Contacts of the helix formed by residues 453 - 467 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A TYR* 3.4 15.7 + - - -
451A PRO* 3.4 3.2 - - - +
452A SER* 1.3 86.1 + - - +
454A GLU* 1.3 66.8 + - - +
455A ASN* 2.9 21.3 + - - +
456A GLU* 3.1 18.6 + - - +
457A CYS* 3.0 25.3 + - - +
482A VAL* 4.4 7.6 - - + -
484A VAL* 3.7 29.4 - - + +
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Residues in contact with GLU 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A PRO* 5.4 3.5 - - + +
321A TYR* 3.6 11.7 - - + -
324A ILE* 3.8 24.5 - - + +
453A ASP* 1.3 75.0 - - - +
455A ASN* 1.3 66.2 + - - +
457A CYS* 3.4 5.8 - - - +
458A ARG* 3.2 26.7 + - - +
481A ALA* 3.0 33.7 - - + +
482A VAL 3.1 9.9 + - - -
483A GLY* 2.9 10.2 + - - -
484A VAL* 2.6 37.9 + - - +
486A LEU* 3.7 17.0 - - + -
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Residues in contact with ASN 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A ASP* 2.9 10.9 + - - +
454A GLU* 1.3 77.8 - - - +
456A GLU* 1.3 73.2 + - + +
458A ARG* 3.1 8.9 + - - +
459A GLN* 3.0 35.2 + - - +
484A VAL* 4.5 6.5 - - + +
485A GLU 3.5 20.5 + - - +
486A LEU* 3.1 15.2 - - + +
487A THR* 2.7 51.1 + - - +
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Residues in contact with GLU 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A PRO* 3.8 14.1 - - + -
452A SER* 3.7 20.8 + - - +
453A ASP* 3.1 23.1 + - - +
455A ASN* 1.3 86.4 + - + +
457A CYS* 1.3 58.3 + - - +
459A GLN* 3.3 8.4 + - - +
460A MSE 2.8 42.4 + - - +
492A LEU* 4.5 2.9 - - - +
531A ASP* 4.2 5.6 - - - +
533A ARG* 2.7 57.3 + - - +
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Residues in contact with CYS 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A TYR* 4.0 18.2 - - + -
324A ILE* 4.3 10.1 - - + -
325A PHE 5.6 0.2 - - - -
451A PRO* 3.4 17.2 - - + +
453A ASP 3.0 13.6 + - - +
454A GLU* 3.4 15.5 - - - +
456A GLU* 1.3 77.6 - - - +
458A ARG* 1.3 63.0 + - - +
460A MSE 3.7 2.9 - - - +
461A LEU* 2.9 42.6 + - - +
474A VAL* 4.4 1.9 - - - +
476A TYR* 3.9 29.4 - - - -
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Residues in contact with ARG 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ILE* 3.7 22.1 + - + -
327A ASP* 5.0 3.6 - - - +
328A TRP* 4.0 23.9 + - + +
331A GLU* 3.1 41.0 + - - -
454A GLU 3.2 6.7 + - - +
455A ASN* 3.1 9.4 + - - +
457A CYS* 1.3 77.4 - - - +
459A GLN* 1.3 58.6 + - + +
461A LEU* 3.2 10.3 + - - +
462A TYR* 2.9 30.0 + - - +
486A LEU* 3.9 42.0 - - - +
487A THR 5.1 5.1 + - - -
489A LEU* 3.6 30.5 - - + +
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Residues in contact with GLN 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A ASN* 3.0 29.2 + - - +
456A GLU* 3.6 11.7 - - - +
458A ARG* 1.3 76.0 - - - +
460A MSE 1.3 51.9 + - - +
462A TYR* 3.3 7.5 - - - +
463A THR* 2.7 37.9 + - - -
487A THR* 3.1 31.4 + - - +
488A PRO 3.2 11.6 + - - +
489A LEU* 3.5 5.8 - - - +
490A GLU* 2.7 44.4 + - - +
492A LEU* 4.0 23.1 - - + +
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Residues in contact with MSE 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A MSE 3.4 35.5 - - + +
450A THR 3.8 4.3 - - - +
451A PRO* 3.4 36.8 - - - -
456A GLU* 2.8 31.8 + - - +
457A CYS 3.7 2.9 - - - +
459A GLN* 1.3 72.8 - - - +
461A LEU* 1.3 57.3 + - - +
462A TYR 3.1 0.2 - - - -
463A THR* 4.1 2.5 - - - -
464A GLY 2.7 29.8 + - - -
474A VAL* 3.8 13.0 - - + -
