Contacts of the helix formed by residues 455 - 469 (chain F) in PDB entry 1ZMD
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 LEU 455 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427E GLU* 2.8 27.2 + - + +
388F PHE* 3.9 5.5 - - + -
391F ASN* 3.5 21.3 - - - +
393F ARG* 4.0 10.7 - - + +
394F ALA* 3.6 27.1 - - + +
397F ASN* 5.9 0.9 - - - +
423F PRO* 3.5 38.8 - - + +
424F GLY* 4.2 7.6 - - - +
428F MET* 3.3 22.8 - - + +
454F THR* 1.3 72.7 - - - +
456F SER* 1.3 63.3 + - - +
458F ALA* 3.0 20.4 + - - +
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Residues in contact with SER 456 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427E GLU* 2.9 13.0 + - - -
430E ASN* 2.8 34.4 + - - -
428F MET* 4.1 12.8 - - - -
431F GLU* 4.0 7.0 - - - -
450F HIS* 3.2 18.4 - - - +
454F THR* 2.8 17.9 + - - -
455F LEU* 1.3 77.4 - - - +
457F GLU* 1.3 56.2 + - - +
459F PHE* 2.9 23.5 + - - +
460F ARG 3.0 9.5 + - - -
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Residues in contact with GLU 457 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329E HIS* 5.3 0.5 - - - +
332E GLU* 4.4 8.7 - - - +
386F PHE* 5.4 0.7 - - - -
391F ASN* 3.8 6.9 + - - +
392F SER* 4.6 2.9 + - - -
450F HIS* 4.3 12.3 - - + +
451F ALA 3.5 21.0 - - - +
452F HIS* 2.8 40.7 + - - +
453F PRO* 3.2 2.1 - - - +
454F THR* 3.0 31.3 + - - +
455F LEU 3.0 0.2 - - - -
456F SER* 1.3 76.3 + - - +
458F ALA* 1.3 60.1 + - - +
460F ARG* 3.1 12.9 + - + +
461F GLU* 2.8 37.3 + - + +
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Residues in contact with ALA 458 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386F PHE* 3.7 34.0 - - + +
388F PHE* 3.7 26.9 - - + -
391F ASN* 3.6 7.5 - - + +
404F VAL* 3.9 11.3 - - + +
455F LEU 3.0 12.9 + - - +
457F GLU* 1.3 77.9 - - - +
459F PHE* 1.3 62.2 + - - +
462F ALA* 2.9 26.7 + - - +
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Residues in contact with PHE 459 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434E LEU* 6.0 0.2 - - + -
404F VAL* 4.0 22.2 - - + +
406F ILE* 3.7 13.7 - - + -
415F VAL* 6.2 1.1 - - + -
418F ALA* 4.1 3.8 - - + -
420F ILE* 5.1 3.6 - - + -
428F MET* 3.8 27.8 - - + -
431F GLU* 3.4 41.3 - - + -
432F ALA* 3.8 35.7 - - + -
435F ALA* 5.0 0.9 - - + -
445F ILE* 3.5 29.2 - - + -
450F HIS* 4.3 0.7 - - - -
455F LEU 3.9 0.6 + - - -
456F SER* 2.9 11.0 + - - +
458F ALA* 1.3 80.8 - - - +
460F ARG* 1.3 62.2 + - - +
462F ALA* 3.9 1.6 - - - +
463F ASN* 3.0 44.3 + - - -
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Residues in contact with ARG 460 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329E HIS* 5.2 1.4 + - - +
332E GLU* 5.9 1.4 + - - +
333E ASP* 2.8 38.9 + - - +
336E ILE* 5.6 7.1 - - - +
445F ILE* 4.5 6.5 - - - -
446F ALA* 2.9 31.9 + - - +
447F ARG* 4.0 5.1 + - - +
448F VAL 3.0 17.4 + - - -
449F CYS* 3.7 1.4 - - - +
450F HIS* 3.3 59.3 + - + +
456F SER 3.0 8.1 + - - +
457F GLU* 3.3 14.5 + - - +
459F PHE* 1.3 78.5 - - - +
461F GLU* 1.3 61.1 + - + +
463F ASN* 3.3 5.5 + - - +
464F LEU* 3.0 25.8 + - + +
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Residues in contact with GLU 461 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386F PHE* 3.2 34.3 - - + -
457F GLU* 2.8 25.7 + - + +
458F ALA 3.9 0.2 - - - +
460F ARG* 1.3 75.2 - - + +
462F ALA* 1.3 59.7 + - - +
464F LEU* 3.1 15.7 + - - +
465F ALA* 2.8 29.8 + - - +
471F SER* 3.1 10.7 - - - -
