Contacts of the strand formed by residues 387 - 393 (chain B) in PDB entry 3UAJ
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 LEU 387 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B LYS* 5.8 5.8 - - - -
306B PHE* 3.5 24.6 + - + +
307B SER* 4.6 4.9 - - - -
308B ILE* 3.8 43.3 - - + +
324B VAL* 5.3 2.0 - - + -
378B ILE 3.4 2.8 - - - +
379B VAL* 3.5 2.4 - - - +
380B ILE* 2.8 52.2 + - + +
385B SER 3.8 3.2 + - - +
386B ALA* 1.3 70.7 - - - +
388B THR* 1.3 63.8 + - - +
389B LEU* 3.9 16.2 - - + -
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Residues in contact with THR 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LYS* 3.7 30.8 + - - +
377B TYR* 3.7 31.6 - - + -
378B ILE 3.4 6.7 - - - +
379B VAL* 4.5 11.6 - - + +
386B ALA* 3.8 8.4 + - - +
387B LEU* 1.3 78.4 + - - +
389B LEU* 1.3 67.2 + - - +
390B HIS 4.5 0.2 + - - -
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Residues in contact with LEU 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ILE* 3.9 27.1 - - + -
311B GLU* 5.8 4.3 - - + -
312B MET* 4.9 21.1 - - + +
322B VAL* 5.1 4.7 - - + -
377B TYR* 3.5 6.7 - - - -
378B ILE* 2.8 50.7 + - + +
380B ILE* 3.8 27.6 - - + -
387B LEU* 3.9 23.3 - - + -
388B THR* 1.3 76.8 - - - +
390B HIS* 1.3 65.2 + - - +
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Residues in contact with HIS 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B MET* 5.1 0.5 - - - +
342B VAL* 5.9 0.9 - - + -
375B ASP* 3.2 39.1 + - + -
376B SER 3.8 2.7 + - - -
377B TYR* 3.3 43.9 + + + -
388B THR 4.4 0.8 + - - -
389B LEU* 1.3 75.5 - - - +
391B TRP* 1.3 80.5 + - - +
392B PHE* 4.9 4.7 - - + +
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Residues in contact with TRP 391 (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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107A LEU* 6.1 2.2 - - + -
311B GLU* 5.2 4.5 - - - -
312B MET* 3.5 56.1 - - + -
313B ALA* 4.4 1.3 - - - -
314B GLU* 3.6 45.1 + - + -
320B THR* 3.5 16.1 - - + +
371B PRO* 3.7 26.0 - - + +
374B GLY 3.4 0.9 - - - +
375B ASP* 3.5 2.4 - - - -
376B SER* 2.9 45.2 + - - +
378B ILE* 4.7 4.9 - - + -
390B HIS* 1.3 85.1 - - - +
392B PHE* 1.3 86.8 + - - +
393B ARG* 4.3 2.4 - - + +
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Residues in contact with PHE 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLU* 4.6 1.6 - - - +
374B GLY* 3.4 26.2 - - - -
375B ASP* 3.5 29.8 - - - +
390B HIS* 4.9 4.7 + - + +
391B TRP* 1.3 92.4 + - - +
393B ARG* 1.3 70.2 - - - +
394B LYS* 4.2 10.6 + - + -
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Residues in contact with ARG 393 (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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314B GLU* 3.5 19.5 - - - +
317B HIS 3.8 19.4 + - - -
318B GLY* 3.9 24.6 + - - -
370B GLU* 4.2 21.0 + - - +
371B PRO* 2.9 29.2 + - - +
372B PRO* 3.5 20.4 - - - +
373B PHE* 3.7 39.1 - - + +
374B GLY* 3.0 28.1 + - - -
391B TRP* 4.3 7.4 - - + +
392B PHE* 1.3 78.7 - - - +
394B LYS* 1.3 68.2 + - + +
395B GLY 3.9 1.0 + - - -
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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