Contacts of the strand formed by residues 388 - 393 (chain B) in PDB entry 1JXQ
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 GLY 388 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A ASN 3.7 2.9 - - - -
393A PHE* 3.3 30.8 - - - -
329B VAL 3.9 0.2 - - - +
330B SER* 3.6 1.2 + - - -
331B TYR 2.9 35.9 + - - -
386B MET 3.7 0.2 + - - -
387B PRO* 1.3 76.6 - - - +
389B CYS* 1.3 68.0 + - - -
390B PHE* 4.2 6.3 - - - -
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Residues in contact with CYS 389 (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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390A PHE* 3.5 1.2 - - - -
392A ASN* 2.8 51.6 + - + +
393A PHE* 5.0 0.2 - - - -
328B PHE* 3.8 32.1 - - + -
329B VAL 3.3 4.0 - - - -
330B SER* 4.4 5.6 - - - -
367B GLN* 6.4 0.4 - - - -
370B LEU* 3.9 27.8 - - - -
387B PRO* 5.8 1.6 - - - -
388B GLY* 1.3 78.8 - - - -
390B PHE* 1.3 65.9 + - - +
392B ASN* 3.3 6.0 + - + +
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Residues in contact with PHE 390 (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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240A GLN* 3.7 16.4 - - + -
389A CYS 3.8 4.5 - - - -
390A PHE* 3.3 41.3 - + + +
393A PHE* 4.5 10.5 - + - -
240B PHE* 3.5 64.8 - - + +
258B VAL* 5.1 0.9 - - + -
327B ILE* 4.0 1.9 - - - +
328B PHE* 3.6 5.2 - - - -
329B VAL* 2.9 55.1 + - + +
331B TYR* 4.1 21.8 - + + -
388B GLY 4.5 6.5 - - - -
389B CYS* 1.3 74.8 - - - +
392B ASN* 1.3 60.8 + - - +
393B PHE* 3.7 5.0 + - - -
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Residues in contact with ASN 392 (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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367A GLN* 4.2 11.7 + - - +
371A LEU* 4.2 7.9 - - - +
388A GLY* 3.2 3.6 - - - -
389A CYS* 2.8 47.5 + - - +
392A ASN* 5.4 2.7 - - + -
328B PHE* 3.6 29.9 - - + -
367B GLN* 3.3 26.5 + - - +
389B CYS* 4.5 5.2 - - + +
390B PHE* 1.3 71.7 - - - +
393B PHE* 1.3 60.7 + - - +
394B LEU* 2.9 28.7 + - - +
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Residues in contact with PHE 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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331A TYR* 4.5 5.6 - + + -
333A THR 4.4 1.6 - - - -
334A PHE* 3.3 35.9 - + + -
335A PRO* 3.8 17.3 - - + -
386A MET* 3.2 37.0 - - + +
387A PRO 3.5 4.5 - - - -
388A GLY* 3.3 29.4 - - - -
389A CYS 4.1 7.9 - - - -
390A PHE* 3.8 27.4 - + - -
240B PHE* 4.1 14.8 - - - -
324B PRO 4.5 2.9 - - - +
325B SER 4.2 0.2 - - - -
326B ASP 3.2 20.6 + - - -
327B ILE* 3.0 28.3 + - + +
390B PHE 4.3 2.5 - - - -
392B ASN* 1.3 77.5 + - - +
394B LEU* 1.3 64.2 - - - +
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Residues in contact with LEU 394 (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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371A LEU* 3.5 15.5 - - + +
374A ALA* 3.8 14.0 - - - +
387A PRO 4.9 0.2 - - - +
153B TYR* 3.3 22.9 - - + +
277B PRO* 4.3 8.5 - - + -
279B LEU* 4.6 4.3 - - + -
326B ASP* 3.7 27.1 - - - +
328B PHE* 3.7 38.8 - - + -
366B LEU* 4.3 13.9 - - + -
367B GLN* 5.9 3.1 - - + +
392B ASN* 2.9 14.1 + - - +
393B PHE* 1.3 82.8 - - - +
395B ARG* 1.3 63.0 + - - +
396B LYS 3.8 17.3 - - - +
398B LEU* 4.7 8.1 - - + +
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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