Contacts of the helix formed by residues 455 - 469 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388G PHE* 3.9 5.1 - - + -
391G ASN* 3.7 9.4 - - - +
393G ARG* 4.0 10.4 - - + +
394G ALA* 3.6 38.1 - - + +
397G ASN* 5.1 4.7 - - - +
423G PRO* 3.4 41.3 - - + +
424G GLY* 4.0 9.6 - - - +
428G MET* 3.5 19.8 - - + +
454G THR* 1.3 73.2 - - - +
456G SER* 1.3 63.1 + - - +
458G ALA* 3.0 23.7 + - - +
427H GLU* 2.8 27.5 + - + +
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Residues in contact with SER 456 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428G MET* 4.1 13.4 - - - +
431G GLU* 4.0 8.1 - - - -
450G HIS* 3.2 18.5 - - - -
454G THR* 2.8 10.6 + - - -
455G LEU* 1.3 77.4 - - - +
457G GLU* 1.3 56.0 + - - +
459G PHE* 2.9 28.2 + - - +
460G ARG 3.1 4.9 + - - -
427H GLU* 2.9 12.9 + - - -
430H ASN* 2.8 40.2 + - - -
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Residues in contact with GLU 457 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386G PHE* 5.4 0.4 - - - -
391G ASN* 3.9 8.5 + - - +
392G SER* 4.7 1.8 - - - -
450G HIS* 4.2 13.0 - - + +
451G ALA 3.4 22.2 - - - +
452G HIS* 3.1 36.9 + - - +
453G PRO* 3.1 2.6 - - - +
454G THR* 2.9 30.0 + - - +
455G LEU 3.0 0.6 + - - -
456G SER* 1.3 78.3 + - - +
458G ALA* 1.3 57.3 + - - +
460G ARG* 3.2 15.4 + - + +
461G GLU* 2.8 37.8 + - + +
329H HIS* 5.2 0.3 - - - +
332H GLU* 4.1 10.7 - - - +
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Residues in contact with ALA 458 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386G PHE* 3.6 33.3 - - + +
388G PHE* 3.6 27.4 - - + -
391G ASN* 3.8 7.1 - - - +
404G VAL* 3.7 11.4 - - + +
455G LEU 3.0 14.0 + - - +
457G GLU* 1.3 78.3 - - - +
459G PHE* 1.3 56.4 + - - +
461G GLU 3.5 0.2 + - - -
462G ALA* 2.9 32.1 + - - +
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Residues in contact with PHE 459 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404G VAL* 3.9 22.0 - - + +
406G ILE* 3.7 13.0 - - + -
415G VAL* 6.1 1.6 - - + -
418G ALA* 4.0 3.8 - - + -
420G ILE* 5.0 3.1 - - + -
428G MET* 3.8 27.4 - - + -
431G GLU* 3.6 36.1 - - + -
432G ALA* 3.8 36.6 - - + -
435G ALA* 4.9 0.7 - - + -
445G ILE* 3.5 33.4 - - + -
450G HIS* 4.3 1.3 - - - -
455G LEU 4.0 0.6 + - - -
456G SER* 2.9 13.1 + - - +
458G ALA* 1.3 80.1 - - - +
460G ARG* 1.3 59.5 + - - +
462G ALA* 3.4 2.4 + - - +
463G ASN* 3.0 45.0 + - - -
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Residues in contact with ARG 460 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445G ILE* 4.0 15.0 - - - +
446G ALA* 3.0 28.5 + - - +
447G ARG* 4.1 4.4 + - - +
448G VAL 3.0 17.2 + - - -
449G CYS* 4.7 0.2 - - - -
450G HIS* 3.3 56.0 + - + +
456G SER 3.1 4.0 + - - -
457G GLU* 3.4 16.8 + - - +
459G PHE* 1.3 78.1 - - - +
461G GLU* 1.3 59.9 + - - +
463G ASN* 3.3 5.0 + - - +
464G LEU* 2.9 26.4 + - + +
329H HIS* 5.2 1.8 + - - +
332H GLU* 5.4 5.3 + - - -
333H ASP* 3.0 41.5 + - - +
336H ILE* 5.5 8.7 - - - +
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Residues in contact with GLU 461 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386G PHE* 3.3 31.6 - - + -
457G GLU* 2.8 26.1 + - + +
458G ALA 3.8 0.2 - - - +
460G ARG* 1.3 73.3 - - + +
462G ALA* 1.3 60.2 + - - +
464G LEU* 3.1 13.0 + - - +
465G ALA 2.8 24.6 + - - -
471G SER* 3.2 15.3 + - - -
472G ILE* 2.7 30.1 + - - +
473G ASN* 2.7 48.3 + - - +
