Contacts of the helix formed by residues 490 - 496 (chain E) in PDB entry 1Q57
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 GLY 490 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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443E ASP* 4.0 0.4 - - - -
489E SER* 1.3 82.6 - - - +
491E ALA* 1.3 64.7 + - - +
492E LEU 3.3 2.5 - - - -
493E ARG* 3.2 26.8 + - - +
494E GLN* 2.9 27.9 + - - +
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Residues in contact with ALA 491 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443E ASP* 3.1 50.1 + - + +
446E MET* 3.3 17.0 - - + -
447E THR* 4.8 2.2 - - + -
490E GLY* 1.3 77.9 - - - +
492E LEU* 1.3 52.4 + - - +
494E GLN* 3.1 0.8 + - - -
495E LEU* 2.5 51.7 + - + +
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Residues in contact with LEU 492 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309E MET* 3.9 26.2 - - + -
426E ILE* 4.7 7.0 - - + -
442E ILE* 3.0 40.4 - - + -
446E MET* 3.3 29.1 - - + +
464E CYS* 4.4 17.5 - - - -
486E LEU* 4.3 7.6 - - + -
487E ARG* 3.5 10.8 - - + +
488E GLY* 3.4 17.9 - - - +
491E ALA* 1.3 74.9 - - - +
493E ARG* 1.3 63.1 + - + +
494E GLN 2.5 22.7 + - - -
496E SER* 2.9 19.0 + - - +
499E ILE* 4.9 3.2 - - - +
520E LYS* 4.7 0.5 + - - -
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Residues in contact with ARG 493 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467E LYS* 5.0 2.4 - - - +
483E ILE* 4.0 27.3 + - + +
484E THR* 4.5 5.1 + - - -
486E LEU* 3.0 48.0 + - + +
487E ARG 3.1 19.6 + - - +
488E GLY 3.3 12.3 + - - -
489E SER* 3.9 14.9 + - - +
490E GLY* 3.2 33.2 - - - +
492E LEU* 1.3 73.4 - - + +
494E GLN* 1.3 54.7 + - - +
499E ILE* 5.9 4.0 - - - -
520E LYS* 3.8 11.9 + - - +
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Residues in contact with GLN 494 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343D GLU* 6.0 2.5 - - - +
490E GLY 2.9 15.9 + - - +
491E ALA* 3.4 2.4 - - - +
492E LEU 2.5 6.2 + - - -
493E ARG* 1.3 73.9 - - - +
495E LEU* 1.3 75.7 + - + +
496E SER 2.9 8.2 + - - +
520E LYS* 2.8 24.6 + - - +
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Residues in contact with LEU 495 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307E VAL* 4.3 1.3 - - - +
446E MET* 3.4 18.4 - - + +
447E THR* 3.1 56.1 - - + +
450E LYS* 3.5 36.8 + - + +
491E ALA* 2.5 25.1 + - + +
494E GLN* 1.3 93.5 - - + +
496E SER* 1.3 58.5 + - - +
497E ASP* 3.2 12.0 - - - +
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Residues in contact with SER 496 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307E VAL* 3.5 18.6 - - - -
309E MET* 3.7 8.6 - - - +
446E MET* 3.1 21.0 - - - +
492E LEU* 2.9 16.1 + - - -
494E GLN 2.9 6.6 + - - +
495E LEU* 1.3 73.8 - - - +
497E ASP* 1.3 62.0 + - - +
499E ILE* 3.2 28.1 - - - +
520E LYS* 2.7 28.9 + - - -
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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