Contacts of the helix formed by residues 449 - 463 (chain B) in PDB entry 2JGN
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 THR 449 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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447B VAL* 3.8 1.5 - - - +
448B GLU* 1.3 104.5 - - + +
450B LYS* 1.3 59.1 + - - +
451B LYS* 3.6 8.2 + - - +
452B GLY* 2.9 22.4 + - - -
453B ALA 2.9 24.4 + - - -
497B THR* 3.5 11.6 - - - +
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Residues in contact with LYS 450 (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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449B THR* 1.3 71.5 - - - +
451B LYS* 1.3 63.5 + - - +
453B ALA* 3.3 2.3 + - - +
454B ASP* 3.1 29.7 + - - +
471B HIS* 3.6 33.4 + - + +
472B GLY* 3.8 11.9 - - - +
473B ASP* 3.6 42.6 + - - +
497B THR* 3.9 3.8 - - + +
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Residues in contact with LYS 451 (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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449B THR* 3.3 8.0 + - - +
450B LYS* 1.3 78.6 - - - +
452B GLY* 1.3 56.1 + - - +
454B ASP* 3.7 8.1 - - + +
455B SER* 3.1 36.7 + - - -
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Residues in contact with GLY 452 (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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427B ARG* 5.2 0.6 + - - -
447B VAL* 4.0 10.8 - - - +
449B THR* 2.9 20.6 + - - -
451B LYS* 1.3 74.1 - - - +
453B ALA* 1.3 63.8 + - - +
455B SER* 4.0 3.3 - - - -
456B LEU* 3.0 28.1 + - - +
516B ASP* 6.1 0.2 - - - -
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Residues in contact with ALA 453 (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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447B VAL* 3.5 24.3 - - + +
449B THR 2.9 13.3 + - - +
450B LYS 3.3 6.7 + - - +
452B GLY* 1.3 72.3 - - - +
454B ASP* 1.3 58.9 + - - +
457B GLU* 3.0 29.5 + - - +
469B SER* 4.5 5.6 - - - -
470B ILE 4.7 5.2 - - - +
471B HIS* 3.9 17.3 - - + +
495B VAL* 3.8 18.1 - - + +
497B THR* 4.1 10.1 - - + +
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Residues in contact with ASP 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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450B LYS* 3.1 16.3 + - - +
451B LYS* 3.7 7.8 - - + +
453B ALA* 1.3 75.7 - - - +
455B SER* 1.3 57.1 + - - +
457B GLU* 3.4 6.1 + - - +
458B ASP* 3.1 36.6 + - - +
471B HIS* 3.0 19.1 + - - -
474B ARG* 2.6 39.0 + - - +
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Residues in contact with SER 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B ARG* 2.4 33.7 + - - -
451B LYS* 3.1 21.3 + - - -
452B GLY* 4.0 4.0 - - - -
454B ASP* 1.3 77.6 - - - +
456B LEU* 1.3 60.1 + - - +
458B ASP* 3.4 8.0 + - - +
459B PHE* 2.9 26.3 + - - +
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Residues in contact with LEU 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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427B ARG* 3.7 13.5 - - + +
430B LEU* 3.9 22.4 - - + -
445B VAL* 4.0 20.2 - - + -
447B VAL* 3.6 26.9 - - + -
452B GLY 3.0 18.6 + - - +
453B ALA 3.9 2.9 - - - +
455B SER* 1.3 75.1 - - - +
457B GLU* 1.3 60.3 + - - +
459B PHE* 3.1 20.6 + - + +
460B LEU* 2.8 35.0 + - + +
495B VAL* 4.3 10.5 - - + -
515B PHE* 4.0 26.5 - - + -
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Residues in contact with GLU 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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453B ALA 3.0 17.9 + - - +
454B ASP* 3.8 5.9 - - - +
456B LEU* 1.3 76.4 - - - +
458B ASP* 1.3 65.3 + - - +
461B TYR* 2.8 35.6 + - + +
467B CYS* 3.7 26.5 - - - +
468B THR* 3.7 17.9 + - - -
469B SER* 2.7 35.3 + - - -
474B ARG* 3.5 11.8 + - - -
495B VAL* 4.6 9.3 - - + +
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Residues in contact with ASP 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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454B ASP* 3.1 22.2 + - - +
455B SER* 3.8 7.2 - - - +
456B LEU 3.2 0.2 - - - -
457B GLU* 1.3 84.0 - - - +
459B PHE* 1.3 55.7 + - - +
461B TYR* 3.2 13.9 + - - +
462B HIS* 2.9 44.2 + - + +
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Residues in contact with PHE 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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427B ARG* 3.2 68.9 - - + +
428B SER* 5.4 0.4 - - - -
430B LEU* 5.4 0.9 - - + -
431B LEU* 3.5 44.4 - - + -
455B SER 2.9 8.6 + - - +
456B LEU* 3.2 19.5 - - + +
458B ASP* 1.3 77.2 - - - +
460B LEU* 1.3 63.3 + - + +
462B HIS* 3.4 6.4 + - + +
463B GLU* 3.1 46.9 + - + +
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Residues in contact with LEU 460 (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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430B LEU* 4.1 21.5 - - + -
431B LEU* 3.8 21.1 - - + -
434B LEU* 3.6 26.0 - - + -
445B VAL* 5.2 1.3 - - + -
456B LEU* 2.8 21.7 + - + +
459B PHE* 1.3 76.0 - - + +
461B TYR* 1.3 62.4 - - - +
463B GLU* 3.3 7.5 + - - +
464B GLY 3.4 0.5 + - - -
465B TYR* 2.9 38.5 + - + +
467B CYS* 3.8 14.4 - - - -
493B ILE* 3.9 31.0 - - + -
495B VAL* 4.1 18.6 - - + -
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Residues in contact with TYR 461 (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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457B GLU* 2.8 22.0 + - + +
458B ASP* 3.6 14.8 - - + +
460B LEU* 1.3 74.4 - - - +
462B HIS* 1.3 67.2 + + - +
464B GLY* 3.4 12.2 + - - -
465B TYR 3.6 16.1 + - - +
466B ALA* 5.8 1.3 - - - -
467B CYS* 4.0 7.1 - - - -
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Residues in contact with HIS 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B ASP* 2.9 29.6 + - + +
459B PHE* 3.5 8.5 - - + +
461B TYR* 1.3 81.0 - + - +
463B GLU* 1.3 62.3 + - + +
464B GLY* 3.1 5.4 + - - -
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Residues in contact with GLU 463 (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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431B LEU* 3.7 42.1 - - + +
459B PHE* 3.1 34.9 + - + +
460B LEU 3.9 5.2 - - - +
461B TYR 3.3 0.8 - - - -
462B HIS* 1.3 77.7 - - - +
464B GLY* 1.3 56.7 + - - +
465B TYR* 3.6 14.6 - - + -
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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