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Residues in contact with ALA 462 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384G GLY* 3.6 12.6 - - - +
385G LYS 4.4 1.6 - - - -
386G PHE* 3.8 11.1 - - + +
404G VAL* 3.7 37.5 - - + +
406G ILE* 3.7 11.1 - - + +
458G ALA 2.9 18.0 + - - +
459G PHE 3.8 0.9 - - - +
460G ARG 3.3 0.2 - - - -
461G GLU* 1.3 75.7 - - - +
463G ASN* 1.3 58.0 + - - +
465G ALA* 3.4 8.0 + - - +
466G ALA* 3.1 23.4 + - - +
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Residues in contact with ASN 463 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406G ILE* 3.5 28.5 - - - +
415G VAL* 3.6 2.4 - - - +
442G CYS* 3.5 34.5 - - - +
445G ILE* 3.3 35.5 - - + +
446G ALA 4.2 1.1 - - - +
459G PHE* 3.0 42.2 + - - +
460G ARG 3.5 7.9 - - - +
462G ALA* 1.3 75.8 - - - +
464G LEU* 1.3 65.2 + - - +
466G ALA 3.3 0.8 + - - +
467G SER* 2.9 27.0 + - - -
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Residues in contact with LEU 464 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446G ALA* 3.6 24.2 - - + +
460G ARG* 2.9 14.4 + - + +
461G GLU* 3.1 29.1 + - - +
463G ASN* 1.3 75.4 - - - +
465G ALA* 1.3 56.2 + - - +
467G SER* 4.5 1.8 - - - -
468G PHE* 2.8 49.3 + - + +
470G LYS 3.4 16.1 - - - +
471G SER 4.3 0.2 - - - -
472G ILE* 3.8 24.9 - - + +
24H LYS* 4.2 13.0 - - - +
336H ILE* 5.5 4.5 - - + -
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Residues in contact with ALA 465 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383G VAL 4.8 2.3 - - - +
384G GLY* 4.1 12.1 - - - -
385G LYS 4.2 10.3 - - - +
461G GLU 2.8 7.5 + - - +
462G ALA 3.5 9.6 - - - +
464G LEU* 1.3 77.0 - - - +
466G ALA* 1.3 56.9 + - - +
469G GLY* 2.9 31.1 + - - +
470G LYS* 3.8 14.1 + - - +
471G SER* 3.5 22.7 - - - +
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Residues in contact with ALA 466 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382G LYS* 3.0 36.8 + - + +
383G VAL* 4.1 7.2 - - - -
384G GLY* 3.6 25.9 - - - +
406G ILE* 4.1 10.5 - - + +
408G GLY 5.2 0.2 - - - +
413G ASP* 4.5 0.2 - - - -
442G CYS* 3.9 18.6 - - - -
462G ALA 3.1 12.8 + - - +
463G ASN 3.3 4.2 + - - +
465G ALA* 1.3 75.4 - - - +
467G SER* 1.3 59.5 + - - +
469G GLY* 4.7 1.0 + - - -
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Residues in contact with SER 467 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382G LYS* 3.7 8.2 + - - +
413G ASP* 2.9 26.0 + - - -
442G CYS* 3.6 13.2 - - - +
443G GLU* 3.3 23.1 + - - +
446G ALA* 5.2 0.7 - - - -
463G ASN 2.9 18.0 + - - -
464G LEU* 3.8 5.2 - - - -
466G ALA* 1.3 80.2 - - - +
468G PHE* 1.3 61.7 + - - +
469G GLY 3.5 0.4 + - - -
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Residues in contact with PHE 468 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464G LEU* 2.8 27.5 + - + +
467G SER* 1.3 75.0 - - - +
469G GLY* 1.3 57.7 + - - +
470G LYS* 3.8 23.3 - - + -
24H LYS* 3.6 29.8 - - - -
27H GLN* 3.6 39.5 - - + -
28H LEU* 4.0 22.0 - - + -
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Residues in contact with GLY 469 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464G LEU 3.7 0.2 + - - -
465G ALA* 2.9 24.0 + - - +
466G ALA 4.7 0.9 + - - -
467G SER 3.5 1.4 + - - -
468G PHE* 1.3 79.1 - - - +
470G LYS* 1.3 64.2 + - - +
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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