Contacts of the helix formed by residues 452 - 471 (chain C) in PDB entry 1FSX
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 452 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C ASP* 2.6 47.6 + - - +
449C SER* 3.0 16.4 + - - -
450C HIS 3.5 0.2 - - - -
451C GLY* 1.3 79.3 - - - +
453C ALA* 1.3 61.6 + - - +
454C GLN* 3.1 16.6 + - - +
455C VAL* 3.3 16.7 + - - +
456C LYS* 3.2 22.2 + - - +
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Residues in contact with ALA 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C ASP* 5.1 0.6 + - - -
451C GLY 3.4 4.0 + - - +
452C SER* 1.3 73.6 + - - +
454C GLN* 1.3 60.8 + - + +
456C LYS* 3.8 8.4 - - - +
457C GLY* 3.0 24.1 + - - -
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Residues in contact with GLN 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C HIS* 3.8 10.1 + - - +
446C PHE* 3.4 43.2 - - + -
447C ASP* 2.8 33.0 + - + +
452C SER* 3.1 9.1 + - - +
453C ALA* 1.3 76.9 - - + +
455C VAL* 1.3 61.2 + - - +
457C GLY* 3.4 1.3 + - - -
458C HIS* 2.9 31.0 + - - +
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Residues in contact with VAL 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C ALA* 4.1 19.0 - - + +
429C LEU* 4.1 8.9 - - + +
430C GLU* 4.7 8.5 - - + +
433C PHE* 4.2 21.8 - - + -
446C PHE* 4.5 7.0 - - + -
447C ASP 3.6 9.6 - - - +
448C LEU* 3.7 25.6 - - + +
449C SER 4.9 1.3 - - - +
452C SER* 3.3 27.5 + - - +
454C GLN* 1.3 76.7 - - - +
456C LYS* 1.3 62.2 + - - +
458C HIS* 3.3 3.0 + - - +
459C GLY* 2.9 22.3 + - - -
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Residues in contact with LYS 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C ALA 4.9 1.1 - - - +
423C GLU* 5.0 20.0 + - - +
426C ALA* 3.9 23.9 - - + +
451C GLY* 4.8 11.4 - - - +
452C SER 3.2 21.4 + - - +
453C ALA* 3.8 8.3 - - - +
455C VAL* 1.3 75.3 - - + +
457C GLY* 1.3 64.7 + - - +
459C GLY* 3.2 2.8 + - - -
460C ALA* 3.1 20.3 + - - +
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Residues in contact with GLY 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453C ALA 3.0 15.0 + - - -
454C GLN* 3.7 1.3 - - - -
456C LYS* 1.3 80.3 - - - +
458C HIS* 1.3 60.8 + - - +
460C ALA* 3.2 18.1 + - - +
461C LYS* 3.3 22.0 + - - +
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Residues in contact with HIS 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C LEU* 3.9 11.9 - - + -
443C PHE* 3.9 12.0 - + - -
446C PHE* 3.9 20.5 - + + -
454C GLN 2.9 17.4 + - - +
455C VAL 3.9 2.5 - - - +
457C GLY* 1.3 72.8 - - - +
459C GLY* 1.3 59.9 + - - +
461C LYS* 3.2 18.1 + - + +
462C VAL* 2.9 35.2 + - + +
542C CMO 2.8 34.6 + - - -
543C HEM 3.4 58.3 + + + +
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Residues in contact with GLY 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C ALA 4.1 2.0 - - - +
425C GLY* 3.7 7.3 - - - -
426C ALA 3.6 20.0 - - - -
429C LEU* 3.6 18.7 - - - +
455C VAL 2.9 12.3 + - - -
456C LYS 3.2 4.0 + - - -
458C HIS* 1.3 76.9 - - - +
460C ALA* 1.3 57.6 + - - +
462C VAL* 3.4 3.1 + - - +
463C ALA* 3.0 28.4 + - - +
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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
----------------------------------------------------------
422C ALA* 3.8 28.0 + - + +
456C LYS 3.1 11.0 + - - +
457C GLY* 3.3 13.0 - - - +
458C HIS 3.1 0.6 - - - -
459C GLY* 1.3 76.2 - - - +
461C LYS* 1.3 58.2 + - + +
463C ALA* 3.4 3.8 + - - +
464C ALA* 2.9 28.7 + - - +
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Residues in contact with LYS 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C GLY* 3.5 19.5 - - - +
458C HIS* 3.2 17.3 + - - +
460C ALA* 1.3 75.0 - - + +
462C VAL* 1.3 63.0 - - - +
464C ALA* 3.4 8.4 + - - +
465C ALA 3.2 13.7 + - - -
543C HEM 3.1 58.9 + - + +
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Residues in contact with VAL 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C GLY* 5.1 8.5 - - - +
429C LEU* 4.3 8.7 - - + -
458C HIS* 2.9 30.1 + - + +
