Contacts of the strand formed by residues 453 - 459 (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 ASN 453 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411B LEU 3.3 9.6 - - - +
412B LYS* 4.5 11.3 - - - +
413B LYS* 3.7 4.0 - - - -
449B GLN* 3.3 7.8 - - - +
450B THR* 2.9 45.8 + - - +
451B LYS 3.8 0.6 - - - -
452B GLU* 1.3 87.9 - - - +
454B LEU* 1.3 63.2 + - - +
455B PHE* 3.5 33.0 - - + -
677B PHE* 3.7 19.5 - - + +
678B ALA* 3.3 29.6 + - - +
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Residues in contact with LEU 454 (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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409B LYS 3.6 0.9 - - - +
410B ALA* 3.4 5.5 - - - -
411B LEU* 2.8 49.3 + - + +
413B LYS* 3.7 31.2 - - + -
416B VAL* 4.4 4.5 - - + -
425B THR* 3.8 19.5 - - + -
448B PHE 3.9 1.6 - - - -
449B GLN* 3.8 4.7 - - + -
453B ASN* 1.3 73.9 - - - +
455B PHE* 1.3 62.2 + - - +
456B PHE* 4.5 4.1 - - + -
691B PHE* 3.5 40.8 - - + -
694B PHE* 3.7 38.1 - - + -
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Residues in contact with PHE 455 (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* 3.7 31.0 - - + -
408B ILE* 3.9 17.9 - - + -
409B LYS 3.3 1.8 - - - +
410B ALA* 3.8 13.2 - - + -
447B THR* 3.1 10.1 - - - -
448B PHE* 2.9 77.6 + + + +
450B THR* 3.9 20.0 - - + -
453B ASN* 3.5 35.7 - - + -
454B LEU* 1.3 78.3 - - - +
456B PHE* 1.3 63.2 - - - +
457B VAL 4.1 0.7 - - - -
677B PHE* 3.8 30.3 - + + -
694B PHE* 3.5 1.4 - - - -
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Residues in contact with PHE 456 (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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407B ALA 3.6 0.3 - - - +
408B ILE* 3.4 5.6 - - - -
409B LYS* 2.9 74.3 + - + -
411B LEU* 3.9 13.2 - - + -
425B THR* 4.1 15.9 - - + -
428B GLU* 4.3 7.4 - - + -
429B LYS* 4.2 22.4 - - - -
432B LEU* 3.7 23.3 - - + -
444B MET* 4.8 0.7 - - + -
446B CYS 3.7 4.0 - - - -
447B THR* 3.8 13.5 - - + -
454B LEU* 4.5 4.0 - - + -
455B PHE* 1.3 78.3 - - - +
457B VAL* 1.3 62.7 + - - +
458B MET* 3.5 16.7 + - - +
694B PHE* 3.6 31.0 - + - -
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Residues in contact with VAL 457 (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* 4.1 15.9 - - + -
406B PHE* 3.7 36.6 - - + -
407B ALA 4.0 2.0 - - - -
408B ILE* 3.9 19.3 - - + -
444B MET* 3.6 3.1 - - - +
445B PHE* 2.8 36.7 + - + +
446B CYS* 2.7 32.0 + - - +
448B PHE* 3.6 30.3 - - + -
456B PHE* 1.3 72.3 - - - +
458B MET* 1.3 57.8 + - - +
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Residues in contact with MET 458 (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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406B PHE* 3.4 10.2 - - - +
407B ALA* 2.8 41.7 + - + +
409B LYS 4.9 1.8 - - - +
432B LEU* 3.6 26.7 - - + -
442B THR* 3.2 35.7 - - + -
443B HIS 3.5 13.7 - - - +
444B MET* 3.7 24.9 - - - -
445B PHE* 4.0 4.5 - - - -
456B PHE* 3.8 15.7 - - + +
457B VAL* 1.3 74.7 - - - +
459B GLU* 1.3 67.6 + - - +
1712B LG8 3.6 31.0 - - + +
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Residues in contact with GLU 459 (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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405B PHE 5.4 0.4 - - - -
406B PHE* 4.8 1.3 - - - -
407B ALA* 3.9 0.6 - - - +
441B LEU 3.7 0.3 - - - +
442B THR* 3.7 2.5 - - - +
443B HIS* 2.9 47.7 + - + +
445B PHE* 3.5 24.6 - - + -
458B MET* 1.3 70.3 - - + +
460B TYR* 1.3 60.3 + - - +
461B LEU* 3.8 23.0 - - + +
513B ASP* 5.2 0.3 - - - +
519B LYS* 2.9 37.7 + - - -
1712B LG8 2.8 25.5 + - - -
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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