Contacts of the helix formed by residues 466 - 474 (chain B) in PDB entry 5ZR1
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 ASP 466 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B LEU 4.4 0.4 + - - -
465B TRP* 1.3 74.4 - - - +
467B ASN* 1.3 60.7 + - - +
468B MET* 3.8 11.2 + - - +
469B LYS* 3.1 31.8 + - - +
470B ALA* 3.0 26.5 + - - +
422E GLN* 4.0 8.3 - - - -
425E SER* 3.4 22.1 + - - +
426E GLU* 3.4 21.4 - - - +
429E THR* 3.4 23.2 + - - +
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Residues in contact with ASN 467 (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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466B ASP* 1.3 78.2 - - - +
468B MET* 1.3 60.7 + - - +
470B ALA* 4.1 0.7 - - - +
471B GLN* 3.2 23.0 + - - +
309C ASN* 3.2 27.5 + - - +
310C THR 5.5 0.4 - - - +
311C ASN* 4.3 9.3 - - - +
312C HIS* 3.6 23.2 - - + +
422E GLN* 2.7 38.6 + - - +
423E ASN* 4.2 11.7 + - - +
426E GLU* 3.0 38.8 + - - +
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Residues in contact with MET 468 (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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443B PHE* 5.5 11.4 - - + -
466B ASP* 3.3 12.5 + - - +
467B ASN* 1.3 78.7 - - - +
469B LYS* 1.3 64.4 + - + +
471B GLN* 3.4 17.2 + - - +
472B ASN* 2.9 55.0 + - - +
111C ASP* 4.2 15.0 - - - +
113C THR* 4.9 11.4 - - + +
312C HIS* 3.8 26.8 - - - +
426E GLU* 4.1 2.4 + - - +
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Residues in contact with LYS 469 (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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435B ASN* 2.5 32.0 + - - +
438B GLN* 3.5 22.7 - - + +
439B THR* 3.6 22.1 + - - +
442B SER* 3.7 21.3 + - - +
464B LEU* 4.2 18.1 + - - +
465B TRP* 4.1 13.5 - - + -
466B ASP* 3.1 22.6 + - - +
468B MET* 1.3 75.3 - - + +
470B ALA* 1.3 61.3 + - - +
472B ASN* 4.0 4.2 - - - +
473B TYR* 3.0 35.7 + - + -
443E TYR* 6.1 2.0 - - - -
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Residues in contact with ALA 470 (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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465B TRP* 4.3 13.8 - - + +
466B ASP 3.0 19.6 + - - +
469B LYS* 1.3 75.1 - - - +
471B GLN* 1.3 60.4 + - - +
473B TYR* 4.4 4.7 - - - -
474B ASN* 3.0 26.3 + - - +
475B PHE* 4.6 4.3 + - + -
315C GLN* 4.8 0.9 - - - +
319C LYS* 4.8 3.3 + - - -
422E GLN* 3.4 26.7 - - + +
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Residues in contact with GLN 471 (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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467B ASN 3.2 16.6 + - - +
468B MET* 3.5 20.1 - - - +
469B LYS 3.2 0.4 - - - -
470B ALA* 1.3 76.3 - - - +
472B ASN* 1.3 69.3 + - - +
474B ASN* 3.5 18.7 + - - +
111C ASP* 5.0 0.2 - - - +
312C HIS* 3.0 38.7 + - + -
315C GLN* 3.5 47.6 + - + +
422E GLN* 5.3 0.2 - - - +
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Residues in contact with ASN 472 (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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442B SER* 3.3 32.2 - - - +
443B PHE* 4.7 14.9 - - - -
445B SER* 3.6 22.3 - - - +
446B VAL* 3.3 27.4 + - + +
468B MET* 2.9 45.2 + - - +
469B LYS* 4.1 2.1 - - - +
471B GLN* 1.3 81.1 - - - +
473B TYR* 1.3 63.3 + - - +
474B ASN* 4.5 2.4 - - - +
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Residues in contact with TYR 473 (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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313B SER* 3.2 20.5 + - - -
427B LEU* 4.2 8.7 - - + +
438B GLN* 2.9 20.3 + - - -
441B LEU* 3.3 41.0 - - + +
442B SER* 3.1 20.7 + - - -
445B SER* 3.2 19.3 - - - +
452B ILE* 5.3 5.2 - - + -
465B TRP* 3.4 31.9 - + + -
469B LYS 3.0 23.3 + - - +
470B ALA* 4.2 2.2 - - - +
472B ASN* 1.3 79.9 - - - +
474B ASN* 1.3 73.3 + - - +
475B PHE* 3.4 46.4 - + + -
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Residues in contact with ASN 474 (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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311B GLY 3.1 24.7 + - - +
312B PHE* 3.6 20.7 - - - -
313B SER 3.6 8.3 + - - -
445B SER 5.6 0.5 - - - +
470B ALA 3.0 18.2 + - - +
471B GLN 3.5 7.6 + - - +
472B ASN 4.5 2.2 - - - +
473B TYR* 1.3 89.7 - - - +
475B PHE* 1.3 68.0 + - - +
315C GLN* 3.3 31.4 - - - +
319C LYS* 3.6 16.3 + - + +
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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