Contacts of the strand formed by residues 388 - 392 (chain B) in PDB entry 4J15
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 PHE 388 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B ALA* 3.8 14.6 - - + -
310B MET* 3.7 24.7 - - + -
311B VAL* 4.5 2.7 - - + -
314B PHE* 3.5 30.3 - + + -
337B PHE* 3.9 8.3 - - + -
338B LYS 3.5 0.4 + - - -
339B PHE* 4.3 10.8 - - + -
340B LEU 5.2 1.1 + - - -
343B THR* 3.5 35.9 - - + +
344B LEU* 4.6 2.9 + - - +
386B THR* 2.6 24.0 + - - +
387B ASP* 1.3 80.2 - - - +
389B TYR* 1.3 65.9 + - - +
390B ILE* 5.3 0.2 - - + -
418B MET* 3.9 37.2 - - + -
419B PHE 3.2 15.3 - - - -
420B MET* 4.2 2.7 - - + -
425B ILE* 4.2 13.0 - - + -
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Residues in contact with TYR 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B THR* 4.3 3.8 - - - -
344B LEU* 3.6 27.1 - - + +
346B LEU* 4.3 16.2 - - + -
368B LEU* 5.4 0.2 - - - +
373B GLU 4.5 1.9 + - - -
376B LEU* 3.4 31.5 - - + +
377B GLY* 4.0 14.4 + - - -
380B VAL* 3.7 36.6 - - + -
387B ASP 5.1 3.4 - - - -
388B PHE* 1.3 80.5 - - - +
390B ILE* 1.3 77.3 + - - +
391B LEU* 4.3 6.5 - - + -
418B MET* 3.4 5.7 - - - +
419B PHE* 3.1 74.7 + + + -
422B GLY* 5.5 0.9 - - - -
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Residues in contact with ILE 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B MET* 3.8 41.3 - - + +
304B GLU* 5.9 0.4 - - + -
307B ALA* 3.8 16.4 - - + -
343B THR* 3.7 27.1 - - + +
344B LEU 2.9 12.8 + - - +
345B ARG* 3.5 13.4 - - + -
346B LEU* 2.8 27.0 + - - -
389B TYR* 1.3 85.6 - - - +
391B LEU* 1.3 72.3 + - - +
392B ASP 4.3 0.4 - - - +
416B TYR* 4.0 7.0 - - + -
417B ASP 3.5 9.9 - - - +
418B MET* 3.9 22.0 - - + -
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Residues in contact with LEU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU* 3.2 20.0 - - + +
347B GLU 3.7 20.6 - - - +
348B TYR* 3.7 17.5 - - + +
351B ALA* 3.9 11.2 - - + -
368B LEU* 3.7 23.6 - - + -
376B LEU* 4.1 11.7 - - + -
389B TYR* 4.2 4.9 + - + -
390B ILE* 1.3 74.6 - - - +
392B ASP* 1.3 59.4 + - - +
394B TYR* 3.4 32.3 - - + +
416B TYR* 3.3 4.9 - - - +
417B ASP 2.9 28.5 + - - +
419B PHE* 3.7 18.1 - - + -
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Residues in contact with ASP 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B TYR* 2.7 26.4 + - - -
300B HIS* 2.7 28.7 + - - -
303B MET* 4.2 9.2 - - - -
345B ARG* 2.9 31.3 + - + +
346B LEU 2.8 12.5 + - - +
347B GLU* 3.5 1.3 - - - -
348B TYR* 2.8 28.1 + - - +
390B ILE* 4.7 1.3 - - + -
391B LEU* 1.3 74.5 - - - +
393B LYS* 1.3 76.5 + - + +
394B TYR* 3.7 1.6 - - - -
415B SER 3.2 10.0 - - - +
416B TYR* 4.4 2.0 - - - +
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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
------------------------------------------------------------
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