Contacts of the helix formed by residues 473 - 481 (chain B) in PDB entry 4Z4Q
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 473 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460B ILE* 3.6 41.0 + - + +
469B ASP 3.5 6.9 + - - +
470B ILE 3.4 15.5 - - - +
471B LEU 3.1 3.0 - - - -
472B LYS* 1.3 76.0 - - - +
474B GLU* 1.3 67.6 + - - +
475B GLU* 3.2 27.0 + - - +
476B ILE* 3.5 11.8 + - + -
477B ASN* 2.9 28.5 + - - +
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Residues in contact with GLU 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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415B LYS* 5.6 3.8 - - - +
456B ARG* 2.7 36.6 + - - -
472B LYS 3.5 4.8 + - - -
473B ASN* 1.3 73.2 + - - +
475B GLU* 1.3 69.5 + - + +
477B ASN* 4.1 3.1 - - - +
478B THR* 2.6 44.8 + - + +
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Residues in contact with GLU 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B LEU* 6.0 1.8 - - + -
454B PRO 4.0 4.0 - - - +
455B LEU* 3.6 25.1 - - + +
456B ARG* 3.2 42.9 + - - +
457B GLY 5.8 0.4 - - - -
458B LYS 6.0 0.9 - - - +
459B VAL* 5.3 16.3 - - + +
460B ILE 5.9 0.4 - - - +
473B ASN* 3.3 14.5 - - - +
474B GLU* 1.3 91.2 - - + +
476B ILE* 1.3 68.0 + - + +
478B THR* 2.9 16.7 + - - -
479B MET* 3.0 20.8 + - - +
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Residues in contact with ILE 476 (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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459B VAL* 4.9 9.6 - - + -
460B ILE* 3.6 27.4 - - + -
462B THR* 4.0 8.3 - - + -
470B ILE* 4.0 23.3 - - + +
473B ASN* 3.5 8.1 + - + +
475B GLU* 1.3 73.9 - - + +
477B ASN* 1.3 64.9 + - - +
479B MET* 3.0 16.5 + - - +
480B ILE* 3.0 24.3 + - + +
518B LEU* 6.4 0.2 - - + -
521B PHE* 3.2 59.0 - - + -
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Residues in contact with ASN 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B ILE 5.6 0.2 - - - -
471B LEU* 3.2 28.0 + - - -
472B LYS 5.5 0.2 - - - -
473B ASN 2.9 20.6 + - - +
474B GLU* 4.1 3.6 - - - +
476B ILE* 1.3 75.4 - - - +
478B THR* 1.3 61.9 + - + +
480B ILE* 3.4 6.9 + - - +
481B TYR* 3.2 24.5 + - - +
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Residues in contact with THR 478 (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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415B LYS* 4.7 16.2 - - + +
416B LEU* 5.4 0.9 - - - +
453B LEU* 3.8 25.9 - - - +
474B GLU* 2.6 37.7 - - + +
475B GLU* 2.9 8.9 + - - -
477B ASN* 1.3 73.1 - - + +
479B MET* 1.3 56.8 + - - +
481B TYR* 3.9 4.3 - - - +
482B THR* 2.6 42.8 + - - +
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Residues in contact with MET 479 (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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429B LEU* 5.9 0.9 - - + -
431B LEU* 3.6 26.7 - - + -
453B LEU* 4.0 16.8 - - + -
455B LEU* 4.3 14.4 - - + -
459B VAL* 5.9 1.1 - - - -
475B GLU* 3.0 24.2 + - - +
476B ILE* 3.6 19.3 - - - +
478B THR* 1.3 75.0 - - - +
480B ILE* 1.3 64.3 + - - +
481B TYR 3.1 2.1 + - - -
482B THR* 4.4 4.0 - - - -
483B ILE* 3.3 37.3 + - + +
518B LEU* 3.8 14.8 - - + -
521B PHE* 5.0 10.8 - - + -
522B PHE* 3.6 32.1 - - + -
526B MET* 5.7 1.3 - - - -
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Residues in contact with ILE 480 (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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476B ILE* 3.0 16.0 + - + +
477B ASN* 3.8 11.0 - - - +
479B MET* 1.3 76.6 - - - +
481B TYR* 1.3 57.5 + - + +
483B ILE* 4.3 1.8 - - - +
484B GLY* 3.2 21.5 + - - -
485B ALA 4.0 5.0 + - - -
486B GLY* 4.2 14.4 + - - +
487B VAL* 4.8 18.4 - - + +
521B PHE* 5.6 4.6 - - + -
526B MET* 5.3 7.6 - - - -
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Residues in contact with TYR 481 (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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477B ASN 3.2 16.2 + - - +
478B THR* 4.6 3.4 - - - +
479B MET 3.1 0.6 - - - -
480B ILE* 1.3 78.1 - - + +
482B THR* 1.3 64.0 + - + +
483B ILE 3.6 0.4 - - - -
484B GLY* 4.0 8.7 + - - +
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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