Contacts of the helix formed by residues 455 - 469 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427G GLU* 2.8 26.6 + - + +
388H PHE* 3.8 4.4 - - + -
391H ASN* 3.7 8.1 - - - +
393H ARG* 3.8 12.5 - - + +
394H ALA* 3.6 38.1 - - + +
397H ASN* 4.8 7.0 - - - +
423H PRO* 3.4 43.1 - - + +
424H GLY* 3.9 8.7 - - - +
428H MET* 3.5 19.9 - - + +
454H THR* 1.3 67.2 - - - +
456H SER* 1.3 56.8 + - - +
457H GLU 2.9 5.6 - - - -
458H ALA* 2.9 30.1 + - - +
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Residues in contact with SER 456 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427G GLU* 2.9 18.2 + - - -
430G ASN* 3.0 20.7 + - - -
428H MET* 4.0 13.6 - - - +
431H GLU* 4.1 10.1 - - - -
450H HIS* 3.0 24.4 - - - -
454H THR* 2.9 16.4 + - - -
455H LEU* 1.3 77.9 - - - +
457H GLU* 1.3 55.3 + - - +
458H ALA 3.1 0.2 - - - -
459H PHE* 2.9 10.3 + - - +
460H ARG 2.9 22.9 + - - -
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Residues in contact with GLU 457 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329G HIS* 5.1 1.0 - - - +
332G GLU* 4.2 9.4 - - - +
386H PHE* 5.3 0.7 - - - -
391H ASN* 3.6 7.7 + - - +
392H SER* 4.7 3.7 + - - -
450H HIS* 4.3 12.4 - - + +
451H ALA 3.4 21.4 - - - +
452H HIS* 2.9 39.3 + - - +
453H PRO* 3.2 2.6 - - - +
454H THR* 3.1 30.9 + - - +
455H LEU 2.9 0.4 + - - -
456H SER* 1.3 78.9 + - - +
458H ALA* 1.3 56.0 + - - +
460H ARG* 3.7 14.3 + - - +
461H GLU* 2.9 37.9 + - + +
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Residues in contact with ALA 458 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386H PHE* 3.6 32.2 - - + +
388H PHE* 3.4 28.0 - - + -
391H ASN* 3.3 9.2 - - + +
404H VAL* 3.7 12.2 - - + +
455H LEU 2.9 12.9 + - - +
457H GLU* 1.3 76.1 - - - +
459H PHE* 1.3 57.8 + - - +
461H GLU 3.4 0.2 + - - -
462H ALA* 2.9 30.7 + - - +
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Residues in contact with PHE 459 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434G LEU* 5.9 0.2 - - + -
404H VAL* 3.9 21.7 - - + +
406H ILE* 3.9 13.2 - - + -
415H VAL* 6.2 1.6 - - + -
418H ALA* 4.0 4.9 - - + -
420H ILE* 4.7 4.9 - - + -
428H MET* 3.7 29.8 - - + -
431H GLU* 3.3 38.6 - - + -
432H ALA* 3.8 36.3 - - + -
435H ALA* 5.4 0.2 - - + -
445H ILE* 3.6 26.9 - - + -
450H HIS* 4.4 1.6 - - - -
455H LEU 3.9 0.4 + - - -
456H SER* 2.9 10.2 + - - +
458H ALA* 1.3 78.7 - - - +
460H ARG* 1.3 63.7 + - - +
462H ALA* 3.6 1.7 + - - +
463H ASN* 2.9 44.2 + - - -
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Residues in contact with ARG 460 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329G HIS* 5.1 2.4 - - - +
332G GLU* 5.6 4.2 + - - +
333G ASP* 2.9 40.4 + - - +
336G ILE* 5.6 7.4 - - - +
445H ILE* 3.7 19.5 - - - +
446H ALA* 2.8 28.1 + - - +
447H ARG* 4.1 3.2 - - - +
448H VAL 3.2 13.4 + - - -
450H HIS* 3.2 54.4 + - + +
456H SER 2.9 9.2 + - - +
457H GLU* 3.7 15.7 + - - +
458H ALA 3.3 0.2 - - - -
459H PHE* 1.3 80.1 - - - +
461H GLU* 1.3 59.7 + - - +
463H ASN* 3.3 5.7 + - - +
464H LEU* 3.0 24.4 + - + +
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Residues in contact with GLU 461 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386H PHE* 3.4 28.2 - - + -
457H GLU* 2.9 26.7 + - + +
460H ARG* 1.3 76.1 - - + +
462H ALA* 1.3 60.6 + - - +
463H ASN 3.1 2.0 - - - -
464H LEU* 3.2 11.6 + - + +
465H ALA* 2.9 24.8 + - - +
471H SER* 3.0 19.5 - - - -
472H ILE* 2.7 31.4 + - - +
473H ASN* 2.8 43.4 + - - +
