Contacts of the strand formed by residues 457 - 464 (chain C) in PDB entry 2O2C
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 CYS 457 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389C HIS* 4.7 0.4 - - - -
390C ALA* 3.5 14.8 - - - -
392C LEU* 3.8 21.1 - - + -
448C ILE* 3.9 23.1 - - - -
455C ILE 3.4 16.1 + - - -
456C PRO* 1.3 74.5 - - - +
458C ASP* 1.3 65.9 + - - +
459C PHE* 3.5 24.7 - - + -
487C LEU* 4.4 5.2 - - + -
525C PRO 3.5 11.6 + - - +
526C SER* 3.2 2.7 - - - +
527C ASN* 2.8 27.5 + - - +
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Residues in contact with ASP 458 (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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373C LEU* 4.3 7.1 - - - +
389C HIS* 3.0 26.0 + - - -
390C ALA 2.8 14.3 + - - +
391C ILE* 3.8 5.7 - - + +
392C LEU* 2.8 31.5 + - - +
457C CYS* 1.3 71.8 - - - +
459C PHE* 1.3 63.0 + - - +
460C ILE* 3.9 3.5 + - + +
527C ASN* 3.0 36.3 + - - +
529C LEU* 4.6 7.6 - - + -
546C TYR* 2.7 37.6 + - - +
549C LYS* 4.4 0.9 + - - -
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Residues in contact with PHE 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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392C LEU* 3.5 20.2 - - + -
394C TYR* 3.5 37.2 - + - -
445C TYR* 3.8 8.3 - + - -
457C CYS* 3.5 30.3 - - + -
458C ASP* 1.3 71.2 - - - +
460C ILE* 1.3 55.7 + - - +
480C PHE* 3.6 19.6 - + + -
483C GLN* 3.6 31.0 - - + -
484C THR* 3.6 25.1 - - + -
487C LEU* 3.9 20.6 - - + -
526C SER* 4.2 5.2 - - - -
527C ASN 2.8 13.4 + - - +
528C THR* 3.4 3.4 - - - +
529C LEU* 2.7 33.6 + - - +
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Residues in contact with ILE 460 (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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391C ILE* 4.4 11.2 - - + -
392C LEU 3.2 6.3 + - - -
393C PRO* 3.5 9.6 - - + +
394C TYR* 2.6 35.2 + - - +
395C ASP* 5.4 0.5 - - - +
398C LEU* 4.3 13.5 - - + -
401C LEU* 3.9 24.9 - - + -
458C ASP 4.5 4.7 - - - +
459C PHE* 1.3 74.6 - - - +
461C GLY* 1.3 63.6 + - - +
480C PHE* 3.5 4.2 - - - -
529C LEU* 3.3 28.9 - - + +
531C ILE* 5.5 3.8 - - + -
542C ILE* 4.3 26.5 - - + -
546C TYR* 3.6 29.6 - - + +
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Residues in contact with GLY 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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394C TYR 4.0 10.1 - - - -
395C ASP* 5.8 1.8 - - - -
460C ILE* 1.3 77.0 - - - +
462C ALA* 1.3 59.7 + - - -
477C MET* 4.5 4.0 - - - -
480C PHE* 3.5 15.0 - - - -
529C LEU 2.9 9.3 + - - +
530C LEU* 3.4 10.3 - - - -
531C ILE* 3.0 30.9 + - - +
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Residues in contact with ALA 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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394C TYR 4.5 5.6 + - - +
395C ASP* 4.5 14.5 + - - +
461C GLY* 1.3 74.5 - - - -
463C ILE* 1.3 60.8 + - - +
464C GLN 3.7 17.9 - - - +
473C HIS* 3.1 24.1 + - - +
477C MET* 3.2 13.7 - - - +
530C LEU* 4.4 0.2 - - - -
531C ILE* 3.4 19.3 - - + -
533C SER* 4.1 9.0 - - - -
534C LEU 4.2 5.4 - - - +
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Residues in contact with ILE 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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600B MET* 3.9 19.3 - - + +
601B PHE* 3.4 41.4 - - + +
604B LEU* 3.7 15.0 - - + +
605B SER* 3.6 22.9 - - - +
98C PHE* 3.7 29.6 - - + -
462C ALA* 1.3 72.9 - - - +
464C GLN* 1.3 55.7 + - + +
473C HIS* 2.8 21.6 + - - -
530C LEU* 3.9 25.8 - - + -
531C ILE 3.0 17.0 + - - +
532C LYS* 3.6 10.3 - - - +
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Residues in contact with GLN 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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604B LEU 2.9 27.1 + - - +
605B SER 4.0 14.5 + - - +
606B HIS 4.7 6.1 + - - +
462C ALA* 3.7 16.3 - - - +
463C ILE* 1.3 81.1 - - + +
465C SER* 1.3 61.7 + - - +
466C GLN* 4.2 2.3 + - - +
468C LYS* 4.0 13.2 + - - +
473C HIS* 4.0 3.6 - - - -
532C LYS* 2.8 41.1 + - + +
533C SER* 3.9 24.5 + - - -
534C LEU 4.6 0.5 + - - -
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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