Contacts of the strand formed by residues 427 - 433 (chain B) in PDB entry 2AB5
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 THR 427 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417B ILE* 3.5 7.6 - - - +
418B TYR* 3.1 52.6 + - + +
419B LYS 5.9 0.8 - - - -
425B MSE 5.2 0.7 + - - -
426B LYS* 1.3 79.4 + - - +
428B ALA* 1.3 64.3 + - - +
467B LYS* 3.6 34.3 - - + +
504B ILE* 4.5 1.1 - - - -
506B LYS* 3.9 10.9 + - - +
507B TYR* 3.6 17.3 - - - +
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Residues in contact with ALA 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B SER 3.6 4.5 - - - -
417B ILE* 3.3 22.2 - - + -
427B THR* 1.3 76.3 - - - +
429B SER* 1.3 60.9 + - - +
467B LYS* 3.1 28.6 - - - +
472B ILE* 3.8 6.1 - - + +
497B PHE* 3.7 8.1 - - + -
501B LEU* 3.6 23.8 - - + -
507B TYR* 3.1 16.0 + - + -
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Residues in contact with SER 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B CYS 3.8 2.1 - - - +
415B PHE* 3.9 2.4 - - - -
416B SER* 3.1 46.1 + - - -
418B TYR* 3.2 26.6 + - - -
428B ALA* 1.3 76.2 - - - +
430B PHE* 1.3 60.3 + - - +
431B GLU* 4.2 3.6 + - - -
465B THR* 3.9 16.4 - - - +
466B THR 3.0 15.3 - - - -
467B LYS* 4.2 1.3 - - - -
472B ILE* 4.0 5.1 - - - +
497B PHE* 4.0 4.6 - - - -
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Residues in contact with PHE 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409B PHE* 3.7 30.3 - + - -
413B SER* 3.6 29.6 - - - -
414B CYS 3.6 3.6 - - - -
415B PHE* 3.4 45.5 - + + -
429B SER* 1.3 74.7 - - - +
431B GLU* 1.3 61.9 + - - +
432B VAL* 3.7 20.6 - - + -
444B ILE* 5.8 0.7 - - + -
448B LEU* 5.3 1.8 - - + -
450B ILE* 5.0 7.6 - - + -
464B MSE 3.7 1.6 - - + +
465B THR* 3.4 3.1 - - - -
466B THR* 3.0 36.1 + - + +
472B ILE* 3.8 15.6 - - + +
475B VAL* 3.6 31.6 - - + -
497B PHE* 6.0 0.4 - - + -
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Residues in contact with GLU 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B SER* 3.2 5.5 - - - -
414B CYS* 2.8 63.3 + - + +
416B SER* 4.7 7.4 + - - -
429B SER* 4.2 2.6 + - - -
430B PHE* 1.3 76.6 - - - +
432B VAL* 1.3 68.7 + - - +
433B SER* 4.7 7.8 + - - +
461B ASN* 5.5 0.7 - - - +
463B LYS* 3.0 31.0 - - + +
464B MSE 3.0 12.6 - - - +
465B THR* 3.6 16.4 + - + +
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Residues in contact with VAL 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B PHE* 3.5 34.3 - - + -
409B PHE* 4.1 14.1 - - + -
412B LYS 3.5 9.2 - - - +
413B SER* 4.4 0.7 - - - +
430B PHE* 3.7 24.7 - - + -
431B GLU* 1.3 78.7 - - - +
433B SER* 1.3 65.2 + - - +
434B MSE 3.3 1.6 + - - -
441B MSE 3.9 21.6 - - + +
444B ILE* 4.6 3.1 - - + -
463B LYS* 4.4 2.0 - - - -
464B MSE 2.9 48.7 + - + +
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Residues in contact with SER 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408B PHE* 4.1 8.0 - - - -
412B LYS* 2.9 48.3 + - - +
414B CYS* 6.1 1.0 - - - +
431B GLU* 4.2 10.7 + - - +
432B VAL* 1.3 76.3 - - - +
434B MSE 1.3 60.3 + - - +
435B ASN* 4.4 5.3 + - - -
461B ASN* 4.7 10.0 + - - -
462B SER 4.1 6.1 - - - -
463B LYS* 4.2 5.8 - - - +
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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