Contacts of the helix formed by residues 450 - 462 (chain B) in PDB entry 2ZXI
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 ASN 450 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445B TYR* 2.8 23.8 - - - +
447B ARG* 3.1 42.6 + - - +
449B ASP* 1.3 75.9 + - - +
451B ALA* 1.3 63.9 + - - +
452B ILE 3.1 2.7 - - - -
453B LEU* 3.1 14.8 + - + +
454B ARG* 2.9 42.4 + - - +
531B TYR* 3.8 5.2 - - - -
535B GLU* 3.7 18.6 - - - +
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Residues in contact with ALA 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ARG* 3.6 44.0 - - + +
63B GLU* 3.8 8.5 - - + +
66B ALA* 3.5 7.7 - - - +
238B TYR* 4.4 2.9 + - - +
447B ARG 3.9 2.6 + - - +
448B GLN 4.2 1.1 + - - +
449B ASP 3.7 1.6 - - - -
450B ASN* 1.3 78.8 - - - +
452B ILE* 1.3 57.1 + - - +
454B ARG* 3.1 27.7 + - - +
455B LEU* 2.9 28.8 + - - +
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Residues in contact with ILE 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ALA* 3.6 21.5 - - + +
230B PHE* 3.7 31.0 - - + -
231B TRP* 3.5 31.4 - - + -
238B TYR* 3.4 19.2 + - + +
450B ASN 4.5 0.4 - - - -
451B ALA* 1.3 80.6 - - - +
453B LEU* 1.3 65.3 + - + +
456B ALA* 3.0 46.1 + - + +
473B VAL* 3.9 12.0 - - + +
531B TYR* 3.5 33.2 - - + +
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Residues in contact with LEU 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445B TYR* 5.5 0.2 + - - -
450B ASN* 3.1 13.1 + - + +
452B ILE* 1.3 86.7 - - + +
454B ARG* 1.3 62.8 + - + +
456B ALA 4.7 0.7 + - - -
457B LYS* 5.6 2.1 + - - +
473B VAL* 4.4 11.9 - - + +
476B LEU* 5.9 0.9 - - + -
477B GLU* 3.4 43.1 - - + +
480B ILE* 4.5 6.7 - - + -
531B TYR* 3.4 31.9 - - + +
535B GLU* 3.8 22.7 - - + +
539B GLN* 3.8 15.7 - - - +
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Residues in contact with ARG 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ILE* 3.9 2.2 - - - +
63B GLU* 2.5 35.9 + - - +
414B GLU* 2.9 39.1 + - + +
415B SER* 3.6 2.0 - - - +
445B TYR* 3.5 48.6 + - + +
446B ILE* 3.5 12.9 - - - +
447B ARG 2.7 27.9 + - - +
450B ASN* 2.9 31.2 + - - +
451B ALA* 3.3 22.6 - - - +
453B LEU* 1.3 81.4 - - + +
455B LEU* 1.3 68.9 + - + +
456B ALA 3.9 0.2 - - - -
457B LYS* 5.4 2.3 + - - +
458B LEU* 5.9 0.3 - - - +
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Residues in contact with LEU 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B GLU* 3.5 43.7 - - + +
66B ALA* 3.8 9.2 - - + +
67B LEU* 3.6 34.6 - - + +
410B LEU* 4.8 9.9 - - + -
414B GLU* 5.0 5.6 - - + +
415B SER* 4.0 23.6 - - - +
417B ILE* 5.3 0.4 - - + -
451B ALA 2.9 12.9 + - - +
454B ARG* 1.3 92.3 - - + +
456B ALA* 1.3 64.4 + - - +
457B LYS 3.3 2.2 - - - -
458B LEU* 3.4 16.4 + - + +
459B GLY* 3.0 18.0 + - - -
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Residues in contact with ALA 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ALA* 3.7 10.8 + - - +
452B ILE* 3.0 25.5 + - + +
453B LEU 4.7 0.8 - - - -
454B ARG 3.9 0.4 - - - -
455B LEU* 1.3 77.5 - - - +
457B LYS* 1.3 58.0 + - - +
459B GLY* 3.2 0.9 + - - -
460B ARG* 2.8 31.4 + - - +
465B LEU* 3.5 12.5 - - + +
470B TYR* 3.8 6.1 - - + -
473B VAL* 4.0 32.3 - - + -
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Residues in contact with LYS 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B LEU 5.6 2.1 + - - +
454B ARG 5.4 2.4 + - - +
455B LEU 3.3 0.6 - - - -
456B ALA* 1.3 78.4 - - - +
458B LEU* 1.3 57.7 + - - +
460B ARG* 3.3 2.9 + - - +
461B GLU* 2.9 36.8 + - + +
470B TYR* 3.6 31.4 - - + +
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Residues in contact with LEU 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LEU* 4.0 12.6 - - + -
396B ILE* 6.1 0.4 - - + -
408B ILE* 3.9 27.1 - - + -
409B TYR 5.4 1.1 - - - +
410B LEU* 3.5 33.0 - - + -
454B ARG 5.8 0.4 + - - +
455B LEU* 3.4 16.2 + - + +
456B ALA 3.3 0.2 - - - -
457B LYS* 1.3 78.4 - - - +
459B GLY* 1.3 64.7 + - - +
461B GLU* 3.1 23.5 + - - +
462B LEU* 2.9 43.9 + - + +
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Residues in contact with GLY 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LEU* 3.5 28.9 - - - +
455B LEU 3.0 14.4 + - - -
456B ALA 3.2 4.2 + - - -
458B LEU* 1.3 79.4 - - - +
460B ARG* 1.3 57.1 + - - +
462B LEU* 3.6 4.4 + - - +
463B GLY 3.3 2.6 + - - -
464B LEU* 3.1 29.1 + - - +
465B LEU* 3.2 10.7 + - - -
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Residues in contact with ARG 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456B ALA 2.8 16.1 + - - +
457B LYS 3.8 3.6 - - - +
459B GLY* 1.3 73.5 - - - +
461B GLU* 1.3 67.6 + - - +
463B GLY* 3.0 19.5 + - - -
465B LEU* 2.7 38.5 + - + +
466B SER* 3.3 12.5 - - - +
467B GLU* 3.3 45.9 + - - +
470B TYR* 3.7 35.2 - - + +
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Residues in contact with GLU 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408B ILE* 5.4 5.5 - - - +
457B LYS* 2.9 26.8 + - + +
458B LEU* 3.4 23.9 - - - +
460B ARG* 1.3 78.2 - - - +
462B LEU* 1.3 66.1 + - - +
463B GLY* 4.6 0.3 - - - -
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Residues in contact with LEU 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B MET* 3.6 34.0 - - + +
67B LEU* 5.3 1.8 - - + -
396B ILE* 3.5 50.5 - - + -
400B LEU* 4.4 11.2 - - + -
408B ILE* 3.9 19.5 - - + -
458B LEU* 2.9 34.0 + - + +
459B GLY* 3.9 5.4 - - - +
460B ARG 3.2 0.2 - - - -
461B GLU* 1.3 84.1 - - - +
463B GLY* 1.3 59.2 + - - +
464B LEU* 3.4 14.8 - - + -
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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