Contacts of the helix formed by residues 487 - 495 (chain A) in PDB entry 1DQU
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 VAL 487 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471A PHE* 3.3 41.1 - - + -
483A TYR* 2.5 50.3 + - + +
486A LEU* 1.3 77.4 - - + +
488A GLN* 1.3 64.2 + - - +
490A PRO* 3.2 9.3 - - - +
491A GLU* 3.3 26.2 + - - +
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Residues in contact with GLN 488 (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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483A TYR* 2.8 46.2 + - + -
484A GLY* 3.3 20.9 + - - +
487A VAL* 1.3 69.0 - - - +
489A GLU* 1.3 55.9 + - - +
490A PRO* 2.8 5.8 - - - -
491A GLU* 2.7 32.7 + - + +
492A MET* 2.8 46.7 + - + +
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Residues in contact with GLU 489 (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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484A GLY 3.3 4.8 + - - +
485A GLU* 3.2 36.7 - - - +
488A GLN* 1.3 75.6 - - - +
490A PRO* 1.3 74.6 - - + +
492A MET* 3.7 7.8 - - - +
493A ALA* 2.3 46.3 + - + +
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Residues in contact with PRO 490 (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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485A GLU 3.4 9.9 - - - +
486A LEU 3.2 23.1 - - - +
487A VAL 3.2 5.4 - - - +
488A GLN 2.8 6.7 - - - -
489A GLU* 1.3 102.8 - - + +
491A GLU* 1.3 57.9 + - - +
493A ALA* 2.9 7.6 + - + -
494A ASN* 2.4 51.0 + - - +
496A VAL* 5.4 0.2 - - - -
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Residues in contact with GLU 491 (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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483A TYR* 5.0 4.9 + - - -
487A VAL* 3.3 24.5 + - - +
488A GLN* 2.7 18.5 + - + +
490A PRO* 1.3 73.7 - - - +
492A MET* 1.3 63.6 + - + +
494A ASN 3.4 0.2 + - - -
495A GLY 2.9 18.4 + - - -
496A VAL* 3.1 32.8 + - + +
498A VAL* 3.1 33.4 - - - +
499A VAL* 3.2 31.8 - - + +
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Residues in contact with MET 492 (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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488A GLN* 2.8 57.8 + - + +
489A GLU* 3.7 6.1 - - - +
491A GLU* 1.3 71.6 - - + +
493A ALA* 1.3 66.1 + - - +
495A GLY* 2.7 18.6 + - - -
499A VAL* 4.1 21.1 - - + +
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Residues in contact with ALA 493 (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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489A GLU* 2.3 39.6 + - + +
490A PRO* 3.4 7.6 - - + +
492A MET* 1.3 68.9 - - - +
494A ASN* 1.3 63.1 + - - +
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Residues in contact with ASN 494 (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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490A PRO* 2.4 41.4 + - - +
491A GLU 4.3 1.3 - - - +
492A MET 2.8 2.2 + - - -
493A ALA* 1.3 74.5 - - - +
495A GLY* 1.3 59.0 + - - +
496A VAL* 3.6 11.6 - - + +
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Residues in contact with GLY 495 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A LYS* 4.1 6.8 + - - -
491A GLU 2.9 1.3 + - - -
492A MET* 2.7 20.6 + - - -
494A ASN* 1.3 74.2 - - - +
496A VAL* 1.3 65.6 + - - +
497A ASP* 3.3 3.3 + - - +
499A VAL* 4.3 2.0 - - - -
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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