459C GLY* 3.8 6.7 - - - +
461C LYS* 1.3 74.6 - - - +
463C ALA* 1.3 63.6 + - - +
465C ALA* 3.3 5.2 + - - +
466C LEU* 3.2 32.3 + - + +
501C LEU* 4.9 11.4 - - + -
505C LEU* 5.3 4.0 - - + -
542C CMO 3.3 30.5 - - - +
543C HEM 4.1 31.9 - - + +
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Residues in contact with ALA 463 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C TRP* 3.9 4.0 - - + -
421C ALA* 3.0 42.6 - - + +
422C ALA* 4.0 2.2 - - - +
425C GLY* 4.5 4.2 - - - -
459C GLY 3.0 16.3 + - - +
460C ALA 3.6 4.3 - - - +
462C VAL* 1.3 76.4 - - - +
464C ALA* 1.3 58.3 + - - +
466C LEU* 3.2 12.7 + - - +
467C THR* 2.9 33.8 + - - -
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Residues in contact with ALA 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460C ALA 2.9 17.7 + - - +
461C LYS* 3.5 11.4 - - - +
462C VAL 3.2 0.2 - - - -
463C ALA* 1.3 76.1 - - - +
465C ALA* 1.3 56.3 + - - +
467C THR* 3.4 8.1 + - - -
468C LYS* 3.0 27.5 + - - +
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Residues in contact with ALA 465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C LYS 3.2 10.6 + - - +
462C VAL 3.3 8.0 + - - +
464C ALA* 1.3 76.2 - - - +
466C LEU* 1.3 61.6 + - - +
467C THR 3.3 0.2 - - - -
468C LYS* 3.8 8.4 - - + +
469C ALA* 3.0 26.9 + - - +
480C LEU* 3.9 8.8 - - + +
483C LEU* 3.5 31.4 - - + -
543C HEM 3.8 17.0 - - + -
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Residues in contact with LEU 466 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C TRP* 3.8 28.7 - - + -
425C GLY* 6.2 1.8 - - - -
462C VAL* 3.2 25.8 + - + +
463C ALA* 3.2 10.3 + - - +
465C ALA* 1.3 73.3 - - - +
467C THR* 1.3 67.1 + - - +
469C ALA* 3.3 6.3 + - + +
470C VAL* 3.0 28.9 + - - +
505C LEU* 3.8 28.3 - - + -
528C PHE* 4.1 13.5 - - + -
529C LEU* 4.1 22.9 - - + -
532C VAL* 4.7 9.4 - - + -
543C HEM 4.2 22.9 - - + -
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Residues in contact with THR 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C TRP* 2.8 33.8 + - + +
421C ALA* 4.5 6.6 - - - +
463C ALA 2.9 20.3 + - - -
464C ALA* 3.5 8.4 - - - -
466C LEU* 1.3 77.7 - - - +
468C LYS* 1.3 61.8 + - - +
470C VAL* 3.1 5.5 + - - +
471C GLU* 3.0 43.1 + - + +
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Residues in contact with LYS 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464C ALA 3.0 17.6 + - - +
465C ALA* 3.9 8.3 - - - +
467C THR* 1.3 75.4 - - - +
469C ALA* 1.3 62.1 + - - +
471C GLU* 3.5 11.4 + - - +
472C HIS* 2.9 46.1 + - + +
479C ALA* 3.1 37.1 + - + +
480C LEU* 5.5 5.0 - - + +
482C GLU* 5.9 1.6 + - - -
483C LEU* 6.3 1.6 - - - +
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Residues in contact with ALA 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465C ALA 3.0 18.4 + - - +
466C LEU* 3.5 9.0 - - + +
467C THR 3.3 0.2 - - - -
468C LYS* 1.3 76.9 - - - +
470C VAL* 1.3 57.3 + - - +
472C HIS* 3.3 2.1 - - - +
473C LEU* 3.2 18.8 + - - +
476C LEU* 3.1 38.2 - - + +
479C ALA* 5.0 2.0 - - - -
480C LEU* 4.2 20.3 - - + +
528C PHE* 4.4 10.5 - - + -
532C VAL* 4.5 5.6 - - + -
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Residues in contact with VAL 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C VAL* 3.7 14.6 - - + -
411C LYS* 3.9 31.0 - - + +
414C TRP* 4.2 31.6 - - + -
466C LEU 3.0 18.2 + - - +
467C THR* 3.1 10.7 + - - +
469C ALA* 1.3 73.6 - - - +
471C GLU* 1.3 62.6 + - + +
472C HIS 3.0 8.4 + - - -
473C LEU* 3.5 23.6 + - + +
528C PHE* 3.5 22.2 - - + -
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Residues in contact with GLU 471 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C THR* 3.0 34.1 + - + +
468C LYS* 4.0 12.0 - - - +
469C ALA 3.5 0.2 - - - -
470C VAL* 1.3 80.2 - - + +
472C HIS* 1.3 74.9 + - + +
473C LEU 3.7 0.2 - - - -
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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
------------------------------------------------------------
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