Contacts of the helix formed by residues 455 - 469 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388A PHE* 4.0 6.7 - - + -
391A ASN* 3.8 8.5 - - - +
393A ARG* 3.9 11.4 - - + +
394A ALA* 3.8 27.1 - - + +
397A ASN* 6.0 4.5 - - - +
423A PRO* 3.4 52.0 - - + +
424A GLY* 3.7 10.8 - - - +
428A MET* 3.4 22.9 - - + +
454A THR* 1.3 72.1 - - - +
456A SER* 1.3 62.9 + - - +
457A GLU 2.9 1.6 + - - -
458A ALA* 3.0 18.0 + - - +
427B GLU* 2.7 26.2 + - + +
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Residues in contact with SER 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A MET* 4.0 13.9 - - - +
431A GLU* 3.8 13.7 - - - -
450A HIS* 3.2 18.9 - - - -
454A THR* 2.7 14.9 + - - -
455A LEU* 1.3 76.7 - - - +
457A GLU* 1.3 61.5 + - - +
458A ALA 3.1 0.4 - - - -
459A PHE* 3.0 17.1 + - - +
460A ARG 3.1 9.4 + - - -
427B GLU* 2.8 16.6 + - - -
430B ASN* 2.6 31.3 + - - -
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Residues in contact with GLU 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A ASN* 3.5 8.7 + - - +
392A SER* 5.1 2.2 - - - -
393A ARG 5.2 0.2 + - - -
450A HIS* 4.3 12.3 - - + +
451A ALA 3.4 20.1 - - - +
452A HIS* 2.8 38.5 + - - +
453A PRO* 3.1 2.1 - - - +
454A THR* 2.8 35.0 + - - +
456A SER* 1.3 76.6 + - - +
458A ALA* 1.3 58.8 + - - +
460A ARG* 3.2 16.7 + - + +
461A GLU* 2.9 38.1 + - + +
473A ASN* 5.9 1.0 + - - -
329B HIS* 5.5 0.3 - - - +
332B GLU* 4.2 9.5 - - - +
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Residues in contact with ALA 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A PHE* 3.7 32.0 - - + +
388A PHE* 3.6 27.6 - - + -
391A ASN* 3.4 7.5 - - - +
404A VAL* 3.7 11.6 - - + +
455A LEU 3.0 12.7 + - - +
457A GLU* 1.3 78.4 - - - +
459A PHE* 1.3 57.2 + - - +
461A GLU 3.3 0.3 + - - -
462A ALA* 2.9 32.4 + - - +
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Residues in contact with PHE 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A VAL* 3.9 15.6 - - + +
406A ILE* 3.7 24.9 - - + -
415A VAL* 6.1 2.0 - - + -
418A ALA* 4.1 4.3 - - + -
420A ILE* 5.1 3.8 - - + -
428A MET* 3.8 27.1 - - + -
431A GLU* 3.4 38.1 - - + -
432A ALA* 3.7 35.0 - - + -
435A ALA* 5.0 0.7 - - + -
445A ILE* 3.6 29.6 - - + -
450A HIS* 4.4 1.8 - - - -
455A LEU 4.0 0.6 + - - -
456A SER* 3.0 11.8 + - - +
458A ALA* 1.3 80.6 - - - +
460A ARG* 1.3 61.5 + - - +
462A ALA* 3.5 1.9 + - - +
463A ASN* 3.0 37.7 + - - -
434B LEU* 5.4 0.2 - - + -
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Residues in contact with ARG 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445A ILE* 4.0 14.8 - - - +
446A ALA* 2.9 29.6 + - - +
447A ARG* 4.2 2.4 + - - +
448A VAL 3.2 18.4 + - - -
449A CYS* 3.8 0.2 - - - +
450A HIS* 3.4 48.5 + - + +
456A SER 3.1 6.0 + - - +
457A GLU* 3.4 17.2 + - - +
459A PHE* 1.3 79.6 - - - +
461A GLU* 1.3 59.3 + - - +
463A ASN* 3.2 5.9 + - - +
464A LEU* 3.0 27.3 + - + +
329B HIS* 5.2 1.4 - - - +
332B GLU* 5.3 6.1 + - - +
333B ASP* 2.7 44.7 + - - -
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Residues in contact with GLU 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A PHE* 3.3 31.4 - - + -
457A GLU* 2.9 27.4 + - + +
460A ARG* 1.3 73.2 - - + +
462A ALA* 1.3 61.1 + - - +
464A LEU* 3.3 13.2 + - - +
465A ALA* 2.8 24.8 + - - +
471A SER* 3.4 12.3 - - - -
472A ILE* 2.8 29.6 + - - +
