Contacts of the helix formed by residues 451 - 470 (chain B) in PDB entry 3E8R
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 SER 451 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B ASP* 2.6 30.3 + - - -
423B CYS* 3.8 13.0 - - - -
433B TYR* 3.3 38.6 - - - +
435B MET 5.9 0.2 - - - +
450B PHE* 1.3 76.6 - - - +
452B GLN* 1.3 62.9 + - - +
453B CYS* 3.3 2.8 + - - +
454B SER* 3.1 16.6 + - - -
455B LYS* 3.1 24.2 + - - +
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Residues in contact with GLN 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B ASN* 2.5 46.8 + - - +
422B GLU* 4.5 24.0 - - + +
423B CYS* 4.1 8.9 - - - -
433B TYR* 5.1 3.9 - - + +
451B SER* 1.3 74.0 - - - +
453B CYS* 1.3 57.3 + - - +
455B LYS* 3.3 15.2 + - - +
456B GLN* 3.0 30.3 + - - +
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Residues in contact with CYS 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B HIS 5.9 0.9 - - - +
416B ASP* 3.8 9.9 - - - +
417B PRO* 4.5 11.4 - - + -
422B GLU* 5.3 1.6 - - - -
423B CYS* 2.0 50.7 - - - -
451B SER* 3.2 4.7 - - - +
452B GLN* 1.3 78.7 - - - +
454B SER* 1.3 62.8 + - - +
456B GLN* 3.4 11.0 + - - +
457B SER* 3.2 25.2 + - - -
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Residues in contact with SER 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B TRP* 5.1 0.2 - - - -
413B ALA* 4.0 15.3 - - - +
414B GLU 4.4 2.6 + - - +
416B ASP* 3.5 2.3 + - - -
435B MET* 3.1 28.6 - - - +
450B PHE* 3.6 26.1 - - - -
451B SER* 3.1 21.3 + - - -
453B CYS* 1.3 75.0 - - - +
455B LYS* 1.3 58.5 + - - +
457B SER* 3.2 2.9 + - - -
458B ILE* 2.8 36.3 + - - +
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Residues in contact with LYS 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B THR* 3.7 19.1 - - + +
266B ALA* 3.5 23.7 + - - +
267B TRP* 3.7 37.8 - - + +
269B ASN* 3.3 21.1 + - - +
450B PHE* 3.9 15.8 + - + +
451B SER 3.1 25.0 + - - +
452B GLN* 3.6 23.6 - - - +
454B SER* 1.3 75.7 - - - +
456B GLN* 1.3 58.2 + - - +
459B TYR* 2.7 35.5 + - - +
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Residues in contact with GLN 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B TRP 5.1 0.9 - - - -
452B GLN 3.0 16.8 + - - +
453B CYS* 3.6 10.9 - - - +
455B LYS* 1.3 78.6 - - - +
457B SER* 1.3 65.2 + - - +
459B TYR* 3.7 7.4 - - - +
460B LYS* 3.4 31.1 + - - +
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Residues in contact with SER 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B ALA* 3.7 14.3 - - - +
359B ASN* 3.0 31.0 + - - -
412B GLY 3.9 19.1 - - - -
413B ALA* 4.0 9.0 - - - -
414B GLU* 4.7 6.2 + - - +
453B CYS 3.2 13.0 + - - -
454B SER* 3.2 6.2 + - - -
456B GLN* 1.3 78.6 - - - +
458B ILE* 1.3 62.3 + - - +
460B LYS* 3.2 15.9 - - - +
461B THR 3.3 0.2 + - - -
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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
----------------------------------------------------------
267B TRP* 3.4 42.6 - - + -
408B GLY 3.9 1.8 - - - +
411B PHE* 3.6 43.7 - - + +
413B ALA* 3.8 25.4 - - + +
450B PHE* 3.9 22.0 - - + -
454B SER 2.8 21.4 + - - +
457B SER* 1.3 70.2 - - - +
459B TYR* 1.3 55.7 + - - +
461B THR* 3.0 3.1 + - - -
462B ILE* 2.8 48.2 + - + +
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Residues in contact with TYR 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B TRP* 3.7 24.4 - - + +
268B ASP* 4.1 23.5 + - + +
272B PHE* 3.3 46.9 - + - -
455B LYS 2.7 22.7 + - - +
456B GLN* 3.7 8.1 - - - +
458B ILE* 1.3 73.0 - - - +
460B LYS* 1.3 63.3 + - + +
462B ILE* 4.6 2.0 - - - +
463B GLU* 3.1 31.2 + - + +
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Residues in contact with LYS 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B ASN* 4.1 21.8 + - + +
456B GLN* 3.4 24.0 + - + +
457B SER* 3.2 11.1 + - - +
459B TYR* 1.3 81.1 - - + +
461B THR* 1.3 64.6 + - - +
463B GLU* 3.6 4.9 + - - +
464B SER* 3.4 21.8 + - - -
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Residues in contact with THR 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B ASN* 2.8 25.9 + - - +
364B VAL* 3.8 15.0 - - + -
411B PHE* 2.6 35.6 + - + +
412B GLY* 3.6 1.4 - - - -
