Contacts of the helix formed by residues 453 - 466 (chain C) in PDB entry 2O1S
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 453 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321C TYR* 3.6 17.1 - - - -
451C PRO* 3.5 1.9 - - - +
452C SER* 1.3 82.2 + - - +
454C GLU* 1.3 68.2 + - - +
455C ASN* 3.0 8.2 + - - +
456C GLU* 2.8 41.4 + - - +
457C CYS* 3.0 26.3 + - - +
482C VAL* 3.8 17.5 - - + -
484C VAL* 3.6 22.8 - - + +
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Residues in contact with GLU 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C PRO* 5.5 3.9 - - + +
321C TYR* 3.7 9.6 - - + -
324C ILE* 3.7 25.7 - - + +
453C ASP* 1.3 72.4 - - - +
455C ASN* 1.3 64.4 + - - +
457C CYS* 3.4 4.4 - - - +
458C ARG* 3.0 31.2 + - - +
481C ALA* 2.9 31.6 - - + +
482C VAL 3.1 9.0 + - - -
483C GLY* 2.7 28.0 + - - -
484C VAL* 3.0 19.9 + - + +
486C LEU* 3.9 16.8 - - + -
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Residues in contact with ASN 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453C ASP* 3.0 9.7 + - - +
454C GLU* 1.3 77.8 - - - +
456C GLU* 1.3 72.0 + - + +
457C CYS 3.2 0.2 + - - -
458C ARG* 3.2 7.0 + - - +
459C GLN* 2.9 37.6 + - - +
484C VAL* 3.8 7.9 - - + -
485C GLU 3.4 21.5 - - - +
486C LEU* 3.3 14.1 - - + +
487C THR* 3.0 46.6 + - - +
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Residues in contact with GLU 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451C PRO* 4.0 3.6 - - + -
452C SER* 3.6 36.0 + - - +
453C ASP* 2.8 21.9 + - - +
455C ASN* 1.3 80.5 - - - +
457C CYS* 1.3 53.4 + - - +
459C GLN* 3.1 9.9 + - - +
460C MSE 2.8 47.0 + - - +
492C LEU* 4.6 3.7 - - - +
498C ILE* 4.8 3.0 - - - +
531C ASP* 4.2 5.4 - - - +
533C ARG* 2.7 51.7 + - - +
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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
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321C TYR* 4.1 18.2 - - + -
324C ILE* 4.3 10.8 - - + -
325C PHE 5.4 0.2 - - - -
451C PRO* 3.5 16.8 - - + +
453C ASP 3.0 14.3 + - - +
454C GLU* 3.4 15.3 - - - +
456C GLU* 1.3 75.5 - - - +
458C ARG* 1.3 58.8 + - - +
460C MSE 2.9 5.3 + - - +
461C LEU* 2.8 47.0 + - - +
474C VAL* 4.4 1.9 - - - +
476C TYR* 4.0 27.6 - - - -
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Residues in contact with ARG 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C ILE* 3.5 24.7 + - + +
327C ASP* 5.9 2.2 - - - +
328C TRP* 4.2 20.2 + - + +
331C GLU* 2.6 44.5 + - - -
454C GLU 3.0 12.3 + - - +
455C ASN* 3.7 6.2 - - - +
457C CYS* 1.3 76.2 - - - +
459C GLN* 1.3 57.3 + - - +
461C LEU* 3.3 10.6 + - - +
462C TYR* 3.0 30.3 + - - +
486C LEU* 3.5 42.7 - - - +
487C THR 4.5 8.7 + - - -
489C LEU* 3.2 38.0 - - + +
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Residues in contact with GLN 459 (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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455C ASN* 2.9 34.1 + - - +
456C GLU* 3.1 13.7 + - - +
458C ARG* 1.3 76.5 - - - +
460C MSE 1.3 54.7 + - - +
462C TYR* 3.7 3.9 - - - +
463C THR* 2.6 36.8 + - - -
487C THR* 3.1 30.5 + - - +
488C PRO 3.2 11.2 + - - +
489C LEU* 3.6 8.4 - - - +
490C GLU* 2.9 42.4 + - - +
492C LEU* 4.0 19.9 - - + +
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Residues in contact with MSE 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449C MSE 3.5 30.4 - - + +
450C THR 4.1 2.2 - - - +
451C PRO* 3.4 40.4 - - - -
