Contacts of the strand formed by residues 424 - 430 (chain B) in PDB entry 6O4X
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 ARG 424 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324B LEU 3.0 8.7 + - - +
325B GLN* 3.3 22.9 - - + +
326B VAL* 2.9 25.6 + - - +
422B GLY 3.9 1.4 + - - -
423B ALA* 1.3 71.6 - - - +
425B VAL* 1.3 61.6 + - - +
426B TYR* 2.8 47.3 + - + -
486B THR 5.5 3.6 + - - -
487B GLY 3.7 15.7 + - - -
488B ASP* 3.9 11.1 + - - +
502B PRO* 4.2 18.8 - - + -
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Residues in contact with VAL 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B VAL* 3.2 17.7 - - + +
328B VAL* 3.8 27.4 - - + -
415B ALA* 3.9 16.4 - - + +
418B LEU* 3.8 15.9 - - + -
419B ALA* 3.7 30.5 - - - +
423B ALA* 3.8 5.1 + - + +
424B ARG* 1.3 78.9 - - - +
426B TYR* 1.3 61.9 + - - +
502B PRO* 3.3 7.9 - - - +
503B TYR* 2.4 49.8 + - + +
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Residues in contact with TYR 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B GLN* 5.7 0.2 - - + -
326B VAL 2.9 12.8 + - - +
327B LEU* 3.4 20.6 - - + +
328B VAL* 2.8 30.1 + - - +
424B ARG* 2.8 45.6 + - + -
425B VAL* 1.3 77.3 - - - +
427B ALA* 1.3 60.4 + - - +
483B PHE* 4.4 5.8 - + - -
487B GLY 3.7 15.5 - - - -
488B ASP* 3.2 13.9 + - - -
489B PRO* 3.6 33.4 - - + -
490B ASN* 3.9 3.8 + - - -
500B TRP* 3.3 39.7 - + + +
502B PRO* 3.9 21.5 - - + +
503B TYR 4.2 1.8 - - - +
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Residues in contact with ALA 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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328B VAL* 3.1 17.3 - - + +
329B GLY* 5.6 0.4 - - - -
426B TYR* 1.3 75.6 - - - +
428B TYR* 1.3 62.4 + - - +
500B TRP* 3.0 20.4 + - - +
501B PRO 5.2 0.4 + - - -
503B TYR* 3.7 29.0 - - + +
509B GLN 4.1 1.8 + - - +
510B TYR* 3.4 19.8 - - + +
511B VAL 3.2 13.3 + - - -
524B LEU* 4.3 11.0 - - + -
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Residues in contact with TYR 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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227B LEU 5.0 0.2 - - - -
228B GLN* 3.3 38.7 + - + +
229B SER* 4.7 0.5 + - - -
327B LEU* 4.2 15.3 - - + -
328B VAL* 3.1 31.3 + - - -
329B GLY* 3.2 33.0 - - - -
330B VAL* 3.3 16.8 + - - +
427B ALA* 1.3 76.4 - - - +
429B VAL* 1.3 71.2 + - - +
430B PHE* 3.9 16.6 - + + -
450B GLU* 4.3 10.0 + - + +
480B TRP* 3.7 28.1 - + - -
500B TRP* 3.6 11.9 - + + -
510B TYR* 4.4 1.6 - - - -
511B VAL* 3.3 11.4 - - + +
513B LEU* 3.6 28.0 - - + -
524B LEU* 4.6 3.3 - - - +
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Residues in contact with VAL 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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330B VAL* 3.4 16.2 - - + +
331B VAL 4.5 2.2 - - - +
332B LYS* 4.5 13.5 - - + +
428B TYR* 1.3 81.4 - - - +
430B PHE* 1.3 65.9 + - - +
431B GLU* 3.5 30.0 + - + +
510B TYR* 3.5 29.4 - - + +
511B VAL 2.9 7.2 + - - +
512B SER* 3.6 1.8 - - - -
513B LEU 2.9 22.8 + - - -
524B LEU* 3.7 18.4 - - + -
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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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330B VAL 2.8 16.3 + - - +
331B VAL* 3.5 5.7 - - + -
332B LYS* 2.9 28.2 + - - +
428B TYR* 3.9 9.7 - + + -
429B VAL* 1.3 69.4 - - - +
431B GLU* 1.3 58.6 + - - +
432B HIS* 3.1 28.0 - - + -
445B VAL* 3.9 11.2 - - + +
449B TYR 3.9 6.1 - - - -
450B GLU* 3.5 39.0 - - + -
453B PHE* 3.8 19.7 - + + -
454B ILE* 5.4 2.2 - - + -
472B PHE* 3.5 36.3 - + - -
476B LEU* 3.6 14.8 - - + -
513B LEU* 3.7 22.4 - - + -
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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