Contacts of the helix formed by residues 455 - 469 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427C GLU* 2.7 27.5 + - + +
388D PHE* 4.3 4.0 - - + -
391D ASN* 3.5 21.3 - - - +
393D ARG* 3.6 16.5 - - + +
394D ALA* 3.6 20.4 - - + +
397D ASN* 5.3 4.9 - - - +
423D PRO* 3.4 41.7 - - + +
424D GLY* 3.9 9.2 - - - +
428D MET* 3.3 18.1 - - + +
454D THR* 1.3 71.6 - - - +
456D SER* 1.3 56.8 + - - +
458D ALA* 2.9 30.1 + - - +
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Residues in contact with SER 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C GLU* 2.9 11.9 + - - -
430C ASN* 2.8 28.1 + - - -
428D MET* 4.0 13.4 - - - +
431D GLU* 3.8 12.8 - - - -
450D HIS* 3.1 19.9 - - - -
454D THR* 2.7 21.3 + - - -
455D LEU* 1.3 76.9 - - - +
457D GLU* 1.3 60.9 + - - +
459D PHE* 2.9 16.6 + - - +
460D ARG 3.1 9.9 + - - -
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Residues in contact with GLU 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C HIS* 5.1 0.7 - - - +
332C GLU* 4.3 9.0 - - - +
386D PHE* 5.7 0.4 - - - -
391D ASN* 3.6 9.5 + - - +
392D SER* 4.9 2.4 + - - -
393D ARG 5.2 0.2 + - - -
450D HIS* 4.3 12.3 - - + +
451D ALA 3.3 22.7 - - - +
452D HIS* 2.7 43.8 + - - +
453D PRO* 3.3 2.4 - - - +
454D THR* 2.8 28.3 + - - +
456D SER* 1.3 77.2 + - - +
458D ALA* 1.3 56.8 + - - +
460D ARG* 3.4 13.7 + - - +
461D GLU* 3.0 39.5 + - + +
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Residues in contact with ALA 458 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386D PHE* 3.8 29.8 - - + +
388D PHE* 3.6 27.1 - - + -
391D ASN* 3.6 8.0 - - + +
404D VAL* 3.9 12.0 - - + +
455D LEU 2.9 13.9 + - - +
457D GLU* 1.3 79.6 - - - +
459D PHE* 1.3 57.2 + - - +
461D GLU 3.4 0.3 + - - -
462D ALA* 3.0 30.8 + - - +
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Residues in contact with PHE 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434C LEU* 5.4 0.4 - - + -
404D VAL* 4.0 15.4 - - + +
406D ILE* 3.8 19.1 - - + -
415D VAL* 6.1 2.0 - - + -
418D ALA* 4.3 4.3 - - + -
420D ILE* 5.2 3.1 - - + -
428D MET* 3.7 27.4 - - + -
431D GLU* 3.2 39.3 - - + -
432D ALA* 3.7 37.5 - - + -
435D ALA* 4.8 2.5 - - + -
445D ILE* 3.6 29.6 - - + -
450D HIS* 4.3 2.0 - - - -
455D LEU 4.0 0.4 + - - -
456D SER* 2.9 10.0 + - - +
458D ALA* 1.3 80.8 - - - +
460D ARG* 1.3 56.7 + - - +
462D ALA* 3.8 1.7 + - - +
463D ASN* 2.7 48.7 + - - -
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Residues in contact with ARG 460 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C HIS* 5.1 2.8 - - - +
332C GLU* 5.7 3.6 + - - +
333C ASP* 2.7 38.5 + - - +
336C ILE* 6.3 1.6 - - - +
445D ILE* 4.0 14.8 - - - +
446D ALA* 2.9 29.0 + - - +
447D ARG* 3.9 3.6 + - - +
448D VAL 3.1 18.0 + - - -
450D HIS* 3.1 58.3 + - + +
456D SER 3.1 7.2 + - - +
457D GLU* 3.6 15.1 + - - +
458D ALA 3.2 0.2 - - - -
459D PHE* 1.3 78.1 - - - +
461D GLU* 1.3 61.1 + - + +
463D ASN* 3.4 4.5 + - - +
464D LEU* 3.0 26.1 + - + +
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Residues in contact with GLU 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386D PHE* 3.3 28.8 - - + -
457D GLU* 3.0 28.4 + - + +
458D ALA 3.8 0.7 - - - +
460D ARG* 1.3 78.6 - - + +
462D ALA* 1.3 58.9 + - - +
463D ASN 3.1 1.3 - - - -
464D LEU* 3.2 14.6 + - - +
465D ALA* 2.8 29.1 + - - +
471D SER* 3.5 6.3 - - - -
472D ILE* 2.9 29.3 + - - +