456C GLU* 2.8 19.6 + - - +
457C CYS 3.6 3.8 - - - +
459C GLN* 1.3 76.5 - - - +
461C LEU* 1.3 59.6 + - - +
462C TYR 3.2 1.3 - - - -
463C THR* 4.1 1.3 - - - -
464C GLY 2.8 24.4 + - - -
474C VAL* 3.5 20.4 - - + +
492C LEU* 3.7 17.0 - - + -
533C ARG* 3.0 58.8 - - + +
534C PHE* 4.7 1.8 - - + -
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Residues in contact with LEU 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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324C ILE* 5.1 1.1 - - + +
325C PHE* 3.7 50.9 - - + -
328C TRP* 3.5 32.8 - - + -
415C LEU* 3.8 15.5 - - + +
417C ALA* 4.6 7.0 - - + -
457C CYS* 2.8 33.1 + - - +
458C ARG* 3.7 5.2 - - - +
460C MSE 1.3 76.7 - - - +
462C TYR* 1.3 58.0 + - - +
464C GLY* 3.7 0.3 - - - -
465C TYR* 2.8 31.4 + - - +
474C VAL* 4.0 25.8 - - + -
476C TYR* 4.9 2.5 - - + -
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Residues in contact with TYR 462 (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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328C TRP* 3.9 16.8 - + - +
332C THR* 5.9 2.0 - - + -
335C LYS* 5.5 6.7 - - - -
458C ARG 3.0 16.7 + - - +
459C GLN 3.7 4.0 - - - +
461C LEU* 1.3 77.7 - - - +
463C THR* 1.3 63.9 + - - +
465C TYR* 3.2 2.0 + + - +
466C HIS* 3.0 61.9 + + - -
489C LEU* 3.7 37.5 + - + -
490C GLU* 3.8 15.9 - - - -
491C LYS* 3.5 38.6 - - + +
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Residues in contact with THR 463 (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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449C MSE 4.3 11.2 - - + -
459C GLN 2.6 24.4 + - - -
460C MSE 3.7 7.6 - - - -
461C LEU 3.3 0.2 - - - -
462C TYR* 1.3 80.7 - - - +
464C GLY* 1.3 61.8 + - - +
466C HIS* 3.3 4.0 + - - +
467C TYR* 3.1 21.0 + - - +
491C LYS* 3.6 13.6 - - + +
492C LEU* 3.0 46.9 + - + +
494C ILE* 3.8 21.1 - - + -
534C PHE* 4.8 0.2 - - + -
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Residues in contact with GLY 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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415C LEU* 4.0 6.5 - - - -
449C MSE 3.8 11.6 - - - +
460C MSE 2.8 19.9 + - - -
461C LEU 3.8 0.4 - - - -
463C THR* 1.3 73.4 - - - +
465C TYR* 1.3 62.6 + - - +
467C TYR* 3.2 12.0 + - - +
472C SER* 3.3 28.2 + - - -
2003C K 3.0 14.7 - - - -
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Residues in contact with TYR 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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328C TRP* 3.7 24.7 - + + -
332C THR* 3.9 18.8 - - + -
336C ASP* 3.0 31.2 + - + -
339C LEU* 3.3 37.0 + - + +
386C LYS* 2.5 72.7 + - + +
388C ILE* 4.0 10.5 - - + -
415C LEU* 4.0 7.5 - - + +
461C LEU 2.8 18.4 + - - +
462C TYR* 3.2 5.6 + + - +
464C GLY* 1.3 77.4 - - - +
466C HIS* 1.3 76.3 + + - +
2003C K 3.1 10.0 - - - -
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Residues in contact with HIS 466 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C THR* 5.8 1.4 - - - +
336C ASP* 4.9 5.2 - - - -
386C LYS* 4.0 7.1 + - - +
462C TYR* 3.0 64.7 + + - +
463C THR 3.6 3.1 - - - +
464C GLY 3.2 0.2 - - - -
465C TYR* 1.3 103.9 + + - +
467C TYR* 1.3 58.8 + - - +
468C ASN* 3.2 14.6 + - - +
491C LYS* 3.7 36.7 + - + -
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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
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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