472F ILE* 2.7 29.9 + - - +
473F ASN* 2.8 42.8 + - - +
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Residues in contact with ALA 462 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384F GLY* 3.6 16.5 - - - +
385F LYS 4.3 4.3 - - - -
386F PHE* 3.8 11.8 - - + +
404F VAL* 3.6 37.2 - - + +
406F ILE* 3.8 7.0 - - + +
458F ALA 2.9 18.2 + - - +
459F PHE 3.4 0.9 + - - +
461F GLU* 1.3 76.5 - - - +
463F ASN* 1.3 57.8 + - - +
465F ALA* 3.6 1.1 + - - -
466F ALA* 3.1 26.7 + - - +
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Residues in contact with ASN 463 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406F ILE* 3.4 25.3 - - - +
415F VAL* 3.6 1.6 - - - +
442F CYS* 3.4 28.0 - - - +
445F ILE* 3.2 41.6 - - + +
446F ALA 4.2 0.7 - - - +
459F PHE* 3.0 45.5 + - - -
460F ARG 3.6 8.1 - - - +
461F GLU 3.2 0.4 - - - -
462F ALA* 1.3 74.5 - - - +
464F LEU* 1.3 61.6 + - - +
466F ALA* 3.4 1.2 + - - -
467F SER* 2.9 31.7 + - - -
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Residues in contact with LEU 464 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E LYS* 4.2 13.7 - - - +
336E ILE* 5.6 3.8 - - + -
446F ALA* 3.6 22.6 - - + +
460F ARG* 3.0 15.2 + - + +
461F GLU* 3.1 29.1 + - - +
463F ASN* 1.3 76.5 - - - +
465F ALA* 1.3 54.7 + - - +
467F SER* 3.2 2.2 + - - -
468F PHE* 2.7 54.1 + - + +
470F LYS 3.4 11.4 - - - +
471F SER* 4.1 0.4 - - - -
472F ILE* 3.8 28.5 - - + +
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Residues in contact with ALA 465 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383F VAL 4.8 1.9 - - - +
384F GLY* 4.1 13.0 - - - -
385F LYS 4.2 15.0 - - - +
461F GLU 2.8 19.2 + - - +
462F ALA 3.8 4.7 - - - +
464F LEU* 1.3 73.4 - - - +
466F ALA* 1.3 57.2 + - - +
469F GLY* 2.7 32.4 + - - +
470F LYS* 3.8 14.3 + - - +
471F SER* 4.0 13.9 - - - +
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Residues in contact with ALA 466 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382F LYS* 3.0 36.7 + - + +
383F VAL 4.3 5.6 - - - -
384F GLY* 3.6 21.9 - - - +
406F ILE* 4.0 10.1 - - + +
408F GLY 5.2 0.4 - - - +
413F ASP* 4.4 0.2 - - - -
442F CYS* 4.0 17.9 - - - -
462F ALA 3.1 18.3 + - - +
463F ASN 3.8 4.3 - - - +
464F LEU 3.3 0.2 - - - -
465F ALA* 1.3 77.5 - - - +
467F SER* 1.3 60.0 + - - +
469F GLY* 4.7 0.5 + - - -
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Residues in contact with SER 467 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382F LYS* 3.9 7.8 + - - -
413F ASP* 2.7 35.5 + - - -
442F CYS* 3.7 1.1 - - - +
443F GLU* 3.2 27.7 + - - +
446F ALA* 5.3 1.1 - - - -
463F ASN 2.9 17.3 + - - -
464F LEU* 3.9 3.8 - - - -
466F ALA* 1.3 81.2 - - - +
468F PHE* 1.3 61.0 + - - +
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Residues in contact with PHE 468 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E LYS* 3.4 28.9 - - - -
27E GLN* 3.8 37.2 - - + -
28E LEU* 4.1 20.2 - - + -
464F LEU* 2.7 31.4 + - + +
467F SER* 1.3 75.3 - - - +
469F GLY* 1.3 56.1 + - - +
470F LYS* 3.7 24.4 - - + +
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Residues in contact with GLY 469 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465F ALA* 2.7 29.5 + - - +
466F ALA 4.5 0.8 + - - -
467F SER 3.6 0.6 - - - -
468F PHE* 1.3 73.6 - - - +
470F LYS* 1.3 64.6 + - - +
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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