Contacts of the strand formed by residues 422 - 430 (chain B) in PDB entry 4PO2
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 422 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414B ILE* 3.8 38.8 - - + -
418B SER* 4.6 2.8 + - - +
419B THR 3.4 19.0 + - - +
420B ILE* 3.9 3.3 - - + +
421B PRO* 1.3 75.8 - - - +
423B LYS* 1.3 67.5 + - - +
424B GLN* 4.2 14.8 + - + +
479B ASP* 3.6 3.2 - - - +
480B ILE* 2.9 40.9 + - + +
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Residues in contact with LYS 423 (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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422B THR* 1.3 78.4 + - - +
424B GLN* 1.3 81.1 + - - +
425B THR* 4.5 7.0 - - - +
477B THR* 3.6 27.5 - - + +
478B PHE 3.4 5.8 - - - +
479B ASP* 3.2 24.7 - - - +
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Residues in contact with GLN 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B LEU* 3.2 40.6 - - + +
414B ILE* 4.0 13.7 - - + +
422B THR* 4.2 12.4 + - - +
423B LYS* 1.3 84.3 + - - +
425B THR* 1.3 66.7 + - - +
477B THR* 3.4 2.9 - - - +
478B PHE 2.9 33.3 + - - +
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Residues in contact with THR 425 (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 LEU* 4.3 1.6 - - - -
423B LYS* 4.5 7.6 - - - +
424B GLN* 1.3 80.5 + - - +
426B GLN* 1.3 68.9 + - - +
427B ILE* 5.3 3.6 - - + -
475B GLU* 3.6 26.7 - - + +
476B VAL 3.3 6.1 - - - +
477B THR* 2.8 28.9 + - - +
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Residues in contact with GLN 426 (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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411B THR* 4.3 6.8 - - - +
412B ALA 4.7 3.8 - - - +
413B LEU* 3.9 19.7 - - + +
425B THR* 1.3 76.6 - - - +
427B ILE* 1.3 72.5 + - - +
428B PHE* 3.4 43.4 - - + -
476B VAL 2.9 30.8 + - - +
3D LEU* 3.7 22.6 - - - +
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Residues in contact with ILE 427 (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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425B THR* 5.3 3.6 - - + -
426B GLN* 1.3 86.4 + - - +
428B PHE* 1.3 70.1 + - - +
473B GLN* 3.7 14.1 - - + +
474B ILE 3.4 15.3 - - - +
475B GLU* 4.6 20.2 - - + +
493B LYS* 5.7 7.6 - - + -
2D ARG* 3.5 54.9 + - - +
3D LEU 4.6 2.6 + - - -
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Residues in contact with PHE 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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403B LEU* 3.5 23.3 - - + -
405B THR* 3.8 25.4 - - + -
411B THR* 4.2 3.1 - - + -
413B LEU* 4.1 3.8 - - + -
426B GLN* 3.4 58.8 - - + -
427B ILE* 1.3 77.0 - - - +
429B THR* 1.3 62.7 + - - +
473B GLN* 3.6 3.6 - - - -
474B ILE* 2.8 35.8 + - + +
476B VAL* 3.6 27.1 - - + -
2D ARG* 3.7 3.8 - - - +
3D LEU* 3.6 26.2 - - + +
5D LEU* 3.6 27.8 - - + -
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Residues in contact with THR 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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428B PHE* 1.3 73.9 - - - +
430B THR* 1.3 65.3 + - - +
438B VAL* 5.0 3.4 - - - -
470B GLY* 3.0 33.9 - - - +
471B VAL 3.5 0.7 + - - -
472B PRO 2.6 24.1 + - - -
473B GLN* 4.2 1.6 - - - -
474B ILE* 5.0 2.7 - - - +
2D ARG* 3.9 21.1 - - + +
3D LEU 3.0 13.1 + - - +
4D LEU* 3.5 25.5 - - + -
5D LEU* 2.9 30.8 + - - +
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Residues in contact with THR 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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429B THR* 1.3 83.0 + - - +
431B TYR* 1.3 62.2 + - - +
432B SER 3.9 3.4 + - - -
435B GLN* 3.8 38.6 - - + +
438B VAL* 4.4 10.8 - - + -
464B ILE* 4.4 4.7 - - + -
467B ALA 5.1 0.5 + - - -
468B PRO 4.0 0.5 + - - -
469B ARG* 3.7 6.8 - - - +
470B GLY 3.2 25.5 + - - -
472B PRO* 3.4 35.6 - - + +
474B ILE* 5.6 0.7 - - + -
4D LEU* 3.2 16.9 - - - +
5D LEU 3.8 4.3 - - - -
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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