Contacts of the helix formed by residues 491 - 499 (chain A) in PDB entry 3QFS
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 491 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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479A VAL* 2.8 29.4 + - - +
490A LYS* 1.3 70.6 - - - +
492A VAL* 1.3 65.7 + - - +
495A ASN* 2.9 26.0 + - - +
752A FAD 3.2 31.9 - - - -
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Residues in contact with VAL 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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327A PRO* 4.0 16.8 - - + -
328A ALA 3.8 19.1 - - - +
329A ASN* 3.5 25.8 - - - +
381A THR* 3.2 34.8 - - + +
454A LEU* 4.2 9.4 - - + -
457A ARG* 3.7 15.7 - - - +
490A LYS 3.3 1.3 + - - +
491A GLY* 1.3 72.2 - - - +
493A ALA* 1.3 63.1 + - - +
495A ASN* 4.2 0.9 - - - +
496A TRP* 3.1 25.3 + - - +
752A FAD 2.9 11.9 + - - +
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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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325A VAL* 4.5 7.4 - - + -
327A PRO* 3.8 19.3 - - + +
457A ARG* 3.5 22.0 - - + -
459A TYR* 3.4 19.5 - - + +
492A VAL* 1.3 75.1 - - - +
494A THR* 1.3 56.2 + - - +
496A TRP* 3.4 1.8 + - - +
497A LEU* 2.9 35.3 + - + +
752A FAD 2.8 20.7 + - - +
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Residues in contact with THR 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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304A MET* 3.3 15.9 - - + +
459A TYR* 3.6 6.3 - - + +
476A ALA* 4.4 11.9 - - + -
477A VAL 3.4 18.2 - - - +
478A VAL* 3.7 14.8 - - - +
479A VAL* 3.1 19.5 + - - +
491A GLY 3.7 3.3 + - - -
493A ALA* 1.3 76.5 - - - +
495A ASN* 1.3 59.2 + - - +
497A LEU* 4.5 0.7 - - - -
498A ARG* 2.9 25.8 + - - +
752A FAD 2.7 46.7 + - - +
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Residues in contact with ASN 495 (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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478A VAL* 3.7 15.3 - - - +
479A VAL 2.9 28.3 + - - -
480A GLU* 4.3 5.5 - - - +
490A LYS* 3.3 34.3 + - + +
491A GLY* 2.9 29.4 + - - +
492A VAL* 4.3 1.1 - - - +
494A THR* 1.3 75.0 + - - +
496A TRP* 1.3 64.6 + - - +
498A ARG* 3.7 12.8 + - - +
499A ALA* 3.1 24.3 + - - +
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Residues in contact with TRP 496 (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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325A VAL* 4.0 11.0 - - + -
326A TYR 3.3 22.0 - - - -
327A PRO* 3.6 20.4 - - + -
328A ALA* 3.5 42.2 - - + +
376A TYR* 5.8 1.3 - + - -
492A VAL 3.1 20.1 + - - +
493A ALA* 3.6 3.4 - - - +
495A ASN* 1.3 78.2 - - - +
497A LEU* 1.3 92.1 + - + +
499A ALA* 3.3 14.2 + - - +
500A LYS* 3.3 45.3 + - - +
511A LEU 4.2 0.4 - - - -
512A VAL* 3.6 26.2 - - + -
513A PRO* 3.7 14.6 - - + -
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Residues in contact with LEU 497 (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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292A ASN* 3.0 13.9 + - - -
304A MET* 3.8 22.0 - - + -
306A LEU* 3.9 19.7 - - + +
308A LEU* 5.6 0.9 - - + -
325A VAL* 4.9 5.4 - - + -
459A TYR* 4.3 28.3 - - + -
474A ILE* 4.8 21.1 - - + -
476A ALA* 5.3 0.4 - - + -
493A ALA 2.9 25.3 + - - +
494A THR* 4.7 0.7 - - - -
496A TRP* 1.3 99.2 - - + +
498A ARG* 1.3 64.6 + - - +
500A LYS* 3.0 17.0 + - - +
512A VAL* 4.0 23.8 - - + -
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Residues in contact with ARG 498 (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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292A ASN* 3.4 13.6 + - - +
302A HIS* 3.3 59.7 + - - +
304A MET* 3.7 13.9 - - - -
478A VAL* 4.1 12.9 - - + +
480A GLU* 4.1 17.4 + - - -
494A THR 2.9 19.0 + - - +
495A ASN* 3.7 12.0 + - - +
496A TRP 3.3 0.2 - - - -
497A LEU* 1.3 77.1 - - - +
499A ALA* 1.3 59.0 + - - +
500A LYS 4.7 0.2 - - - -
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Residues in contact with ALA 499 (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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495A ASN 3.1 15.5 + - - +
496A TRP* 3.7 7.4 - - + +
497A LEU 3.1 1.0 - - - -
498A ARG* 1.3 76.7 - - - +
500A LYS* 1.3 58.6 + - - +
501A GLU* 3.0 14.1 + - - +
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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