Contacts of the strand formed by residues 453 - 458 (chain A) in PDB entry 3OPY
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 LYS 453 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387A ILE 3.9 3.8 + - - -
388A ASP* 2.9 35.7 + - + +
390A THR* 2.7 41.5 + - - -
391A ALA 4.6 0.2 - - - -
392A ALA* 4.0 24.9 - - + +
398A PHE* 4.7 20.0 - - + -
451A ARG* 2.9 27.8 + - + +
452A ARG* 1.4 80.5 - - - +
454A THR* 1.4 59.3 + - - +
455A THR* 3.0 14.8 + - - +
656A GLU* 5.8 4.7 - - - +
657A ASP* 3.4 29.6 - - - +
659A HIS* 6.5 0.2 - - + -
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Residues in contact with THR 454 (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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396A ARG 3.9 12.4 + - - -
397A ALA* 3.4 6.9 - - + +
398A PHE* 2.8 33.7 + - - -
421A ASP* 3.6 23.9 + - + +
443A CYS* 3.7 30.1 - - + -
447A ARG* 3.5 30.8 + - - +
451A ARG* 4.5 3.7 - - - +
452A ARG 3.7 2.2 + - - -
453A LYS* 1.4 71.6 + - - +
455A THR* 1.3 55.5 + - - +
456A VAL* 5.0 2.9 - - + -
479A LEU* 4.7 5.6 - - + -
484A LEU* 4.5 11.9 - - + -
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Residues in contact with THR 455 (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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384A VAL* 4.3 23.1 - - + -
387A ILE* 5.1 1.6 - - + +
388A ASP* 4.1 12.5 + - - -
398A PHE* 3.4 18.6 - - + +
400A VAL* 4.3 10.3 - - + -
418A THR* 4.9 5.6 + - - +
419A GLY 5.4 0.2 - - - -
420A ALA* 3.7 9.4 - - - -
421A ASP* 2.8 41.6 + - - +
451A ARG* 4.4 2.4 + - - -
453A LYS 3.0 15.2 + - - -
454A THR* 1.3 73.0 + - - +
456A VAL* 1.3 70.1 + - - +
457A ILE* 4.5 11.2 - - + -
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Residues in contact with VAL 456 (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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398A PHE 3.0 8.4 + - - +
399A VAL* 3.5 5.4 - - + +
400A VAL* 2.9 27.2 + - - +
422A TYR* 3.4 18.4 - - + +
424A PHE* 3.6 32.3 - - + -
439A LEU* 3.9 21.8 - - + -
443A CYS* 4.5 6.3 - - - -
454A THR* 5.0 1.1 - - + -
455A THR* 1.3 77.9 - - - +
457A ILE* 1.3 67.8 + - - +
458A VAL* 4.4 2.9 - - + -
475A VAL* 3.7 16.6 - - + -
479A LEU* 3.9 21.8 - - + -
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Residues in contact with ILE 457 (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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384A VAL* 5.3 3.1 - - + -
400A VAL* 3.5 19.5 - - + -
402A VAL* 3.9 23.6 - - + -
411A GLY* 3.8 28.9 - - - +
414A SER* 4.1 18.2 - - - +
415A GLY 4.2 0.2 - - - +
418A THR* 3.4 27.4 - - + +
420A ALA* 3.5 19.7 - - + -
422A TYR 3.1 7.9 + - - -
423A ILE* 3.3 9.6 - - + -
424A PHE* 2.9 28.8 + - - -
455A THR* 4.5 7.2 - - + -
456A VAL* 1.3 76.7 - - - +
458A VAL* 1.3 64.7 + - - +
459A ALA 4.1 0.6 + - - +
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Residues in contact with VAL 458 (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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399A VAL* 3.8 20.6 - - + -
400A VAL 2.9 10.1 + - - +
401A GLU* 3.4 22.1 - - - +
402A VAL* 2.9 29.6 + - - +
424A PHE* 3.8 13.7 - - + -
456A VAL* 4.4 2.0 - - + -
457A ILE* 1.3 74.1 - - - +
459A ALA* 1.3 64.3 + - - +
462A ALA* 3.7 11.9 - - + -
470A ILE 3.4 26.2 - - - +
472A SER* 4.3 6.3 - - - +
475A VAL* 3.8 26.2 - - + -
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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