457B SER 3.3 1.1 + - - -
458B ILE* 3.0 6.6 + - - -
460B LYS* 1.3 76.9 - - - +
462B ILE* 1.3 56.7 + - + +
464B SER* 2.7 11.0 + - - -
465B LYS* 2.7 62.8 + - + +
470B PHE* 5.7 0.4 - - + -
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Residues in contact with ILE 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B TRP* 3.6 31.9 - - + +
272B PHE* 3.8 13.9 - - + -
275B TYR* 3.5 50.9 + - + +
411B PHE* 4.1 14.6 - - + -
458B ILE* 2.8 35.7 + - + +
459B TYR* 4.2 3.6 - - - +
461B THR* 1.3 74.7 - - + +
463B GLU* 1.3 63.8 + - - +
464B SER 3.1 0.9 + - - -
465B LYS* 4.5 1.8 - - - +
466B ALA* 3.4 24.8 + - + +
470B PHE* 4.2 15.0 - - + -
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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
----------------------------------------------------------
272B PHE* 5.7 4.3 - - + -
459B TYR* 3.1 28.5 + - + +
460B LYS* 3.9 5.8 - - - +
462B ILE* 1.3 77.9 - - - +
464B SER* 1.3 60.5 + - - +
467B GLN* 5.5 7.5 + - - +
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Residues in contact with SER 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B LYS 3.4 11.9 + - - -
461B THR* 2.7 14.7 + - - -
463B GLU* 1.3 77.7 - - - +
465B LYS* 1.3 64.0 + - - +
466B ALA 3.8 0.9 - - - -
467B GLN* 4.4 6.7 + - - +
468B GLU* 4.2 14.2 + - - +
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Residues in contact with LYS 465 (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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360B SER 5.3 1.4 + - - -
362B GLY 3.1 24.7 + - - -
363B GLY* 3.9 0.6 - - - -
364B VAL* 2.9 49.3 + - + +
365B CYS* 3.3 20.4 - - + -
410B ASN 4.7 1.2 + - - -
461B THR* 2.7 34.9 + - + +
464B SER* 1.3 76.7 - - - +
466B ALA* 1.3 63.7 + - - +
467B GLN 3.2 2.2 - - - -
468B GLU* 3.1 16.3 + - - +
469B CYS 2.9 20.6 + - - -
470B PHE* 3.8 3.7 + - + -
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Residues in contact with ALA 466 (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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222B LYS* 3.4 28.6 - - + +
275B TYR* 3.9 11.9 - - + +
462B ILE* 3.4 18.6 + - - +
465B LYS* 1.3 76.8 - - - +
467B GLN* 1.3 64.3 + - + +
470B PHE* 2.9 52.6 + - + +
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Residues in contact with GLN 467 (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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221B MET* 5.3 9.4 - - + -
222B LYS* 3.2 35.1 + - + +
462B ILE 5.0 0.4 + - - -
463B GLU 5.5 6.5 + - - +
464B SER 4.4 9.3 + - - +
465B LYS* 3.2 0.4 - - - +
466B ALA* 1.3 78.8 - - + +
468B GLU* 1.3 61.2 + - - +
470B PHE 5.3 0.2 - - - +
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Residues in contact with GLU 468 (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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365B CYS* 3.5 26.1 - - + +
366B PRO* 4.1 11.6 - - - +
367B LYS* 5.3 4.7 - - - +
464B SER 4.2 6.7 + - - +
465B LYS* 3.1 26.1 + - - +
467B GLN* 1.3 82.1 - - - +
469B CYS* 1.3 59.8 + - + +
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Residues in contact with CYS 469 (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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224B THR 4.6 0.5 - - - +
226B LYS* 5.5 0.7 + - - +
332B VAL 5.8 0.2 - - - -
333B CYS* 3.5 31.2 + - + +
365B CYS* 2.0 59.5 - - + -
366B PRO* 4.2 10.3 - - + -
465B LYS 2.9 7.9 + - - -
466B ALA 3.4 0.2 + - - -
468B GLU* 1.3 76.1 - - + +
470B PHE* 1.3 68.2 + - - +
471B GLN* 3.8 12.2 + - - +
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Residues in contact with PHE 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B LYS* 3.2 34.9 - - - +
223B ASN 3.9 9.4 - - - -
224B THR 3.2 9.4 - - - +
225B CYS* 3.8 8.3 - - + -
275B TYR* 3.8 25.4 - + + -
276B GLY 5.1 0.4 - - - -
333B CYS* 3.7 27.6 - - - -
364B VAL* 4.1 18.6 - - + -
411B PHE* 3.7 34.3 - + - -
461B THR* 5.7 0.2 - - + -
462B ILE* 4.2 11.2 - - + -
465B LYS* 4.4 5.2 - - + -
466B ALA* 2.9 36.8 + - + +
467B GLN 5.3 0.2 - - - +
469B CYS* 1.3 85.3 - - - +
471B GLN* 1.3 62.8 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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