Contacts of the helix formed by residues 453 - 466 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321B TYR* 3.5 15.9 + - - -
451B PRO* 3.4 3.2 - - - +
452B SER* 1.3 89.4 + - - +
454B GLU* 1.3 70.2 + - - +
455B ASN* 2.7 13.5 + - - +
456B GLU* 2.7 30.3 + - - +
457B CYS* 3.0 19.2 + - - +
482B VAL* 4.1 6.7 - - + -
484B VAL* 4.0 26.8 - - + +
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Residues in contact with GLU 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B PRO* 5.1 6.2 - - + +
321B TYR* 3.5 11.8 - - + -
324B ILE* 3.4 29.2 - - + +
453B ASP* 1.3 72.8 - - - +
455B ASN* 1.3 63.2 + - + +
457B CYS* 3.3 3.3 - - - +
458B ARG* 3.2 22.3 + - - +
481B ALA* 3.0 24.2 - - + +
482B VAL* 2.9 24.8 + - - +
483B GLY* 2.6 27.7 + - - -
484B VAL* 2.7 20.0 + - - +
486B LEU* 3.7 19.3 - - + -
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Residues in contact with ASN 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B ASP* 2.7 17.8 + - - +
454B GLU* 1.3 75.4 - - - +
456B GLU* 1.3 72.3 + - - +
458B ARG* 3.3 8.6 + - - +
459B GLN* 3.1 35.0 + - - +
484B VAL* 4.8 5.7 - - + +
485B GLU 3.4 21.7 + - - +
486B LEU* 3.4 11.5 - - + -
487B THR* 2.8 46.7 + - - +
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Residues in contact with GLU 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B PRO* 4.0 5.4 - - + -
452B SER* 3.5 30.9 + - - +
453B ASP* 2.7 30.2 + - - +
455B ASN* 1.3 81.9 + - - +
457B CYS* 1.3 57.5 + - - +
459B GLN* 3.1 10.8 + - - +
460B MSE 2.8 42.3 + - - +
492B LEU* 5.2 2.1 - - - +
498B ILE* 5.4 0.2 - - - +
531B ASP* 3.7 11.5 - - - +
533B ARG* 3.0 46.4 + - - +
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Residues in contact with CYS 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B TYR* 4.2 5.8 - - + -
324B ILE* 3.3 31.4 - - + -
325B PHE* 6.0 0.2 - - - -
451B PRO* 3.6 20.8 - - + +
453B ASP 3.0 12.8 + - - +
454B GLU* 3.3 4.0 - - - +
455B ASN 3.1 0.2 - - - -
456B GLU* 1.3 76.7 - - - +
458B ARG* 1.3 56.8 + - - +
460B MSE 3.3 2.3 + - - +
461B LEU* 2.9 44.3 + - - +
474B VAL* 4.3 2.0 - - - +
476B TYR* 3.8 33.4 - - - -
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Residues in contact with ARG 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B ILE* 4.2 27.1 - - + +
328B TRP* 4.3 12.3 + - + +
331B GLU* 4.2 20.6 + - - -
454B GLU 3.2 15.3 + - - +
455B ASN* 3.3 15.3 + - - +
457B CYS* 1.3 72.7 - - - +
459B GLN* 1.3 68.8 + - - +
461B LEU* 3.3 9.4 + - + +
462B TYR* 2.9 24.9 + - - +
486B LEU* 4.0 35.4 - - - +
487B THR 3.1 26.0 + - - -
488B PRO* 5.1 1.4 - - - +
489B LEU* 3.5 33.1 - - + +
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Residues in contact with GLN 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B ASN* 3.1 27.7 + - - +
456B GLU* 3.5 13.7 - - - +
458B ARG* 1.3 79.4 - - - +
460B MSE 1.3 53.1 + - - +
462B TYR* 3.4 5.0 + - - +
463B THR* 2.7 38.4 + - - -
487B THR* 3.0 41.6 + - - -
488B PRO 3.5 6.4 + - - -
489B LEU* 3.5 3.9 - - - +
490B GLU* 2.8 37.7 + - - +
492B LEU* 4.1 25.1 - - + +
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Residues in contact with MSE 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B MSE 3.5 35.0 - - + +
