Contacts of the helix formed by residues 490 - 496 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487E ARG* 6.3 1.3 - - - -
443F ASP* 4.0 0.7 - - - -
489F SER* 1.3 80.5 - - - +
491F ALA* 1.3 64.5 + - - +
492F LEU 3.4 1.8 - - - -
493F ARG* 3.3 26.9 + - - +
494F GLN* 2.9 28.5 + - - +
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Residues in contact with ALA 491 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443F ASP* 3.1 51.3 + - + +
446F MET* 3.3 16.4 - - + -
447F THR* 4.7 2.2 - - + -
490F GLY* 1.3 75.7 - - - +
492F LEU* 1.3 53.7 + - - +
494F GLN* 3.1 1.2 + - - +
495F LEU* 2.5 51.0 + - + +
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Residues in contact with LEU 492 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309F MET* 3.7 27.1 - - + -
426F ILE* 4.7 7.4 - - + -
442F ILE* 3.1 38.4 - - + -
446F MET* 3.2 30.3 - - + +
464F CYS* 4.4 17.5 - - - -
486F LEU* 4.0 7.4 - - + -
487F ARG* 3.6 7.9 - - + +
488F GLY* 3.4 19.7 - - - +
491F ALA* 1.3 72.7 - - - +
493F ARG* 1.3 62.5 + - + +
494F GLN 2.5 23.7 + - - -
496F SER* 2.8 19.4 + - - +
499F ILE* 5.0 2.3 - - - +
520F LYS* 4.9 0.2 + - - -
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Residues in contact with ARG 493 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468E ASN* 6.1 2.6 - - - +
467F LYS* 5.0 2.8 - - - +
483F ILE* 3.9 25.9 + - + +
484F THR* 4.5 6.0 + - - +
486F LEU* 3.0 50.7 + - + +
487F ARG 3.0 20.1 + - - +
488F GLY 3.1 16.5 + - - -
489F SER* 3.9 16.2 + - - +
490F GLY* 3.3 27.2 - - - +
492F LEU* 1.3 72.2 - - + +
494F GLN* 1.3 55.5 - - - +
499F ILE* 6.0 3.4 - - - -
520F LYS* 3.7 12.2 + - - +
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Residues in contact with GLN 494 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343E GLU* 5.6 4.7 - - - +
425E HIS* 3.9 22.2 + - - +
427E SER* 4.3 4.8 - - - -
465E HIS* 4.3 21.6 - - + +
466E LEU 4.9 4.3 - - - +
487E ARG* 3.4 28.4 + - - +
490F GLY* 2.9 16.4 + - - +
491F ALA* 3.4 2.6 - - - +
492F LEU 2.5 5.4 + - - -
493F ARG* 1.3 73.8 - - - +
495F LEU* 1.3 69.2 + - + +
496F SER 2.8 16.8 + - - +
520F LYS* 2.9 21.1 + - - +
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Residues in contact with LEU 495 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343E GLU* 5.6 9.2 - - - +
428E ILE* 6.1 5.4 - - + -
307F VAL* 4.6 1.8 - - - -
446F MET* 3.4 18.6 - - + +
447F THR* 3.0 57.2 - - + +
450F LYS* 3.4 39.2 + - + +
491F ALA* 2.5 24.5 + - + +
494F GLN* 1.3 89.8 - - + +
496F SER* 1.3 59.3 + - - +
497F ASP* 3.3 12.1 - - - +
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Residues in contact with SER 496 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307F VAL* 3.5 17.5 - - - -
309F MET* 3.7 10.1 - - - -
446F MET* 3.1 19.6 - - - +
492F LEU* 2.8 17.2 + - - -
494F GLN 2.8 7.0 + - - +
495F LEU* 1.3 73.4 - - - +
497F ASP* 1.3 54.2 + - - +
499F ILE* 3.1 28.3 - - - -
520F LYS* 2.7 36.0 + - - -
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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