Contacts of the strand formed by residues 405 - 412 (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 PHE 405 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B HIS* 4.3 16.6 - + - -
396B LEU* 3.8 22.4 - - + -
397B ALA 3.3 9.9 - - - -
398B GLU* 4.1 28.7 - - + -
403B ASN 3.8 17.5 - - - -
404B GLN* 1.3 74.9 - - - +
406B PHE* 1.3 71.6 + - - +
459B GLU* 5.4 0.2 - - - -
460B TYR* 4.1 15.5 + - + +
658B PRO* 3.6 55.4 - - + -
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Residues in contact with PHE 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B PHE* 4.0 17.7 - + + -
395B PHE 3.6 0.5 - - - +
396B LEU* 3.7 7.3 - - - +
397B ALA* 2.8 32.9 + - - +
399B PHE* 3.8 14.4 - + + -
404B GLN* 3.5 46.0 - - + -
405B PHE* 1.3 78.6 - - - +
407B ALA* 1.3 62.1 + - - +
408B ILE* 4.5 5.8 - - + -
445B PHE* 3.5 43.3 - + + -
457B VAL* 3.7 22.7 - - + -
458B MET 3.4 15.5 - - - +
459B GLU* 4.7 0.7 - - - -
460B TYR* 3.7 8.1 - - - -
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Residues in contact with ALA 407 (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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386B LEU* 4.1 7.0 - - + -
394B VAL* 3.9 15.5 - - + -
395B PHE 3.3 5.8 - - - -
406B PHE* 1.3 71.7 - - - +
408B ILE* 1.3 61.9 + - - +
409B LYS 4.1 0.4 - - - -
456B PHE 3.6 0.2 - - - +
458B MET* 2.8 39.1 + - + +
459B GLU 3.9 4.9 - - - +
460B TYR* 3.8 3.7 - - - +
1712B LG8 3.6 38.6 - - + +
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Residues in contact with ILE 408 (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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377B ILE* 4.9 7.0 - - + -
380B PHE* 3.8 35.7 - - + -
382B LEU* 4.8 7.0 - - + -
393B LYS 3.7 0.9 - - - +
394B VAL* 3.3 3.6 - - - -
395B PHE* 2.7 49.4 + - + +
397B ALA* 3.7 26.9 - - + -
406B PHE* 4.5 2.0 - - + -
407B ALA* 1.3 77.1 - - - +
409B LYS* 1.3 69.4 + - - +
410B ALA* 3.7 2.3 + - + +
448B PHE* 5.3 0.9 - - + -
455B PHE* 3.9 25.6 - - + -
456B PHE 3.4 8.5 - - - +
457B VAL* 3.9 21.3 - - + -
677B PHE* 6.4 0.2 - - + -
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Residues in contact with LYS 409 (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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390B SER 5.4 0.2 + - - -
391B PHE* 2.7 36.4 + - - +
393B LYS 3.2 9.2 - - - +
394B VAL* 4.1 11.3 - - + +
407B ALA 4.1 1.0 + - - -
408B ILE* 1.3 73.2 - - - +
410B ALA* 1.3 65.8 + - - +
411B LEU* 3.8 16.2 - - - +
428B GLU* 3.0 33.9 + - - +
455B PHE* 3.3 5.5 - - - -
456B PHE* 2.9 69.3 + - + -
458B MET* 4.9 1.7 - - + +
522B ASP* 5.5 0.4 + - - -
1712B LG8 3.7 27.1 - - + -
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Residues in contact with ALA 410 (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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393B LYS* 2.8 32.0 + - + +
395B PHE* 4.1 13.5 - - + -
408B ILE* 3.7 1.9 + - + +
409B LYS* 1.3 74.2 - - - +
411B LEU* 1.3 67.9 + - - +
454B LEU 3.4 4.0 - - - -
455B PHE* 3.8 12.8 - - + -
677B PHE* 3.5 35.9 - - + -
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Residues in contact with LEU 411 (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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391B PHE 4.4 0.9 - - - +
392B GLY* 3.9 22.9 - - - +
409B LYS* 3.8 28.3 - - - +
410B ALA* 1.3 81.2 - - - +
412B LYS* 1.3 61.5 + - - +
416B VAL* 4.0 22.7 - - + -
425B THR* 3.9 30.7 - - + +
428B GLU* 5.4 0.7 - - - +
453B ASN* 3.3 8.3 - - - +
454B LEU* 2.8 41.6 + - + -
456B PHE* 3.9 7.6 - - + -
677B PHE* 6.4 0.4 - - - -
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Residues in contact with LYS 412 (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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393B LYS* 4.9 13.3 - - - +
411B LEU* 1.3 71.0 - - - +
413B LYS* 1.3 59.6 + - - +
414B ASP* 4.2 0.2 - - + -
415B VAL* 3.2 29.6 + - + +
416B VAL* 3.0 29.9 + - - +
452B GLU 3.6 4.7 - - - -
453B ASN* 4.5 10.5 - - - +
677B PHE* 6.2 5.6 - - + -
680B ARG* 3.4 53.4 - - - +
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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