Contacts of the helix formed by residues 469 - 479 (chain A) in PDB entry 3U0Z
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 469 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468A ALA* 1.3 72.0 - - - +
470A PRO* 1.4 63.5 - - - +
471A ASN* 2.9 30.1 + - - +
472A PHE* 2.8 36.1 + - + +
473A VAL* 3.1 10.2 + - - +
565A TYR* 3.8 17.3 - - + -
568A MET* 5.8 1.4 - - - -
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Residues in contact with PRO 470 (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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452A ASN* 5.1 0.9 - - - +
468A ALA 3.0 14.1 - - - +
469A ASP* 1.4 82.4 - - - +
471A ASN* 1.3 60.4 + - - +
473A VAL* 3.5 12.1 - - + +
474A THR* 2.8 32.2 + - - -
453B PHE* 4.9 17.7 - - + -
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Residues in contact with ASN 471 (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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448A GLU* 5.5 4.2 + - - -
469A ASP* 2.9 18.7 + - - +
470A PRO* 1.3 82.4 + - - +
472A PHE* 1.3 55.3 + - - +
474A THR* 3.2 11.2 + - - +
475A ALA* 2.7 32.2 + - - +
565A TYR* 3.4 19.0 + - + +
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Residues in contact with PHE 472 (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* 4.7 0.4 - - + -
465A PHE* 3.9 19.5 - + - -
468A ALA* 4.2 7.2 - - + -
469A ASP* 2.8 15.9 + - + +
471A ASN* 1.3 74.7 - - - +
473A VAL* 1.3 81.3 + - + +
475A ALA* 3.1 3.1 + - - +
476A MET* 2.8 54.2 + - + +
561A VAL* 3.9 17.7 - - + -
562A LEU* 4.1 8.7 - - + -
565A TYR* 3.5 44.2 + + + -
568A MET* 3.3 45.3 - - + -
572A PHE* 4.4 8.3 - + - -
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Residues in contact with VAL 473 (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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452A ASN* 4.4 5.8 - - - +
459A VAL* 3.6 34.5 - - + -
465A PHE* 3.5 39.3 - - + +
468A ALA* 4.3 2.5 - - + +
469A ASP 3.1 9.6 + - - +
470A PRO* 3.5 14.1 - - + +
472A PHE* 1.3 87.9 - - + +
474A THR* 1.3 65.3 + - - +
476A MET* 2.8 13.1 + - - +
477A LEU* 2.9 26.3 + - + +
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Residues in contact with THR 474 (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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448A GLU* 3.6 40.8 - - + +
451A VAL* 6.4 1.6 - - + -
452A ASN* 3.2 29.8 + - - +
470A PRO 2.8 23.1 + - - -
471A ASN* 3.2 14.8 + - - -
473A VAL* 1.3 72.3 - - - +
475A ALA* 1.3 67.4 + - - +
477A LEU* 3.4 6.2 + - + +
478A SER* 2.9 27.8 + - - +
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Residues in contact with ALA 475 (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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471A ASN 2.7 17.7 + - - +
472A PHE 3.1 8.0 + - - +
474A THR* 1.3 74.4 - - - +
476A MET* 1.3 65.8 + - - +
478A SER* 3.1 18.2 + - - -
479A LYS* 3.7 10.8 - - - +
561A VAL* 4.1 25.4 - - + -
564A GLU* 4.6 6.7 - - - +
565A TYR* 4.3 11.4 - - + +
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Residues in contact with MET 476 (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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465A PHE* 4.0 30.5 - - + -
472A PHE* 2.8 56.2 + - + +
473A VAL 2.8 8.1 + - - +
475A ALA* 1.3 71.2 - - - +
477A LEU* 1.3 65.1 + - - +
478A SER 2.9 1.7 + - - -
479A LYS* 3.0 15.0 + - - +
480A LEU* 3.7 15.6 + - + +
503A PHE* 4.2 5.2 - - + -
553A LEU* 3.9 31.3 - - + +
558A PHE* 5.2 3.8 - - + -
561A VAL* 4.1 22.0 - - + -
562A LEU* 5.7 1.6 - - + -
572A PHE* 4.1 19.7 - - + -
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Residues in contact with LEU 477 (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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451A VAL* 3.6 31.5 - - + +
452A ASN* 3.7 27.6 - - - +
455A CYS* 3.9 30.6 - - + -
458A LEU* 4.7 2.9 - - + -
459A VAL* 4.0 14.6 - - + -
465A PHE* 3.9 26.5 - - + -
473A VAL* 2.9 27.8 + - + +
474A THR* 3.8 4.7 - - + +
476A MET* 1.3 72.9 - - - +
478A SER* 1.3 61.1 + - - +
479A LYS 3.2 0.5 + - - -
480A LEU* 3.4 30.3 + - + +
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Residues in contact with SER 478 (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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436A GLU* 5.6 0.2 - - - +
448A GLU* 5.3 4.5 - - - +
451A VAL* 4.5 11.0 - - - +
474A THR* 2.9 22.4 + - - +
475A ALA* 3.1 12.2 + - - -
476A MET 2.9 1.4 + - - -
477A LEU* 1.3 76.0 - - - +
479A LYS* 1.3 76.5 + - - +
480A LEU 3.9 1.9 + - - +
481A ARG* 4.4 10.6 + - - -
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Residues in contact with LYS 479 (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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475A ALA* 3.7 15.3 - - - +
476A MET 3.0 3.4 + - - +
478A SER* 1.3 96.4 + - - +
480A LEU* 1.3 61.7 + - - +
481A ARG* 3.6 25.8 + - - +
552A SER 3.9 2.3 - - - +
553A LEU* 3.8 20.9 - - + +
554A SER 5.2 0.2 + - - -
557A ASN* 3.3 44.3 + - + +
560A GLU* 3.9 21.1 - - - +
561A VAL* 4.7 12.6 - - + -
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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