Contacts of the helix formed by residues 455 - 469 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388E PHE* 3.8 5.3 - - + -
391E ASN* 3.5 19.1 - - - +
393E ARG* 3.9 11.6 - - + +
394E ALA* 3.6 27.6 - - + +
397E ASN* 5.2 6.5 - - - +
423E PRO* 3.5 40.8 - - + +
424E GLY* 4.1 8.5 - - - +
428E MET* 3.2 20.5 - - + +
454E THR* 1.3 72.9 - - - +
456E SER* 1.3 62.9 + - - +
458E ALA* 3.0 24.1 + - - +
427F GLU* 2.7 26.2 + - + +
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Residues in contact with SER 456 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428E MET* 3.9 13.2 - - - +
431E GLU* 4.1 10.3 - - - -
450E HIS* 3.2 16.9 - - - -
454E THR* 2.8 19.8 + - - -
455E LEU* 1.3 76.2 - - - +
457E GLU* 1.3 58.4 + - - +
459E PHE* 2.8 23.0 + - - +
460E ARG* 2.9 12.1 + - - +
427F GLU* 2.9 16.6 + - - -
430F ASN* 2.9 25.9 + - - -
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Residues in contact with GLU 457 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386E PHE* 5.4 0.4 - - - -
391E ASN* 3.8 6.8 + - - +
392E SER* 4.6 4.6 + - - +
450E HIS* 4.4 11.4 - - + +
451E ALA 3.4 23.6 - - - +
452E HIS* 2.8 39.4 + - - +
453E PRO* 3.2 2.8 - - - +
454E THR* 2.9 28.2 + - - +
456E SER* 1.3 78.1 + - - +
458E ALA* 1.3 58.0 + - - +
460E ARG* 3.6 15.4 + - + +
461E GLU* 2.9 39.7 + - + +
329F HIS* 5.2 0.7 - - - +
332F GLU* 4.3 9.9 - - - +
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Residues in contact with ALA 458 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386E PHE* 3.5 32.8 - - + +
388E PHE* 3.4 28.0 - - + -
391E ASN* 3.2 11.9 - - - +
404E VAL* 3.9 10.0 - - + +
455E LEU 3.0 13.8 + - - +
457E GLU* 1.3 79.7 - - - +
459E PHE* 1.3 56.5 + - - +
461E GLU 3.5 0.2 + - - -
462E ALA* 3.0 26.5 + - - +
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Residues in contact with PHE 459 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404E VAL* 3.9 21.9 - - + +
406E ILE* 3.7 19.5 - - + -
415E VAL* 6.2 2.2 - - + -
418E ALA* 4.1 5.2 - - + -
420E ILE* 4.8 4.3 - - + -
428E MET* 3.7 29.6 - - + -
431E GLU* 3.3 38.6 - - + -
432E ALA* 3.7 36.6 - - + -
435E ALA* 5.4 1.8 - - + -
445E ILE* 3.5 19.3 - - + -
450E HIS* 4.5 1.1 - - - -
455E LEU 4.0 0.4 + - - -
456E SER* 2.8 10.2 + - - +
458E ALA* 1.3 79.0 - - - +
460E ARG* 1.3 63.5 + - - +
462E ALA* 3.4 2.4 + - - +
463E ASN* 3.1 43.8 + - - -
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Residues in contact with ARG 460 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445E ILE* 3.9 15.0 - - - +
446E ALA* 2.8 32.5 + - - +
447E ARG* 4.2 3.4 - - - +
448E VAL 3.3 14.0 + - - -
449E CYS* 4.0 0.2 - - - +
450E HIS* 3.3 54.4 + - + +
456E SER 2.9 9.2 + - - +
457E GLU* 3.3 15.1 + - - +
459E PHE* 1.3 78.0 - - - +
461E GLU* 1.3 60.0 + - + +
463E ASN* 3.4 4.2 + - - +
464E LEU* 3.0 26.9 + - + +
329F HIS* 5.2 2.0 - - - +
332F GLU* 5.4 5.5 + - - -
333F ASP* 2.9 40.7 + - - -
336F ILE* 5.6 7.4 - - - +
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Residues in contact with GLU 461 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386E PHE* 3.3 21.6 - - + -
457E GLU* 2.9 23.4 + - + +
460E ARG* 1.3 79.9 - - + +
462E ALA* 1.3 60.5 + - - +
463E ASN 3.2 0.2 - - - -
464E LEU* 3.2 13.4 + - + +
465E ALA* 2.8 30.8 + - - +
471E SER* 2.8 29.1 + - - +
472E ILE* 2.8 21.3 + - - +
473E ASN* 2.6 44.7 + - - +