450B THR 3.8 5.6 - - - +
451B PRO* 3.3 39.0 - - + -
452B SER 5.5 0.2 - - - +
456B GLU* 2.8 26.3 + - - +
457B CYS 3.8 3.6 - - - +
459B GLN* 1.3 74.8 - - - +
461B LEU* 1.3 56.8 + - - +
463B THR* 4.1 2.5 - - - -
464B GLY* 2.7 30.0 + - - -
474B VAL* 3.5 13.8 - - + +
492B LEU* 3.9 17.3 - - + -
533B ARG* 3.5 52.3 - - + +
534B PHE* 5.1 0.9 - - + -
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Residues in contact with LEU 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B ILE* 5.1 1.1 - - + -
325B PHE* 4.1 28.3 - - + +
328B TRP* 3.6 43.5 - - + -
415B LEU* 3.7 11.8 - - + +
417B ALA* 4.8 5.6 - - + -
457B CYS* 2.9 34.4 + - - +
458B ARG* 3.7 8.7 - - - +
460B MSE 1.3 76.4 - - - +
462B TYR* 1.3 54.0 + - - +
464B GLY 3.7 0.3 - - - -
465B TYR* 2.7 37.6 + - - +
474B VAL* 3.5 36.3 - - + -
476B TYR* 4.7 6.7 - - + -
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Residues in contact with TYR 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B TRP* 3.9 15.0 - + - +
332B THR* 5.8 2.0 - - + -
335B LYS* 4.6 10.8 - - + -
458B ARG 2.9 18.4 + - - +
459B GLN* 3.4 4.9 - - - +
461B LEU* 1.3 77.5 - - - +
463B THR* 1.3 62.4 + - - +
465B TYR* 3.3 1.8 + - - +
466B HIS* 3.1 57.7 + + - +
489B LEU* 3.7 42.2 + - + -
490B GLU* 3.6 24.5 - - - -
491B LYS* 3.5 32.7 - - + +
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Residues in contact with THR 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449B MSE 4.2 14.8 - - + -
459B GLN 2.7 26.2 + - - -
460B MSE 3.7 7.0 - - - -
462B TYR* 1.3 75.1 - - - +
464B GLY* 1.3 66.4 + - - +
466B HIS* 3.1 4.0 + - - +
467B TYR* 3.1 22.7 + - + +
491B LYS* 3.5 12.3 - - + +
492B LEU* 2.8 50.1 + - + +
494B ILE* 4.2 17.5 - - + -
534B PHE* 4.9 1.3 - - + -
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Residues in contact with GLY 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415B LEU* 4.0 7.4 - - - +
449B MSE 3.5 11.4 - - - -
460B MSE 2.7 21.2 + - - -
461B LEU 3.8 0.4 - - - -
463B THR* 1.3 74.1 - - - +
465B TYR* 1.3 57.6 + - - +
467B TYR* 3.4 9.7 + - - +
472B SER* 3.1 29.8 + - - -
2002B K 2.9 17.8 - - - -
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Residues in contact with TYR 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B TRP* 3.8 14.4 - + + -
332B THR* 3.7 18.6 - - + -
336B ASP* 2.7 28.3 + - - -
339B LEU* 3.4 32.4 + - + +
386B LYS* 3.2 61.9 + - + +
387B PRO 5.8 0.4 - - - -
388B ILE* 4.0 20.2 - - + -
415B LEU* 3.9 8.2 - - + +
461B LEU 2.7 22.6 + - - +
462B TYR 3.5 4.0 - - - +
463B THR 3.1 0.2 - - - -
464B GLY* 1.3 74.7 - - - +
466B HIS* 1.3 83.8 + + - +
2002B K 3.0 14.3 - - - -
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Residues in contact with HIS 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B THR* 5.7 2.0 - - + -
335B LYS* 6.6 0.2 - - + -
336B ASP* 5.4 1.2 + - - -
386B LYS* 4.4 7.0 - - - +
462B TYR* 3.1 61.3 + + - +
463B THR 3.1 4.0 + - - +
465B TYR* 1.3 105.3 - + - +
467B TYR* 1.3 61.2 + - - +
468B ASN* 3.5 18.7 + - - +
491B LYS* 4.1 34.0 + - + +
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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