Contacts of the strand formed by residues 454 - 462 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445L LEU* 3.5 25.1 - - + -
448L TYR* 3.5 34.8 - - + +
452L LYS* 4.1 4.3 - - + +
453L PRO* 1.3 78.3 - - - +
455L GLY* 1.3 56.5 + - - +
502L PRO* 3.6 4.7 - - - +
503L LEU* 2.6 42.7 + - + -
509L MET* 3.3 29.2 - - + -
548L VAL* 4.4 10.5 - - + -
549L HIS 4.7 4.3 - - - +
550L ILE* 4.2 9.6 - - + -
551L PRO* 4.1 24.2 - - + -
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Residues in contact with GLY 455 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454L LEU* 1.3 73.6 - - - +
456L LEU* 1.3 63.8 + - - -
457L GLN* 3.8 7.1 + - - +
500L GLU* 4.5 15.7 - - - -
501L ILE 3.5 7.0 - - - -
502L PRO* 4.6 1.1 - - - -
548L VAL* 3.4 20.2 - - - +
549L HIS* 4.7 2.7 + - - -
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Residues in contact with LEU 456 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410L LEU* 4.5 8.5 - - + -
443L VAL* 3.8 29.8 - - + -
454L LEU 4.1 2.2 + - - -
455L GLY* 1.3 72.1 - - - -
457L GLN* 1.3 69.1 + - - +
458L ILE* 4.9 0.7 - - + -
500L GLU* 3.2 6.2 - - - +
501L ILE* 2.7 66.7 + - + +
503L LEU* 3.9 27.0 - - + +
511L ALA* 4.8 1.3 - - + -
513L ILE* 4.9 0.4 - - + -
546L PHE* 4.4 15.0 - - + -
547L ARG 3.5 27.6 - - - +
548L VAL* 4.0 9.9 - - + -
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Residues in contact with GLN 457 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393L SER* 5.1 5.1 + - - -
397L LEU* 5.5 2.9 - - + +
455L GLY 4.4 6.3 - - - +
456L LEU* 1.3 76.0 - - - +
458L ILE* 1.3 65.9 + - - +
459L PHE* 5.3 1.6 - - + -
491L LYS* 3.2 36.0 - - - +
498L VAL* 4.2 13.7 - - + +
499L LEU 3.4 3.8 - - - +
500L GLU* 3.5 13.3 + - + +
546L PHE* 3.2 9.5 - - - +
547L ARG* 2.8 65.4 + - + +
548L VAL* 5.6 0.4 - - - -
549L HIS* 3.7 21.2 + - + -
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Residues in contact with ILE 458 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456L LEU* 4.7 4.3 - - + +
457L GLN* 1.3 82.7 - - - +
459L PHE* 1.3 72.4 + - - +
476L VAL* 3.9 8.2 - - + +
498L VAL* 3.2 4.9 - - - +
499L LEU* 2.7 56.5 + - + +
501L ILE* 3.7 30.7 - - + -
513L ILE* 4.2 11.2 - - + -
515L CYS* 5.4 0.4 - - - -
516L ALA* 4.7 10.5 - - + -
544L LEU* 4.2 16.6 - - + -
545L VAL 3.4 5.2 - - - +
546L PHE* 3.4 34.3 - - + -
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Residues in contact with PHE 459 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397L LEU* 3.7 35.4 - - + -
457L GLN 5.3 0.4 - - - -
458L ILE* 1.3 82.2 - - - +
460L ILE* 1.3 67.5 + - - +
468L LEU* 4.7 3.1 - - + -
469L LYS 4.8 0.9 - - - -
470L PRO* 3.5 37.5 - - + -
476L VAL* 3.2 14.1 - - - -
496L THR* 4.1 17.7 - - + -
497L LYS 4.2 5.2 - - - +
498L VAL* 4.5 5.2 - - + -
543L ARG 3.6 0.3 - - - +
544L LEU* 3.7 2.6 - - - +
545L VAL* 2.7 85.1 + - + +
547L ARG* 4.5 10.8 - - + -
561L GLN* 4.2 11.2 - - - -
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Residues in contact with ILE 460 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459L PHE* 1.3 77.6 - - - +
461L GLY* 1.3 60.4 + - - +
470L PRO* 3.5 6.8 - - - +
471L HIS* 2.9 22.0 + - + +
474L TYR* 3.9 22.0 - - + +
475L GLN* 3.7 7.4 + - - +
476L VAL* 3.6 31.2 - - + +
496L THR* 5.6 1.6 - - - +
497L LYS 5.4 0.2 + - - -
517L GLY 4.9 0.9 - - - +
518L ILE* 4.2 23.1 - - + -
542L VAL* 3.3 39.5 - - + -
543L ARG 3.3 3.1 - - - +
544L LEU* 3.5 31.0 - - + -
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Residues in contact with GLY 461 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459L PHE 3.7 2.0 + - - -
460L ILE* 1.3 75.1 - - - +
462L THR* 1.3 60.5 + - - -
468L LEU* 4.0 3.6 - - - -
469L LYS 3.2 12.1 - - - -
470L PRO* 4.2 0.4 - - - -
471L HIS* 3.8 6.5 - - - +
542L VAL* 3.3 10.2 - - - +
543L ARG 2.6 35.8 + - - -
545L VAL* 3.7 17.2 - - - +
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Residues in contact with THR 462 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461L GLY* 1.3 71.0 - - - -
463L ALA* 1.3 59.3 + - - +
464L ASP* 3.3 28.1 + - - +
466L ARG* 5.4 0.9 - - - +
467L ILE 3.7 4.5 + - - -
468L LEU* 3.2 19.6 - - - +
469L LYS* 2.7 42.2 + - - +
470L PRO 4.0 3.6 - - - +
471L HIS* 3.4 40.4 - - + -
472L ALA 5.0 0.2 - - - +
539L ASN* 5.2 6.7 - - - +
543L ARG* 3.2 7.0 + - - -
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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