Contacts of the helix formed by residues 459 - 469 (chain A) in PDB entry 3QHE
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 459 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455A LYS 4.3 1.3 + - - +
456A LEU* 3.1 15.2 + - + +
458A PHE* 1.3 77.8 - - - +
460A GLU* 1.3 62.5 + - - +
461A GLU* 3.4 16.9 + - - +
462A HIS* 2.6 44.9 + - - +
463A ARG* 2.9 28.8 + - - +
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Residues in contact with GLU 460 (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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458A PHE 4.0 0.8 + - - -
459A ASP* 1.3 73.7 + - - +
461A GLU* 1.3 63.9 + - + +
463A ARG* 3.3 34.3 + - - +
464A HIS* 3.0 28.8 + - + +
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Residues in contact with GLU 461 (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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402A ARG* 3.3 48.2 + - - +
459A ASP* 3.3 13.7 + - - +
460A GLU* 1.3 83.3 - - + +
462A HIS* 1.3 61.6 + - - +
464A HIS* 3.3 9.1 + - - +
465A ALA* 3.2 19.6 + - - +
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Residues in contact with HIS 462 (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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402A ARG* 3.5 34.3 - - + +
405A ARG* 4.9 7.8 + - - -
406A VAL* 4.1 13.3 - - + +
456A LEU* 3.2 62.1 - - + +
459A ASP* 2.6 33.7 + - + +
461A GLU* 1.3 73.5 - - - +
463A ARG* 1.3 65.4 + - - +
465A ALA* 3.1 8.2 + - - +
466A MET* 2.9 30.3 + - + +
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Residues in contact with ARG 463 (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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456A LEU 4.2 1.0 + - - -
457A SER* 2.9 39.5 + - - +
458A PHE* 3.2 23.8 + - - +
459A ASP 2.9 9.2 + - - +
460A GLU* 3.3 39.6 + - - +
462A HIS* 1.3 74.2 - - - +
464A HIS* 1.3 57.7 + - - +
466A MET* 3.2 8.0 + - - +
467A ASN* 3.0 36.5 + - - +
507A ASN 3.5 23.1 + - - -
508A LEU* 4.0 20.8 - - + +
386B TYR* 3.1 38.8 + - - -
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Residues in contact with HIS 464 (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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403A GLU* 5.9 1.0 + - - -
460A GLU* 3.0 14.7 + - + +
461A GLU* 3.4 13.4 + - - +
462A HIS 3.1 0.2 - - - -
463A ARG* 1.3 76.8 - - - +
465A ALA* 1.3 61.8 + - - +
467A ASN* 3.3 13.5 + - + +
468A GLU* 3.1 50.6 + - + +
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Residues in contact with ALA 465 (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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402A ARG* 4.9 4.7 - - + +
403A GLU* 4.1 30.5 - - + +
406A VAL* 4.2 20.4 - - + -
461A GLU 3.2 9.6 + - - +
462A HIS* 3.1 10.5 + - - +
464A HIS* 1.3 78.3 + - - +
466A MET* 1.3 65.7 + - - +
468A GLU* 3.3 9.5 + - - +
469A LEU* 3.2 26.6 + - + +
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Residues in contact with MET 466 (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 VAL* 3.7 22.2 - - + +
410A LEU* 4.8 1.8 - - + -
453A LEU* 3.4 36.8 - - + +
456A LEU* 3.7 19.3 - - + +
457A SER* 3.6 22.4 - - - +
462A HIS* 2.9 20.8 + - + +
463A ARG* 3.3 8.1 - - - +
465A ALA* 1.3 76.3 - - - +
467A ASN* 1.3 55.1 + - - +
469A LEU 3.0 13.5 + - - -
470A GLY 3.0 0.2 + - - -
471A GLY* 2.8 37.1 + - - +
472A LEU 5.4 0.2 - - - +
475A ILE* 4.8 8.3 - - - -
508A LEU* 4.1 32.1 - - + -
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Residues in contact with ASN 467 (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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463A ARG* 3.0 24.2 + - - +
464A HIS* 3.3 14.1 + - + +
466A MET* 1.3 76.7 - - - +
468A GLU* 1.3 61.6 + - + +
469A LEU 3.5 0.3 + - - -
470A GLY* 3.8 8.0 + - - +
471A GLY 4.9 1.1 - - - +
472A LEU* 5.2 3.7 + - - +
508A LEU* 3.6 13.9 + - - +
512A ASP* 3.8 18.0 + - - -
515A ASN* 3.0 29.5 + - - +
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Residues in contact with GLU 468 (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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403A GLU* 5.0 10.3 - - - +
464A HIS* 3.1 41.2 + - + +
465A ALA* 3.7 11.2 - - - +
466A MET 3.2 0.2 - - - -
467A ASN* 1.3 76.3 - - + +
469A LEU* 1.3 66.8 + - + +
470A GLY 3.6 0.2 - - - -
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Residues in contact with LEU 469 (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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403A GLU* 3.9 29.8 - - + +
406A VAL* 4.5 6.5 - - + -
407A LEU* 4.0 38.8 - - + +
410A LEU* 3.5 13.7 - - + +
414A ARG* 2.7 31.1 + - - +
465A ALA* 3.2 16.8 + - + +
466A MET 3.0 2.8 + - - +
468A GLU* 1.3 86.9 - - + +
470A GLY* 1.3 51.5 + - - +
471A GLY 3.3 2.7 + - - -
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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