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Residues in contact with ALA 462 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384E GLY* 3.6 13.0 - - - +
386E PHE* 3.8 12.3 - - + +
404E VAL* 3.4 46.7 - - + +
406E ILE* 3.7 10.7 - - + +
458E ALA 3.0 11.2 + - - +
459E PHE 3.4 1.1 + - - +
461E GLU* 1.3 75.8 - - - +
463E ASN* 1.3 58.1 + - - +
465E ALA* 3.3 6.7 + - - +
466E ALA* 3.0 24.6 + - - +
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Residues in contact with ASN 463 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406E ILE* 3.6 16.9 - - - +
415E VAL* 3.7 10.4 - - - +
442E CYS* 3.3 47.7 - - - +
445E ILE* 3.5 20.0 - - + +
446E ALA 4.3 0.4 - - - +
459E PHE* 3.1 53.7 + - - +
460E ARG 3.5 8.7 - - - +
461E GLU 3.2 0.2 - - - -
462E ALA* 1.3 77.6 - - - +
464E LEU* 1.3 56.0 + - - +
466E ALA* 3.2 2.0 + - - -
467E SER* 2.9 25.5 + - - -
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Residues in contact with LEU 464 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446E ALA* 3.7 24.4 - - + +
460E ARG* 3.0 16.3 + - + +
461E GLU* 3.2 27.1 + - - +
463E ASN* 1.3 75.0 - - - +
465E ALA* 1.3 56.3 + - - +
467E SER* 4.5 2.7 - - - -
468E PHE* 2.8 47.5 + - + +
470E LYS 3.5 15.4 - - - +
471E SER* 4.5 0.2 - - - -
472E ILE* 4.2 21.1 - - + +
24F LYS* 4.1 13.0 - - - +
336F ILE* 5.5 7.0 - - + -
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Residues in contact with ALA 465 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383E VAL 4.6 2.6 - - - +
384E GLY* 4.1 12.4 - - - -
385E LYS 4.5 8.1 - - - +
461E GLU 2.8 16.2 + - - +
462E ALA* 3.6 7.9 - - - +
464E LEU* 1.3 77.3 - - - +
466E ALA* 1.3 58.0 + - - +
469E GLY* 2.8 33.1 + - - +
470E LYS 3.8 12.1 + - - -
471E SER* 3.9 19.1 - - - +
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Residues in contact with ALA 466 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382E LYS* 3.1 37.1 + - + +
383E VAL 4.3 5.8 - - - -
384E GLY* 3.8 21.0 - - - +
406E ILE* 4.1 9.6 - - + +
408E GLY 5.0 0.2 - - - +
413E ASP* 4.6 0.2 - - - -
442E CYS* 3.8 19.1 - - - -
462E ALA 3.0 13.4 + - - +
463E ASN 3.2 7.8 + - - +
465E ALA* 1.3 78.3 - - - +
467E SER* 1.3 61.9 + - - +
469E GLY* 4.3 1.6 + - - -
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Residues in contact with SER 467 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382E LYS* 3.4 21.7 + - - +
413E ASP* 3.1 26.5 + - - -
442E CYS* 3.7 4.0 - - - +
443E GLU* 3.5 22.0 - - - +
446E ALA* 5.3 0.9 - - - -
463E ASN 2.9 16.2 + - - -
464E LEU* 3.8 5.4 - - - -
466E ALA* 1.3 78.2 - - - +
468E PHE* 1.3 63.1 + - - +
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Residues in contact with PHE 468 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464E LEU* 2.8 25.7 + - + +
467E SER* 1.3 75.1 - - - +
469E GLY* 1.3 56.2 + - - +
470E LYS* 3.3 26.4 + - + +
24F LYS* 3.3 30.1 - - - -
27F GLN* 3.8 31.9 - - + -
28F LEU* 3.9 26.2 - - + -
340F GLU* 5.9 1.3 - - - -
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Residues in contact with GLY 469 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465E ALA* 2.8 27.0 + - - +
466E ALA 4.3 1.7 - - - -
467E SER 3.5 1.4 - - - -
468E PHE* 1.3 78.9 - - - +
470E LYS* 1.3 62.1 + - - +
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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