473A ASN* 2.8 46.8 + - - +
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Residues in contact with ALA 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A GLY* 3.4 17.4 - - - +
386A PHE* 3.9 9.1 - - + +
404A VAL* 3.6 29.4 - - + +
406A ILE* 3.5 21.3 - - + +
458A ALA 2.9 16.8 + - - +
459A PHE 3.9 0.9 - - - +
461A GLU* 1.3 77.8 - - - +
463A ASN* 1.3 61.5 + - - +
465A ALA* 3.4 4.7 + - - -
466A ALA* 3.1 19.1 + - - +
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Residues in contact with ASN 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A ILE* 3.2 37.6 - - - +
415A VAL* 3.5 10.7 - - - +
442A CYS* 3.3 33.2 - - - +
445A ILE* 3.2 27.3 - - + +
446A ALA 4.2 0.4 - - - +
459A PHE* 3.0 30.5 + - - -
460A ARG 3.2 9.0 + - - +
462A ALA* 1.3 75.6 - - - +
464A LEU* 1.3 56.7 + - - +
466A ALA* 3.1 1.6 + - - +
467A SER* 2.7 35.7 + - - -
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Residues in contact with LEU 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A ALA* 3.7 23.3 - - + +
460A ARG* 3.0 13.6 + - + +
461A GLU* 3.5 21.1 - - - +
463A ASN* 1.3 75.1 - - - +
465A ALA* 1.3 59.4 + - - +
467A SER* 4.2 2.9 - - - -
468A PHE* 2.7 48.4 + - + +
469A GLY 3.5 1.9 + - - -
470A LYS 3.5 8.0 - - - +
471A SER* 3.7 8.5 - - - -
472A ILE* 3.3 33.0 - - + -
24B LYS* 4.3 11.4 - - - +
336B ILE* 5.5 2.2 - - + -
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Residues in contact with ALA 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A VAL 4.8 1.7 - - - +
384A GLY* 4.0 12.6 - - - -
385A LYS 4.1 14.6 - - - +
461A GLU 2.8 21.1 + - - +
462A ALA 3.7 5.6 - - - +
463A ASN 3.2 0.2 - - - -
464A LEU* 1.3 72.6 - - - +
466A ALA* 1.3 59.1 + - - +
469A GLY* 2.9 32.8 + - - +
470A LYS* 3.8 15.0 + - - +
471A SER* 4.0 13.0 - - - +
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Residues in contact with ALA 466 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382A LYS* 3.1 35.8 - - + +
383A VAL 4.2 5.4 - - - -
384A GLY* 3.6 21.3 - - - +
406A ILE* 4.3 9.0 - - + +
408A GLY 5.1 0.7 - - - +
442A CYS* 4.0 17.3 - - - -
462A ALA 3.1 14.1 + - - +
463A ASN 3.4 8.3 - - - +
465A ALA* 1.3 77.1 - - - +
467A SER* 1.3 61.6 + - - +
469A GLY* 4.7 1.0 + - - -
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Residues in contact with SER 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A LYS* 4.0 8.2 + - - +
413A ASP* 3.5 13.2 + - - -
442A CYS* 3.7 14.6 - - - -
443A GLU* 3.5 32.0 - - - +
446A ALA* 5.2 1.1 - - - -
463A ASN 2.7 19.4 + - - -
464A LEU* 3.7 6.3 - - - -
466A ALA* 1.3 77.3 - - - +
468A PHE* 1.3 64.7 + - - +
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Residues in contact with PHE 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464A LEU* 2.7 29.0 + - + +
467A SER* 1.3 76.6 - - - +
469A GLY* 1.3 54.7 + - - +
470A LYS* 3.6 31.0 - - + +
24B LYS* 3.6 27.1 - - - +
27B GLN* 3.6 41.7 - - + -
28B LEU* 3.9 15.7 - - + -
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Residues in contact with GLY 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464A LEU 3.5 0.2 + - - -
465A ALA* 2.9 25.1 + - - +
466A ALA 5.1 0.9 - - - -
467A SER 3.4 1.2 - - - -
468A PHE* 1.3 78.9 - - - +
470A LYS* 1.3 65.7 + - - +
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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