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Residues in contact with ALA 462 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384H GLY* 3.4 16.6 - - - +
386H PHE* 3.8 10.3 - - + +
404H VAL* 3.4 39.5 - - + +
406H ILE* 3.6 11.8 - - + +
458H ALA 2.9 19.0 + - - +
459H PHE 3.8 1.3 - - - +
461H GLU* 1.3 76.5 - - - +
463H ASN* 1.3 56.5 + - - +
465H ALA* 3.5 4.8 + - - -
466H ALA* 3.0 23.6 + - - +
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Residues in contact with ASN 463 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406H ILE* 3.6 18.2 - - - +
415H VAL* 3.7 6.9 - - - +
442H CYS* 3.2 45.8 - - - +
445H ILE* 3.4 34.4 - - + +
446H ALA 4.3 0.7 - - - +
459H PHE* 2.9 38.2 + - - +
460H ARG 3.4 9.6 - - - +
461H GLU 3.1 0.2 - - - -
462H ALA* 1.3 77.3 - - - +
464H LEU* 1.3 58.4 + - - +
466H ALA* 3.3 1.4 + - - -
467H SER* 2.9 26.0 + - - -
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Residues in contact with LEU 464 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G LYS* 4.1 15.0 - - + +
336G ILE* 5.3 6.3 - - + -
446H ALA* 3.7 22.2 - - + +
460H ARG* 3.0 14.1 + - + +
461H GLU* 3.2 28.7 + - - +
463H ASN* 1.3 74.3 - - - +
465H ALA* 1.3 56.7 + - - +
467H SER* 4.5 2.5 - - - +
468H PHE* 2.8 50.9 + - + +
470H LYS 3.4 14.3 - - - +
471H SER* 4.0 0.2 - - - -
472H ILE* 3.9 23.1 - - + -
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Residues in contact with ALA 465 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383H VAL 4.5 3.4 - - - +
384H GLY* 3.9 11.9 - - - -
385H LYS 4.3 11.2 - - - +
461H GLU 2.9 17.2 + - - +
462H ALA* 3.5 7.9 - - - +
464H LEU* 1.3 78.6 - - - +
466H ALA* 1.3 57.8 + - - +
469H GLY* 2.8 31.9 + - - +
470H LYS* 3.7 14.1 + - - +
471H SER* 3.9 15.0 - - - +
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Residues in contact with ALA 466 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382H LYS* 3.1 34.8 + - + +
383H VAL* 4.1 6.7 - - - -
384H GLY* 3.6 20.4 - - - +
406H ILE* 3.8 21.8 - - + +
408H GLY 5.2 0.2 - - - +
413H ASP* 4.5 0.2 - - - -
442H CYS* 3.8 8.7 - - - -
462H ALA 3.0 18.0 + - - +
463H ASN 3.6 4.7 - - - +
464H LEU 3.3 0.2 - - - -
465H ALA* 1.3 76.9 - - - +
467H SER* 1.3 61.3 + - - +
469H GLY* 4.4 1.4 + - - -
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Residues in contact with SER 467 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382H LYS* 3.4 18.2 + - - +
413H ASP* 3.0 24.0 + - - -
442H CYS* 3.6 7.0 - - - -
443H GLU* 3.4 22.8 + - - +
446H ALA* 5.5 0.4 - - - -
463H ASN 2.9 17.3 + - - -
464H LEU* 3.9 4.9 - - - -
466H ALA* 1.3 79.6 - - - +
468H PHE* 1.3 61.9 + - - +
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Residues in contact with PHE 468 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G LYS* 3.3 32.5 - - - -
27G GLN* 3.9 33.9 - - + -
28G LEU* 4.0 22.9 - - + -
464H LEU* 2.8 26.4 + - + +
467H SER* 1.3 74.7 - - - +
469H GLY* 1.3 58.7 + - - +
470H LYS* 3.8 26.9 - - + +
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Residues in contact with GLY 469 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465H ALA* 2.8 23.2 + - - +
466H ALA 4.4 1.7 + - - -
467H SER 3.5 1.2 - - - -
468H PHE* 1.3 79.7 - - - +
470H LYS* 1.3 65.8 + - - +
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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
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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