Contacts of the helix formed by residues 473 - 482 (chain A) in PDB entry 2QFZ
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 473 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410A HIS* 5.3 0.7 - - - -
471A GLU* 3.2 12.7 + - - +
472A LYS* 1.3 78.1 - - - +
474A PHE* 1.4 65.0 + - - +
475A GLN* 3.4 15.9 + - - +
476A GLU* 3.0 37.9 + - + +
477A LEU* 3.0 25.6 + - - +
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Residues in contact with PHE 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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410A HIS* 3.1 32.3 - - + +
411A GLU* 3.1 28.0 - - + -
412A VAL* 3.5 16.6 - - + -
416A GLN* 4.0 15.0 - - - -
472A LYS 3.9 2.8 + - - -
473A ASP* 1.4 74.1 + - - +
475A GLN* 1.3 68.1 + - + +
477A LEU* 3.6 5.1 - - - +
478A LEU* 3.0 51.0 + - + +
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Residues in contact with GLN 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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473A ASP* 3.4 14.0 + - - +
474A PHE* 1.3 90.3 - - + +
476A GLU* 1.3 62.0 + - - +
478A LEU* 3.7 2.8 + - - +
479A LEU* 3.0 48.4 + - + +
479B LEU* 6.2 1.8 - - - +
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Residues in contact with GLU 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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471A GLU* 3.5 31.9 - - - +
473A ASP* 3.0 22.8 + - - +
475A GLN* 1.3 77.4 - - + +
477A LEU* 1.3 59.8 + - - +
479A LEU* 3.7 14.9 - - + +
480A PHE* 3.0 30.1 + - - +
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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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406A HIS* 4.1 17.9 - - + +
407A LEU* 4.2 9.0 - - + -
410A HIS* 3.8 23.1 - - + -
412A VAL* 3.6 22.7 - - + -
468A ILE* 4.1 25.1 - - + +
471A GLU* 3.6 26.8 - - + +
473A ASP 3.0 19.2 + - - +
474A PHE 3.6 4.9 - - - +
475A GLN 3.3 0.2 - - - -
476A GLU* 1.3 72.9 - - - +
478A LEU* 1.3 66.3 + - - +
480A PHE* 3.4 6.6 + - + +
481A LEU* 3.1 33.9 + - + +
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Residues in contact with LEU 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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412A VAL* 4.3 15.0 - - + +
416A GLN* 3.9 37.7 - - + +
417A PHE* 4.1 8.3 - - + -
474A PHE* 3.0 40.7 + - + +
475A GLN* 4.1 3.4 - - - +
477A LEU* 1.3 79.5 - - - +
479A LEU* 1.3 62.2 + - - +
481A LEU* 3.3 3.9 + - - +
482A GLN* 3.1 58.4 + - + +
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Residues in contact with LEU 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 GLN* 3.0 52.9 + - + +
476A GLU* 3.7 13.5 - - + +
477A LEU 3.4 0.4 - - - -
478A LEU* 1.3 75.0 - - - +
480A PHE* 1.3 57.7 + - - +
482A GLN* 4.4 8.9 + - - +
483A ASN* 2.6 48.6 + - - +
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Residues in contact with PHE 480 (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 TRP* 3.9 22.9 - + + -
467A GLU* 3.5 38.1 - - + -
468A ILE* 4.3 20.0 - - + -
471A GLU* 5.5 5.8 - - + +
476A GLU 3.0 18.0 + - - +
477A LEU* 3.6 9.6 - - + +
479A LEU* 1.3 73.6 - - - +
481A LEU* 1.3 63.1 + - + +
483A ASN* 2.9 21.4 + - - +
484A LEU* 3.2 40.7 + - + +
485A PRO* 3.8 24.2 - - + -
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Residues in contact with LEU 481 (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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407A LEU* 3.7 26.0 - - + -
412A VAL* 4.0 9.4 - - + -
417A PHE* 3.6 37.5 - - + +
421A TRP* 3.7 27.8 + - + -
429A GLU* 4.5 1.0 - - - +
461A LEU* 3.4 30.7 - - + -
468A ILE* 4.0 17.7 - - + -
477A LEU* 3.1 28.0 + - + +
478A LEU* 3.3 4.7 + - - +
480A PHE* 1.3 79.3 - - + +
482A GLN* 1.3 60.2 + - - +
483A ASN 3.3 0.6 + - - -
484A LEU* 3.8 18.6 - - + +
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Residues in contact with GLN 482 (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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416A GLN 3.0 22.4 + - - -
417A PHE* 4.1 2.9 - - + -
420A ARG* 2.8 34.0 + - - +
428A ARG 5.3 0.2 - - - +
429A GLU* 3.8 4.9 - - - +
478A LEU* 3.1 44.3 + - + +
479A LEU* 4.4 9.5 - - - +
481A LEU* 1.3 76.5 - - - +
483A ASN* 1.3 74.9 + - - +
484A LEU 3.9 0.9 - - - -
1006A UNX 3.8 20.0 - - - -
416B GLN* 5.2 9.3 - - - +
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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