Contacts of the strand formed by residues 454 - 462 (chain O) in PDB entry 2O93
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 LEU 454 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445O LEU* 4.2 6.3 - - + -
448O TYR* 3.5 41.5 - - + +
452O LYS* 3.1 14.9 + - + +
453O PRO* 1.3 76.2 - - - +
455O GLY* 1.3 56.1 + - - +
502O PRO* 3.5 2.1 - - - +
503O LEU* 2.4 45.2 + - + +
509O MET* 3.8 15.0 - - + +
548O VAL* 4.0 11.2 - - + -
549O HIS 3.6 15.0 - - - +
550O ILE* 4.0 22.2 - - + -
551O PRO* 3.9 16.6 - - + -
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Residues in contact with GLY 455 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453O PRO 4.2 0.4 + - - -
454O LEU* 1.3 75.9 - - - +
456O LEU* 1.3 60.5 + - - -
457O GLN* 4.0 3.0 + - - +
500O GLU* 3.4 23.6 - - - -
501O ILE 3.5 4.5 - - - -
502O PRO* 4.6 1.6 - - - -
503O LEU* 4.7 0.2 - - - -
548O VAL* 2.9 26.7 - - - +
549O HIS 4.5 2.9 + - - +
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Residues in contact with LEU 456 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410O LEU* 5.0 2.9 - - + -
443O VAL* 3.6 33.0 - - + -
455O GLY* 1.3 73.4 - - - +
457O GLN* 1.3 77.0 + - - +
458O ILE* 3.5 8.7 + - + +
500O GLU* 4.0 4.1 - - - +
501O ILE* 2.9 47.1 + - + +
503O LEU* 3.9 27.4 - - + -
511O ALA* 4.5 4.3 - - + -
513O ILE* 4.7 1.6 - - + -
546O PHE* 3.9 26.0 - - + -
547O ARG 3.9 13.5 - - - +
548O VAL* 4.4 6.7 - - + -
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Residues in contact with GLN 457 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394O SER* 3.9 18.4 + - - -
395O VAL 5.5 0.4 - - - +
397O LEU* 5.7 5.5 - - + +
455O GLY 4.0 2.0 - - - +
456O LEU* 1.3 87.3 - - - +
458O ILE* 1.3 67.3 + - - +
459O PHE* 5.7 1.8 - - + -
491O LYS* 3.1 33.3 - - - +
498O VAL* 4.3 8.9 - - + +
499O LEU 3.3 8.3 - - - +
500O GLU* 4.1 6.9 - - + +
545O VAL 4.4 0.4 - - - -
546O PHE* 3.7 9.9 - - - -
547O ARG* 3.2 48.5 + - + +
549O HIS* 3.7 31.0 + - - +
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Residues in contact with ILE 458 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456O LEU* 3.5 9.9 - - + +
457O GLN* 1.3 86.7 - - - +
459O PHE* 1.3 67.5 + - - +
476O VAL* 3.7 14.1 - - + +
498O VAL* 3.9 2.1 - - - +
499O LEU* 2.7 51.2 + - + +
501O ILE* 4.7 13.0 - - + -
513O ILE* 3.4 39.0 - - + -
515O CYS* 5.9 0.9 - - - -
516O ALA* 5.3 9.6 - - + -
544O LEU* 4.9 13.7 - - + -
545O VAL 3.3 11.4 - - - +
546O PHE* 3.6 19.7 - - + -
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Residues in contact with PHE 459 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397O LEU* 4.0 33.2 - - + -
457O GLN* 5.5 0.9 - - + -
458O ILE* 1.3 79.3 - - - +
460O ILE* 1.3 70.1 + - - +
468O LEU* 4.7 4.9 - - + -
470O PRO* 3.7 37.7 - - + -
476O VAL* 3.5 11.0 - - - -
496O THR* 4.4 5.6 - - + -
497O LYS 4.3 5.6 - - - +
498O VAL* 4.2 20.0 - - + -
545O VAL* 3.1 72.1 + - + +
547O ARG* 4.0 26.7 - - + -
561O GLN* 4.8 0.7 - - - -
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Residues in contact with ILE 460 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459O PHE* 1.3 80.2 - - - +
461O GLY* 1.3 61.7 + - - +
470O PRO* 3.7 6.4 - - - +
471O HIS* 3.0 20.8 + - + +
474O TYR* 3.7 29.5 - - + +
475O GLN 4.2 2.9 - - - -
476O VAL* 3.3 35.1 - - + +
496O THR* 5.4 3.1 - - - +
497O LYS 5.3 0.4 + - - -
517O GLY 5.3 0.4 - - - +
518O ILE* 4.3 20.2 - - + -
542O VAL* 3.6 30.1 - - + -
543O ARG 4.1 6.7 - - - +
544O LEU* 3.8 29.2 - - + -
545O VAL* 4.2 0.7 - - - -
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Residues in contact with GLY 461 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459O PHE* 5.0 0.2 - - - -
460O ILE* 1.3 75.6 - - - +
462O THR* 1.3 62.6 + - - -
468O LEU* 4.4 2.5 - - - -
469O LYS 3.4 11.2 - - - -
470O PRO* 4.1 2.0 - - - -
471O HIS* 3.5 6.1 - - - -
542O VAL* 3.2 7.4 - - - +
543O ARG* 2.8 40.5 + - - -
545O VAL* 3.4 17.1 - - - +
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Residues in contact with THR 462 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461O GLY* 1.3 76.0 - - - -
463O ALA* 1.3 54.4 + - - +
464O ASP* 3.4 25.1 + - - +
466O ARG* 5.3 1.1 - - - +
467O ILE 4.1 2.6 + - - -
468O LEU* 3.8 3.3 - - - +
469O LYS* 2.8 56.4 + - - +
470O PRO 4.0 0.7 - - - -
471O HIS* 3.6 33.0 - - + -
539O ASN* 5.8 3.6 - - - +
543O ARG* 2.8 31.2 + - - -
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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
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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