492A LEU* 3.7 17.3 - - + -
533A ARG* 3.2 55.6 - - + +
534A PHE* 4.7 1.6 - - + -
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Residues in contact with LEU 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ILE* 5.0 1.1 - - + -
325A PHE* 4.0 41.5 - - + +
328A TRP* 3.6 42.1 - - + -
415A LEU* 3.7 9.8 - - + +
417A ALA* 4.4 9.4 - - + -
457A CYS* 2.9 33.0 + - - +
458A ARG* 3.5 8.1 - - - +
460A MSE 1.3 75.1 - - - +
462A TYR* 1.3 54.1 + - - +
464A GLY* 3.2 1.0 + - - -
465A TYR* 2.7 36.9 + - - +
474A VAL* 4.0 26.0 - - + +
476A TYR* 4.8 2.9 - - + -
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Residues in contact with TYR 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A TRP* 3.9 12.3 - + - +
332A THR* 5.7 1.6 - - - -
335A LYS* 5.3 4.9 - - + -
458A ARG 2.9 14.8 + - - +
459A GLN* 3.3 10.8 - - - +
461A LEU* 1.3 77.0 - - - +
463A THR* 1.3 63.5 + - - +
465A TYR* 3.2 2.9 + + - +
466A HIS* 3.1 58.1 + + - -
489A LEU* 3.4 38.5 + - + -
490A GLU* 3.8 18.2 - - - -
491A LYS* 3.6 41.5 - - + +
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Residues in contact with THR 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A MSE 4.3 9.6 - - - -
459A GLN 2.7 26.5 + - - -
460A MSE 3.6 8.3 - - - -
462A TYR* 1.3 76.1 - - - +
464A GLY* 1.3 63.9 + - - +
466A HIS* 3.2 3.6 + - - +
467A TYR* 3.0 22.8 + - + +
491A LYS* 3.5 13.4 - - + +
492A LEU* 2.9 49.0 + - + +
494A ILE* 3.8 21.1 - - + -
534A PHE* 4.8 0.2 - - + -
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Residues in contact with GLY 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415A LEU* 4.0 8.2 - - - +
449A MSE 3.7 11.2 - - - +
460A MSE 2.7 21.6 + - - -
461A LEU 3.6 1.1 - - - -
463A THR* 1.3 73.8 - - - +
465A TYR* 1.3 57.5 + - - +
467A TYR* 3.3 10.6 + - - +
472A SER* 3.3 28.4 + - - -
2001A K 3.0 17.8 - - - -
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Residues in contact with TYR 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A TRP* 3.7 13.9 - + + -
332A THR* 3.8 16.8 - - + -
336A ASP* 2.9 34.3 + - - -
339A LEU* 3.4 34.7 + - + +
386A LYS* 2.8 70.9 + - + +
387A PRO 5.8 0.2 - - - -
388A ILE* 4.0 19.7 - - + -
415A LEU* 3.8 6.8 - - + +
461A LEU 2.7 21.2 + - - +
462A TYR* 3.5 4.9 - + - +
464A GLY* 1.3 72.3 - - - +
466A HIS* 1.3 85.2 + + - +
2001A K 3.3 7.7 - - - -
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Residues in contact with HIS 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A THR* 6.1 0.4 - - - +
336A ASP* 6.3 0.4 - - - -
386A LYS* 4.4 7.1 + - - +
462A TYR* 3.1 63.4 + + - +
463A THR 3.2 2.2 + - - +
465A TYR* 1.3 103.9 + + - +
467A TYR* 1.3 59.0 + - - +
468A ASN* 3.3 20.6 + - - +
491A LYS* 3.7 34.6 + - + +
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Residues in contact with TYR 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A PRO* 3.6 4.9 - - - +
445A GLU 4.9 3.8 + - - -
447A VAL* 3.6 30.7 - - + +
463A THR* 3.0 16.5 + - + +
464A GLY* 3.3 11.0 + - - +
465A TYR 3.4 0.2 - - - -
466A HIS* 1.3 76.0 - - - +
468A ASN* 1.3 59.1 + - - +
469A ASP* 3.5 32.6 + - + +
470A GLY* 3.5 33.6 - - - +
472A SER* 4.3 9.2 - - - +
494A ILE* 4.0 36.3 - - + +
2001A K 3.0 17.2 - - - -
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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
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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