Contacts of the helix formed by residues 455 - 469 (chain B) in PDB entry 1ZMC
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427A GLU* 2.8 26.4 + - + +
388B PHE* 4.2 4.0 - - + -
391B ASN* 3.6 19.1 - - - +
393B ARG* 3.9 12.3 - - + +
394B ALA* 3.8 18.2 - - + +
397B ASN* 5.1 5.8 - - - +
423B PRO* 3.5 48.7 - - + +
424B GLY* 3.9 9.6 - - - +
428B MET* 3.4 18.9 - - + +
454B THR* 1.3 67.3 - - - +
456B SER* 1.3 53.2 + - - +
457B GLU 2.8 5.8 + - - -
458B ALA* 2.7 35.0 + - - +
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Residues in contact with SER 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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427A GLU* 2.9 13.4 + - - -
430A ASN* 2.9 35.7 + - - -
428B MET* 4.0 12.3 - - - +
431B GLU* 3.9 7.0 - - - -
450B HIS* 3.0 22.0 - - - +
454B THR* 2.8 17.5 + - - -
455B LEU* 1.3 75.2 - - - +
457B GLU* 1.3 55.5 + - - +
458B ALA 3.1 0.4 - - - -
459B PHE* 3.1 10.8 + - - +
460B ARG 2.9 22.9 + - - -
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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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329A HIS* 5.3 0.7 - - - +
332A GLU* 4.1 9.2 - - - +
386B PHE* 5.3 0.4 - - - -
391B ASN* 3.6 9.5 + - - +
392B SER* 4.7 2.1 - - - -
450B HIS* 4.2 14.1 - - + +
451B ALA 3.5 20.8 - - - +
452B HIS* 2.9 39.0 + - - +
453B PRO* 3.3 2.4 - - - +
454B THR* 3.1 30.4 + - - +
455B LEU 2.8 1.0 + - - -
456B SER* 1.3 79.3 + - - +
458B ALA* 1.3 56.7 + - - +
460B ARG* 3.7 12.2 + - + +
461B GLU* 2.9 35.9 + - + +
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Residues in contact with ALA 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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386B PHE* 3.6 30.8 - - + +
388B PHE* 3.5 29.6 - - + -
391B ASN* 3.6 6.5 - - - +
404B VAL* 3.6 12.9 - - + +
455B LEU 2.7 12.1 + - - +
457B GLU* 1.3 79.8 - - - +
459B PHE* 1.3 57.7 + - - +
461B GLU 3.5 0.3 + - - -
462B ALA* 2.9 30.0 + - - +
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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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404B VAL* 3.8 20.8 - - + +
406B ILE* 3.7 20.4 - - + -
415B VAL* 6.0 1.3 - - + -
418B ALA* 4.0 5.4 - - + -
420B ILE* 4.7 7.2 - - + -
428B MET* 3.8 27.4 - - + -
431B GLU* 3.4 40.4 - - + -
432B ALA* 3.8 34.8 - - + -
445B ILE* 3.7 21.1 - - + -
450B HIS* 4.5 0.7 - - - -
455B LEU 3.9 0.4 + - - -
456B SER* 3.1 10.2 + - - +
458B ALA* 1.3 77.4 - - - +
460B ARG* 1.3 66.8 + - - +
462B ALA* 3.3 2.6 + - - +
463B ASN* 2.9 43.1 + - - -
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Residues in contact with ARG 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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329A HIS* 5.2 1.0 + - - +
332A GLU* 5.9 0.8 + - - -
333A ASP* 3.0 41.9 + - - +
336A ILE* 5.6 7.6 - - - +
445B ILE* 3.9 16.8 - - - +
446B ALA* 2.8 27.0 + - - +
447B ARG* 3.9 4.4 - - - +
448B VAL 3.0 13.7 + - - -
449B CYS* 3.6 0.2 - - - +
450B HIS* 3.2 59.1 + - + +
456B SER 2.9 12.3 + - - +
457B GLU* 3.7 12.2 + - - +
459B PHE* 1.3 79.7 - - - +
461B GLU* 1.3 59.3 + - - +
463B ASN* 3.3 5.2 + - - +
464B LEU* 3.1 25.8 + - + +
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Residues in contact with GLU 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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386B PHE* 3.4 27.7 - - + -
457B GLU* 2.9 23.9 + - + +
460B ARG* 1.3 76.8 - - + +
462B ALA* 1.3 61.6 + - - +
464B LEU* 3.2 13.9 + - - +
465B ALA 2.9 23.6 + - - -
471B SER* 3.1 18.6 + - - +
472B ILE* 2.8 30.2 + - - +
473B ASN* 2.9 46.4 + - - +
