Contacts of the strand formed by residues 392 - 399 (chain B) in PDB entry 2JED
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 392 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388B LYS* 3.2 7.8 - - - +
389B GLY 2.9 34.0 + - - +
390B SER 3.2 3.0 + - - -
391B PHE* 1.3 81.3 - - - +
393B LYS* 1.3 62.1 + - - -
411B LEU* 3.9 19.1 - - - -
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Residues in contact with LYS 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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385B MET* 4.3 14.4 - - - -
387B GLY 3.6 2.2 - - - -
388B LYS* 3.8 40.6 - - + +
391B PHE 4.1 0.4 + - - -
392B GLY* 1.3 72.1 - - - -
394B VAL* 1.3 63.2 + - - +
395B PHE* 3.8 28.0 - - + -
408B ILE 3.7 0.5 - - - +
409B LYS* 3.2 3.8 - - - +
410B ALA* 2.8 42.5 + - + +
412B LYS* 4.9 14.8 - - - +
677B PHE* 6.2 1.6 - - + -
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Residues in contact with VAL 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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385B MET* 3.6 5.7 - - - +
386B LEU* 2.7 45.5 + - + -
387B GLY 3.0 9.5 + - - -
391B PHE* 3.8 14.4 - - + -
393B LYS* 1.3 78.6 - - - +
395B PHE* 1.3 58.4 + - - +
407B ALA* 3.9 17.3 - - + -
408B ILE 3.3 9.2 - - - +
409B LYS* 4.1 16.4 - - + +
1712B LG8 3.6 55.0 - - + -
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Residues in contact with PHE 395 (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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382B LEU* 3.9 35.2 - - + -
384B LYS 3.3 14.6 - - - +
385B MET* 3.9 17.0 - - + -
386B LEU* 3.9 4.5 - - - -
393B LYS* 3.8 37.7 - - + -
394B VAL* 1.3 75.4 - - - +
396B LEU* 1.3 61.8 + - - +
397B ALA 3.5 0.2 + - - -
407B ALA* 3.3 7.1 - - - -
408B ILE* 2.7 49.8 + - + +
410B ALA* 4.1 8.1 - - + -
675B LEU* 3.7 30.5 - - + -
676B SEP 5.9 0.9 - - - -
677B PHE* 3.8 27.4 - + - -
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Residues in contact with LEU 396 (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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382B LEU* 3.6 3.6 - - - -
383B HIS* 2.9 40.4 + - + -
384B LYS* 2.7 36.6 + - + +
386B LEU* 3.7 14.8 - - + +
395B PHE* 1.3 70.6 - - - +
397B ALA* 1.3 58.6 + - - +
405B PHE* 3.8 25.1 - - + -
406B PHE 3.7 12.6 - - - +
460B TYR* 3.9 37.2 - - + +
658B PRO* 4.1 19.3 - - + -
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Residues in contact with ALA 397 (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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380B PHE* 3.9 8.5 - - + -
381B GLU 3.3 4.5 - - - +
382B LEU* 3.6 23.1 - - + -
383B HIS* 4.5 0.2 - - - -
395B PHE 3.5 0.2 + - - -
396B LEU* 1.3 74.2 - - - +
398B GLU* 1.3 60.0 + - - +
399B PHE 4.1 0.6 + - - -
404B GLN 3.8 0.2 - - - +
405B PHE* 3.3 8.8 - - - +
406B PHE* 2.8 39.4 + - - +
408B ILE* 3.7 32.1 - - + -
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Residues in contact with GLU 398 (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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380B PHE* 3.2 4.1 - - - -
381B GLU* 2.8 40.3 + - + +
383B HIS* 2.8 36.8 + - + +
397B ALA* 1.3 72.9 - - - +
399B PHE* 1.3 61.2 + - - +
400B LYS* 3.0 12.3 + - - +
403B ASN* 3.3 48.9 + - - +
404B GLN 3.5 3.6 - - - +
405B PHE* 4.1 20.4 - - + -
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Residues in contact with PHE 399 (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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376B LYS* 3.2 27.6 - - - -
379B ASP* 3.7 23.1 - - + -
380B PHE* 3.7 33.3 - + + -
398B GLU* 1.3 67.0 - - - +
400B LYS* 1.3 58.7 + - - +
401B LYS* 3.0 32.3 + - + -
402B THR* 3.1 32.3 + - + +
403B ASN 2.8 32.1 + - - -
404B GLN* 2.9 21.9 + - - +
406B PHE* 3.8 10.3 - + + -
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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