 3.7 6.5 - - - +
462C CYS* 1.3 76.2 - - - +
464C GLN* 1.3 61.7 - - - +
466C VAL* 3.4 4.4 + - - -
467C CYS* 3.0 3.3 + - - -
468C ASP* 2.9 70.4 + - + +
470C THR 5.9 0.2 - - - +
475C ARG* 3.8 23.6 - - + +
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Residues in contact with GLN 464 (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 ALA 3.0 14.5 + - - +
461C HIS* 3.0 19.3 - - + +
462C CYS 2.9 0.2 - - - -
463C LEU* 1.3 78.1 - - - +
465C ILE* 1.3 59.0 + - - +
467C CYS* 3.3 14.0 + - - +
468C ASP 5.0 0.2 - - - -
469C TRP* 4.7 6.2 + - - +
472C TYR* 3.9 25.0 + - - -
475C ARG* 4.1 7.1 + - - +
476C MET* 4.7 0.5 - - - +
502C LEU* 4.2 24.9 - - + +
503C TYR* 4.5 15.0 - - + +
841C TYR* 2.9 41.1 + - + +
843C ILE 3.6 14.6 + - - -
844C ASP* 4.8 1.0 - - - +
916C LEU* 4.2 13.7 - - - +
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Residues in contact with ILE 465 (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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430C LYS* 3.8 8.1 - - - +
435C ILE* 4.6 19.5 - - + -
461C HIS* 2.9 49.1 - - + +
462C CYS* 2.6 21.6 + - - +
464C GLN* 1.3 74.0 - - - +
466C VAL* 1.3 60.8 + - + +
467C CYS 3.2 0.8 + - - -
839C GLN* 5.8 2.7 - - - +
840C LEU* 4.3 4.2 - - - +
841C TYR* 3.8 29.7 + - + +
868C PHE 5.6 0.2 - - - +
869C PRO* 3.4 33.9 - - + +
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Residues in contact with VAL 466 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C ILE* 3.8 25.8 - - + -
436C PRO* 5.9 1.6 - - + -
439C ILE* 4.4 11.0 - - + -
462C CYS 3.0 11.6 + - - +
463C LEU* 3.4 13.9 - - - +
465C ILE* 1.3 79.3 - - + +
467C CYS* 1.3 65.7 + - - +
468C ASP* 3.6 14.6 - - + +
869C PRO* 4.8 2.0 - - + -
871C VAL* 3.5 30.1 - - + +
872C GLY* 3.6 15.7 - - - -
875C ASN* 2.7 28.7 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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