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Residues in contact with ALA 462 (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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384B GLY* 3.4 15.2 - - - +
386B PHE* 3.8 9.4 - - + +
404B VAL* 3.4 39.0 - - + +
406B ILE* 3.6 12.4 - - + +
458B ALA 2.9 19.0 + - - +
459B PHE 3.3 1.5 + - - +
461B GLU* 1.3 76.1 - - - +
463B ASN* 1.3 58.1 + - - +
465B ALA* 3.4 4.8 + - - -
466B ALA* 3.0 23.7 + - - +
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Residues in contact with ASN 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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406B ILE* 3.6 30.4 - - - +
415B VAL* 3.7 2.6 - - - +
442B CYS* 3.2 44.5 - - - +
445B ILE* 3.4 33.7 - - + +
446B ALA 4.3 0.4 - - - +
459B PHE* 2.9 33.7 + - - -
460B ARG 3.4 9.0 - - - +
462B ALA* 1.3 75.3 - - - +
464B LEU* 1.3 56.7 + - - +
466B ALA* 3.2 1.8 + - - -
467B SER* 2.8 32.2 + - - -
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Residues in contact with LEU 464 (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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24A LYS* 4.1 16.6 - - - +
27A GLN* 6.0 0.2 - - - +
336A ILE* 5.8 3.8 - - + -
446B ALA* 3.8 24.6 - - + +
460B ARG* 3.1 14.3 + - + +
461B GLU* 3.5 27.8 - - - +
463B ASN* 1.3 74.7 - - - +
465B ALA* 1.3 65.5 + - - +
467B SER* 4.6 2.7 - - - -
468B PHE* 2.8 42.9 + - + +
469B GLY 3.6 0.2 + - - -
470B LYS 3.4 14.8 - - - +
471B SER* 4.1 1.3 - - - -
472B ILE* 4.1 21.3 - - + -
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Residues in contact with ALA 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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383B VAL 4.7 2.9 - - - +
384B GLY* 3.8 12.6 - - - -
385B LYS 4.1 10.5 - - - +
461B GLU 2.9 7.7 + - - +
462B ALA 3.5 9.2 - - - +
464B LEU* 1.3 75.4 - - - +
466B ALA* 1.3 58.8 + - - +
469B GLY* 2.7 33.6 + - - +
470B LYS* 3.8 14.3 + - - +
471B SER* 3.5 21.5 - - - +
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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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382B LYS* 3.2 32.3 + - - +
383B VAL 4.2 6.1 - - - -
384B GLY* 3.5 20.1 - - - +
406B ILE* 3.9 10.8 - - + +
408B GLY 5.0 0.7 - - - +
442B CYS* 3.7 20.0 - - - -
462B ALA 3.0 14.5 + - - +
463B ASN 3.2 7.4 + - - +
465B ALA* 1.3 79.3 - - - +
467B SER* 1.3 62.5 + - - +
469B GLY* 4.4 1.0 + - - -
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Residues in contact with SER 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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382B LYS* 3.6 9.2 + - - +
413B ASP* 2.9 34.2 + - - -
442B CYS* 3.7 0.9 - - - +
443B GLU* 3.2 28.4 + - - +
446B ALA* 5.4 0.7 - - - -
463B ASN 2.8 20.4 + - - -
464B LEU* 4.0 4.9 - - - -
466B ALA* 1.3 77.5 - - - +
468B PHE* 1.3 62.7 + - - +
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Residues in contact with PHE 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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24A LYS* 3.8 31.0 - - - -
27A GLN* 3.9 37.7 - - + -
28A LEU* 4.1 17.9 - - + -
464B LEU* 2.8 24.6 + - + +
467B SER* 1.3 75.8 - - - +
469B GLY* 1.3 57.8 + - - +
470B LYS* 3.6 31.4 - - + +
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Residues in contact with GLY 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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464B LEU 3.6 0.2 + - - -
465B ALA* 2.7 29.3 + - - +
466B ALA 4.4 0.8 + - - -
467B SER 3.6 0.8 - - - -
468B PHE* 1.3 73.3 - - - +
470B LYS* 1.3 65.1 + - - +
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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