Contacts of the strand formed by residues 355 - 361 (chain B) in PDB entry 2FJU
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 CYS 355 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B ILE* 4.5 4.7 - - + -
324B ASN 3.2 3.2 + - - +
325B SER* 3.5 20.9 - - - +
326B SER 2.9 29.8 + - - +
353B CYS* 3.4 4.6 - - - -
354B ARG* 1.3 79.9 - - - +
356B VAL* 1.3 66.1 + - - +
404B ILE* 3.3 24.7 - - + -
406B SER* 4.6 3.1 - - - -
461B LYS* 5.9 0.2 - - - -
598B ARG* 4.2 20.0 - - - -
623B MET* 3.8 27.1 - - - -
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Residues in contact with VAL 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B SER 4.1 2.7 - - - -
329B THR* 3.5 12.1 - - + +
345B TYR* 4.0 22.7 - - + -
348B VAL* 3.7 29.6 - - + -
349B LEU* 4.2 16.4 - - + -
353B CYS* 4.1 6.5 - - - -
354B ARG 4.3 0.4 - - - -
355B CYS* 1.3 78.4 - - - +
357B GLU* 1.3 60.9 + - - +
358B LEU* 4.2 4.7 - - + -
391B ILE* 4.3 4.7 - - + -
403B ILE* 4.9 2.7 - - + -
404B ILE 3.1 2.8 + - - +
405B LEU* 3.6 28.9 - - + -
406B SER* 2.8 30.3 + - - -
598B ARG* 5.5 0.2 - - - -
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Residues in contact with GLU 357 (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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326B SER 4.1 0.9 + - - +
327B HIS* 3.3 8.1 - - - -
328B ASN* 3.0 30.0 + - - +
329B THR* 2.9 19.0 + - - +
330B TYR* 3.8 3.2 - - - -
345B TYR* 2.7 26.0 + - - -
356B VAL* 1.3 74.3 - - - +
358B LEU* 1.3 60.8 + - - +
359B ASP* 3.5 11.0 - - - +
406B SER* 3.4 15.7 + - - +
408B GLU* 3.6 9.1 - - + +
532B ALA* 5.3 1.9 - - - +
598B ARG* 2.7 40.5 + - - +
600B TYR* 6.0 1.0 - - - -
1000B CA 2.5 27.9 - - - -
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Residues in contact with LEU 358 (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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330B TYR* 4.6 0.4 - - - -
345B TYR* 3.4 27.6 - - + +
356B VAL* 4.2 14.8 - - + +
357B GLU* 1.3 82.5 - - - +
359B ASP* 1.3 64.5 + - - +
360B CYS* 3.5 11.5 + - - -
372B ILE* 3.8 22.4 - - + -
384B PHE* 3.9 20.4 - - + -
387B ALA* 4.3 4.9 - - + -
388B ILE* 4.1 17.9 - - + -
391B ILE* 4.3 7.6 - - + -
405B LEU* 4.4 11.7 - - + -
406B SER 3.0 11.6 + - - +
407B PHE* 3.6 12.2 - - + -
408B GLU 2.9 25.2 + - - -
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Residues in contact with ASP 359 (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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328B ASN* 3.3 3.5 + - - +
330B TYR* 2.6 32.0 + - + +
357B GLU* 3.5 5.9 - - - +
358B LEU* 1.3 69.9 - - - +
360B CYS* 1.3 61.1 + - - +
361B TRP* 3.4 9.8 + - - +
372B ILE* 3.1 27.0 - - - +
373B THR 3.1 21.7 + - - +
374B HIS* 4.2 2.6 + - - -
408B GLU* 3.3 29.7 - - - +
531B THR* 3.9 6.2 + - - -
1000B CA 2.6 29.7 - - - -
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Residues in contact with CYS 360 (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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358B LEU* 3.6 21.3 - - - -
359B ASP* 1.3 69.9 - - - +
361B TRP* 1.3 64.1 + - - +
370B PRO* 5.8 0.7 - - + -
371B ILE 3.4 6.1 - - - +
372B ILE* 4.5 0.9 - - - -
384B PHE* 3.8 23.1 - - + -
407B PHE* 4.1 8.3 - - - -
408B GLU 2.9 13.1 + - - +
409B ASN* 4.0 5.2 - - - +
410B HIS* 2.9 35.0 + - - +
411B VAL* 3.6 17.7 - - + -
420B MET* 3.6 26.2 - - + -
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Residues in contact with TRP 361 (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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359B ASP* 3.4 11.0 + - - +
360B CYS* 1.3 76.8 - - - +
362B LYS* 1.3 61.6 + - - +
370B PRO* 3.5 4.0 - - - +
371B ILE* 2.8 49.3 + - + +
373B THR* 3.0 37.8 + - - -
375B GLY* 3.4 25.7 - - - +
376B PHE* 3.8 31.6 - + - -
410B HIS* 3.2 59.9 - + + -
411B VAL* 3.8 6.5 - - - -
517B LEU* 4.2 11.4 - - + -
531B THR* 4.1 8.5 - - + -
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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