Contacts of the strand formed by residues 390 - 395 (chain A) in PDB entry 4BU2
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 MSE 390 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376A VAL* 3.4 3.9 - - - -
377A LEU 3.0 34.0 + - - +
379A ASP* 3.2 22.2 - - - +
388A GLU 3.1 21.3 + - - +
389A LYS* 1.3 75.7 - - - +
391A VAL* 1.3 61.9 + - - +
392A TYR* 3.5 5.5 + - + -
418A ARG* 3.7 27.6 - - + -
419A PHE* 3.0 13.5 - - - +
420A PRO* 3.4 37.9 - - + -
421A LEU* 4.4 5.4 - - - +
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Residues in contact with VAL 391 (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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374A LEU* 4.8 8.7 - - + -
375A THR 3.6 10.3 - - - +
376A VAL* 4.6 1.6 - - + +
390A MSE 1.3 70.5 - - - +
392A TYR* 1.3 67.3 + - - +
393A ILE* 4.8 7.6 - - + -
417A LEU 3.9 0.7 - - - +
418A ARG* 3.7 1.6 - - - -
419A PHE* 2.5 43.6 + - + +
420A PRO 3.9 6.5 - - - +
421A LEU* 3.7 32.8 - - + -
424A LEU* 3.8 29.6 - - + +
427A LEU* 3.5 25.4 - - + -
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Residues in contact with TYR 392 (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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373A VAL 3.8 0.3 - - - +
374A LEU* 3.2 9.4 - - - +
375A THR* 2.8 32.2 + - - -
377A LEU* 3.4 39.9 - - + -
378A PRO 3.2 20.0 - - - -
379A ASP* 2.3 33.6 + - - -
380A GLN* 3.9 4.7 - - + +
390A MSE 3.5 10.1 + - + -
391A VAL* 1.3 74.1 - - - +
393A ILE* 1.3 60.7 + - - +
394A TYR* 4.1 30.5 + + + -
417A LEU 3.5 13.0 - - - -
418A ARG* 3.4 35.6 - - + -
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Residues in contact with ILE 393 (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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372A ILE* 3.9 22.4 - - + -
373A VAL 3.5 1.3 - - - -
374A LEU* 3.6 26.2 - - + -
391A VAL* 4.8 3.6 - - + +
392A TYR* 1.3 73.8 - - - +
394A TYR* 1.3 63.7 + - - +
395A HIS* 5.5 1.3 - - + -
416A GLY* 3.0 6.6 - - - -
417A LEU* 2.8 49.4 + - + +
419A PHE* 4.0 27.4 - - + -
427A LEU* 3.8 21.8 - - + -
431A TRP* 3.9 12.8 - - + -
456A LEU* 5.5 2.5 - - + -
461A LEU* 3.9 19.5 - - + -
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Residues in contact with TYR 394 (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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331A LYS* 6.5 0.2 - - + -
332A LYS* 3.6 39.1 + - + +
335A ILE* 3.9 11.4 - - + +
336A MSE 4.3 13.9 - - + -
372A ILE* 3.6 1.6 - - - +
373A VAL* 2.9 54.6 + - + +
375A THR* 4.6 12.8 - - - -
377A LEU* 4.9 5.2 - - + +
392A TYR* 4.2 36.3 - + + -
393A ILE* 1.3 77.8 - - - +
395A HIS* 1.3 63.5 + - - +
414A PHE* 4.1 22.2 - - + +
415A HIS 3.6 14.4 - - - +
416A GLY* 5.1 0.9 - - - -
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Residues in contact with HIS 395 (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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335A ILE* 3.4 10.6 - - - +
371A HIS 3.3 12.3 - - - +
372A ILE* 4.5 7.0 - - + -
393A ILE* 4.9 1.3 - - + -
394A TYR* 1.3 76.7 - - - +
396A SER* 1.3 59.2 + - - +
397A LEU* 3.2 33.4 + - + +
398A LYS* 4.0 18.8 - - - -
399A ASN* 4.2 4.3 - - - +
415A HIS* 3.3 27.3 + - + +
416A GLY* 3.7 19.6 + - - -
459A GLU* 2.9 45.2 + - + +
461A LEU* 4.2 21.5 - - + -
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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