Contacts of the strand formed by residues 366 - 374 (chain B) in PDB entry 1F1J
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 LYS 366 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364B PHE* 3.2 6.4 - - - +
365B GLU* 1.3 85.5 + - + +
367B LEU* 1.3 59.3 + - - +
368B GLY* 4.2 9.0 - - - +
369B LYS* 5.2 4.8 - - - +
405B GLY 5.4 2.7 - - - +
407B ASP* 3.1 33.5 + - - +
433B ASN* 3.0 36.8 + - - +
434B ALA* 3.1 14.1 - - + -
435B ALA* 3.0 23.9 + - - +
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Residues in contact with LEU 367 (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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362B MET* 4.2 18.8 - - + -
366B LYS* 1.3 72.5 - - - +
368B GLY* 1.3 58.1 + - - +
404B LEU 3.3 26.9 - - - +
405B GLY* 3.3 18.0 + - - +
406B PHE* 3.6 37.0 - - + -
435B ALA* 3.2 6.3 + - + +
436B CYS* 2.9 45.8 + - - +
601B PHE* 4.1 27.6 - - + +
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Residues in contact with GLY 368 (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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366B LYS* 3.4 8.9 - - - +
367B LEU* 1.3 82.4 - - - +
369B LYS* 1.3 66.6 + - - -
405B GLY 4.3 1.2 + - - -
406B PHE* 3.2 11.0 - - - -
407B ASP* 2.9 27.1 + - - +
434B ALA* 3.8 12.8 - - - -
436B CYS 3.4 11.0 - - - -
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Residues in contact with LYS 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B LYS* 5.2 4.0 - - - +
368B GLY* 1.3 75.4 - - - -
370B CYS* 1.3 61.6 + - - +
371B ILE* 3.8 21.8 - - + -
406B PHE* 3.7 3.3 - - - -
407B ASP* 3.1 41.5 + - - +
409B ILE* 3.6 31.2 - - + -
426B ALA* 5.5 1.8 - - + -
429B GLU* 4.8 14.4 + - - +
431B HIS* 4.4 12.6 + - + -
434B ALA* 5.1 1.2 - - - +
436B CYS 4.1 3.2 + - - -
437B PHE* 3.7 19.9 - - + -
438B ALA 3.1 23.6 + - - -
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Residues in contact with CYS 370 (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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369B LYS* 1.3 76.9 - - - +
371B ILE* 1.3 61.8 + - - +
372B ILE* 3.7 7.9 + - - +
401B PHE* 3.4 38.8 - - - -
406B PHE* 3.5 26.2 - - + -
407B ASP 3.3 7.3 + - - -
408B VAL* 3.4 24.6 - - + +
409B ILE 3.4 3.8 + - - +
438B ALA* 3.2 11.4 - - + -
440B ILE* 4.0 16.2 - - - -
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Residues in contact with ILE 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B LYS* 3.8 19.1 - - + -
370B CYS* 1.3 72.5 - - - +
372B ILE* 1.3 63.5 + - - +
373B ILE* 4.2 10.3 - - + -
409B ILE* 3.6 9.2 - - + +
411B TYR* 3.7 33.2 - - + +
422B LEU* 3.7 26.0 - - + +
423B LEU* 4.5 2.5 - - + -
426B ALA* 3.5 32.5 - - + -
437B PHE* 4.2 12.8 - - + -
438B ALA 3.1 8.0 + - - +
439B CYS* 3.2 12.5 - - - -
440B ILE* 2.9 24.9 + - - +
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Residues in contact with ILE 372 (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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370B CYS* 4.1 11.2 - - - +
371B ILE* 1.3 80.4 - - - +
373B ILE* 1.3 64.5 + - - +
374B ASN 4.5 0.2 - - - +
394B ALA* 4.2 7.2 - - + +
397B LEU* 3.9 14.8 - - + +
398B PHE* 3.7 37.0 - - + +
408B VAL* 4.2 9.6 - - + -
409B ILE 2.9 13.7 + - - +
410B VAL* 3.4 14.9 - - + -
411B TYR* 2.8 30.1 + - - +
440B ILE* 3.4 26.7 - - + +
442B LEU* 4.2 22.9 - - + -
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Residues in contact with ILE 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B ILE* 4.3 13.2 - - + -
372B ILE* 1.3 73.5 - - - +
374B ASN* 1.3 60.0 + - - +
375B ASN* 3.7 28.9 - - - +
411B TYR* 3.9 3.6 - - + -
414B CYS* 3.7 18.8 - - + -
419B MET* 4.0 25.6 - - + -
422B LEU* 4.0 26.2 - - + -
423B LEU* 4.7 7.0 - - + -
439B CYS* 4.9 0.9 - - - -
440B ILE 2.9 10.6 + - - +
441B LEU* 3.7 31.0 - - + -
442B LEU* 3.0 30.2 + - - +
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Residues in contact with ASN 374 (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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372B ILE* 3.7 1.3 + - + -
373B ILE* 1.3 71.5 - - - +
375B ASN* 1.3 60.1 + - - +
376B LYS* 3.9 3.4 + - - +
390B THR* 2.8 38.2 + - - +
391B ASP* 3.1 25.5 + - - -
394B ALA* 3.6 23.9 - - + +
410B VAL* 4.4 3.8 - - + -
411B TYR 2.8 16.4 + - - +
412B ASN* 3.1 23.9 + - - +
413B ASP* 2.9 20.6 + - - +
442B LEU* 3.5 8.7 - - + +
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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