Contacts of the helix formed by residues 447 - 461 (chain B) in PDB entry 1JEQ
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 447 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445B ALA 5.1 2.7 - - - +
446B PRO* 1.3 76.5 - - - +
448B GLU* 1.3 59.1 + - - +
449B ALA* 3.2 11.8 + - - +
450B GLN* 2.9 44.6 + - + +
451B LEU* 2.9 27.9 + - - +
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Residues in contact with GLU 448 (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 THR* 1.3 74.2 - - - +
449B ALA* 1.3 63.7 + - - +
451B LEU* 4.3 16.8 - - - +
452B ASN* 2.6 65.1 + - - +
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Residues in contact with ALA 449 (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 THR* 3.2 9.8 + - - +
448B GLU* 1.3 81.2 - - - +
450B GLN* 1.3 57.6 + - + +
452B ASN* 4.7 2.4 - - - +
453B ALA* 3.3 13.9 + - - +
536B LEU* 3.2 36.3 - - + +
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Residues in contact with GLN 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A THR* 3.6 24.1 - - - +
445B ALA 4.6 0.7 - - - +
446B PRO* 3.1 14.0 - - + +
447B THR* 2.9 47.6 + - + +
449B ALA* 1.3 78.9 - - + +
451B LEU* 1.3 66.1 + - - +
453B ALA* 3.1 15.1 - - - +
454B VAL* 3.2 7.3 + - - +
536B LEU* 3.1 30.7 + - + +
537B PHE* 3.3 37.4 - - + +
538B PRO* 4.5 5.9 - - - +
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Residues in contact with LEU 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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384A ALA* 4.1 19.7 - - + +
387A ILE* 4.2 25.6 - - + -
388A LYS* 3.3 23.2 - - - +
391A GLU* 5.8 2.0 - - - +
446B PRO* 3.7 30.1 - - + +
447B THR 2.9 21.8 + - - +
448B GLU* 3.6 18.6 + - - +
449B ALA 3.5 0.4 - - - -
450B GLN* 1.3 73.6 - - - +
452B ASN* 1.3 64.4 + - - +
454B VAL* 3.0 6.7 + - - +
455B ASP 2.8 23.9 + - - -
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Residues in contact with ASN 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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388A LYS* 4.5 8.8 + - - -
448B GLU* 2.6 51.7 + - - +
449B ALA* 4.7 3.0 - - - +
451B LEU* 1.3 75.8 - - - +
453B ALA* 1.3 57.2 + - - +
455B ASP* 3.5 11.0 - - + +
456B ALA* 2.9 29.8 + - - +
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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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449B ALA 3.3 16.4 + - - +
450B GLN* 3.1 13.5 - - - +
451B LEU 3.0 0.4 - - - -
452B ASN* 1.3 79.2 - - - +
454B VAL* 1.3 59.8 + - - +
456B ALA* 3.2 19.5 - - - +
457B LEU 3.2 5.0 + - - -
529B PRO 5.1 1.2 - - - +
532B LYS* 5.4 5.5 - - + +
533B ILE* 3.5 20.6 - - + +
536B LEU* 3.6 20.2 - - + -
537B PHE* 4.1 9.4 - - + -
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Residues in contact with VAL 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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381A LEU* 4.4 10.8 - - + -
384A ALA* 3.8 25.1 - - + -
385A LEU* 3.9 21.3 - - + +
388A LYS* 3.6 26.5 - - + -
450B GLN 3.2 6.5 + - - +
451B LEU 3.0 8.1 + - - +
453B ALA* 1.3 71.8 - - - +
455B ASP* 1.3 67.5 + - - +
456B ALA 3.0 2.0 - - - -
457B LEU* 2.9 3.1 + - + +
458B ILE* 2.9 33.8 + - + +
533B ILE* 3.7 17.5 - - + -
537B PHE* 3.8 11.0 - - + -
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Residues in contact with ASP 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A LYS* 3.4 39.5 + - - +
391A GLU* 4.4 2.6 - - - +
392A LYS* 2.6 45.7 + - - +
451B LEU 2.8 5.8 + - - +
452B ASN* 3.5 15.7 - - + +
454B VAL* 1.3 77.6 - - - +
456B ALA* 1.3 60.4 + - - +
458B ILE* 4.8 0.4 - - - -
459B ASP* 3.0 20.3 + - - +
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Residues in contact with ALA 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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452B ASN 2.9 13.5 + - - +
453B ALA* 3.2 13.5 - - - +
454B VAL 3.0 0.2 - - - -
455B ASP* 1.3 76.5 + - - +
457B LEU* 1.3 66.4 + - - +
459B ASP* 3.3 9.1 + - - +
460B SER* 3.1 22.3 + - - -
529B PRO* 4.4 15.1 - - + +
532B LYS* 6.2 3.6 - - + -
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Residues in contact with LEU 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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263A LEU* 4.2 16.6 - - + -
350A PHE* 4.4 9.6 - - + -
385A LEU* 5.3 5.8 - - + -
453B ALA 3.2 1.8 + - - -
454B VAL 2.9 6.1 + - - +
456B ALA* 1.3 76.7 - - - +
458B ILE* 1.3 67.3 + - - +
460B SER* 2.6 24.0 + - - +
461B MET* 2.8 40.3 + - + +
526B SER 4.5 0.7 - - - +
529B PRO* 3.9 10.9 - - + +
530B LEU* 3.1 40.4 - - + +
533B ILE* 3.3 33.2 - - + -
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Residues in contact with ILE 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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350A PHE* 3.5 40.7 - - + +
385A LEU* 4.4 1.8 - - + -
388A LYS* 3.4 36.1 - - + +
389A CYS* 4.0 21.8 - - - -
392A LYS* 3.6 25.4 - - + +
394A VAL* 3.9 13.7 - - + -
454B VAL* 2.9 27.4 + - + +
457B LEU* 1.3 73.7 - - + +
459B ASP* 1.3 64.9 + - - +
461B MET 3.3 2.3 + - - -
462B SER* 3.3 17.8 + - - -
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Residues in contact with ASP 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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392A LYS* 2.9 29.0 + - - +
455B ASP* 3.0 16.2 + - - +
456B ALA* 3.3 11.8 + - - +
457B LEU 3.1 0.6 - - - -
458B ILE* 1.3 81.9 - - - +
460B SER* 1.3 61.9 + - - +
462B SER* 3.4 18.9 + - - -
525B LYS* 5.8 0.5 - - - +
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Residues in contact with SER 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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456B ALA 3.1 6.9 + - - -
457B LEU* 2.6 31.6 + - - +
459B ASP* 1.3 79.7 - - - +
461B MET* 1.3 59.4 + - - +
462B SER* 3.3 5.2 + - - +
522B VAL* 4.3 8.1 - - - +
525B LYS* 3.2 55.0 + - - +
526B SER* 4.0 0.5 - - - -
529B PRO* 3.5 14.6 - - - +
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Residues in contact with MET 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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263A LEU 4.8 4.3 - - - +
347A LEU* 3.2 37.9 - - + +
348A MET 5.0 1.1 - - - -
349A GLY* 3.2 16.5 - - - -
350A PHE* 2.8 37.4 + - + -
457B LEU* 2.8 40.5 + - + +
458B ILE 3.6 3.8 - - - -
459B ASP 3.3 0.4 - - - -
460B SER* 1.3 75.2 - - - +
462B SER* 1.3 62.5 + - - +
463B LEU* 3.4 1.9 + - - +
522B VAL* 4.0 15.9 - - + -
526B SER* 3.7 30.3 - - - -
530B LEU* 4.2 8.7 - - + -
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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