473D ASN* 2.8 45.9 + - - +
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Residues in contact with ALA 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384D GLY* 3.2 21.1 - - - +
386D PHE* 3.9 10.5 - - + +
404D VAL* 3.6 27.6 - - + +
406D ILE* 3.4 22.5 - - + +
458D ALA 3.0 16.6 + - - +
459D PHE 4.1 0.9 - - - +
460D ARG 3.4 0.2 - - - -
461D GLU* 1.3 77.6 - - - +
463D ASN* 1.3 57.3 + - - +
465D ALA* 3.5 2.6 + - - -
466D ALA* 3.1 23.0 + - - +
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Residues in contact with ASN 463 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406D ILE* 3.3 25.3 - - - +
415D VAL* 3.5 8.0 - - - +
442D CYS* 3.2 31.9 - - - +
445D ILE* 3.2 44.3 - - + +
446D ALA 4.4 0.4 - - - +
459D PHE* 2.7 38.4 + - - -
460D ARG 3.4 8.7 + - - +
461D GLU 3.1 0.4 - - - -
462D ALA* 1.3 78.8 - - - +
464D LEU* 1.3 64.6 + - - +
466D ALA 3.3 0.5 + - - -
467D SER* 3.0 18.5 + - - -
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Residues in contact with LEU 464 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C LYS* 4.6 13.9 - - - +
27C GLN* 6.1 0.2 - - - +
336C ILE* 5.4 5.4 - - + -
446D ALA* 3.7 24.0 - - + +
460D ARG* 3.0 15.1 + - + +
461D GLU* 3.5 29.2 - - - +
463D ASN* 1.3 77.1 - - - +
465D ALA* 1.3 59.1 + - - +
467D SER* 3.0 2.9 + - - -
468D PHE* 2.8 47.2 + - + +
470D LYS 3.4 10.1 - - - +
471D SER* 3.8 11.2 - - - -
472D ILE* 4.0 16.6 - - + -
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Residues in contact with ALA 465 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D VAL 4.5 4.0 - - - +
384D GLY* 4.1 11.4 - - - -
385D LYS 4.2 13.0 - - - +
461D GLU 2.8 16.5 + - - +
462D ALA 3.7 5.4 - - - +
464D LEU* 1.3 78.3 - - - +
466D ALA* 1.3 55.8 + - - +
469D GLY* 3.0 32.1 + - - +
470D LYS* 3.3 18.1 + - - +
471D SER* 4.0 10.3 - - - +
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Residues in contact with ALA 466 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382D LYS* 2.9 40.1 + - + +
383D VAL* 4.1 5.6 - - - -
384D GLY* 3.6 21.5 - - - +
406D ILE* 4.1 8.3 - - + +
408D GLY 5.2 0.4 - - - +
442D CYS* 4.0 18.6 - - - -
462D ALA 3.1 17.8 + - - +
463D ASN 3.7 5.2 - - - +
464D LEU 3.2 0.2 - - - -
465D ALA* 1.3 77.1 - - - +
467D SER* 1.3 59.7 + - - +
469D GLY* 5.3 0.4 - - - -
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Residues in contact with SER 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382D LYS* 3.9 8.9 + - - +
413D ASP* 3.2 26.5 + - - -
443D GLU* 3.3 33.0 + - - +
463D ASN 3.0 16.0 + - - -
464D LEU* 3.6 6.7 - - - -
466D ALA* 1.3 82.8 - - - +
468D PHE* 1.3 66.3 + - - +
469D GLY* 3.5 0.7 + - - -
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Residues in contact with PHE 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C LYS* 3.8 20.6 - - - -
27C GLN* 3.7 48.9 - - + -
28C LEU* 3.9 22.2 - - + -
464D LEU* 2.8 30.4 + - + +
467D SER* 1.3 76.5 + - - +
469D GLY* 1.3 55.1 + - - +
470D LYS* 3.5 26.3 - - + +
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Residues in contact with GLY 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464D LEU 3.6 0.2 + - - -
465D ALA* 3.0 26.4 + - - +
466D ALA 5.3 0.4 - - - -
467D SER 3.3 2.1 - - - -
468D PHE* 1.3 78.7 - - - +
470D LYS* 1.3 64.1 + - - +
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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