Contacts of the helix formed by residues 453 - 462 (chain A) in PDB entry 1QTE
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 TYR 453 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429A TRP* 4.0 18.4 - + - +
451A LEU 3.7 0.8 + - - -
452A ALA* 1.3 87.8 - - + +
454A ASN* 1.3 66.3 + - - +
455A ASP 3.3 2.7 - - - -
456A LEU* 3.1 17.9 + - + +
457A PHE* 3.0 30.8 + - + -
481A TRP* 4.0 13.3 + + - -
483A PRO* 3.4 29.5 - - - +
494A LEU* 3.8 30.1 - - + -
523A PRO* 3.6 29.2 - - + +
527A ILE* 3.9 9.4 - - + -
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Residues in contact with ASN 454 (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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451A LEU* 3.6 29.3 + - + +
452A ALA 3.1 4.7 - - - -
453A TYR* 1.3 74.9 - - - +
455A ASP* 1.3 74.5 + - - +
457A PHE* 3.2 1.8 + - - -
458A LYS* 3.0 28.4 + - - +
468A GLN* 2.9 29.4 + - - +
472A MET* 4.4 9.6 - - - +
602A MET* 4.6 4.5 - - - +
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Residues in contact with ASP 455 (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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453A TYR 3.3 0.6 - - - -
454A ASN* 1.3 87.4 + - - +
456A LEU* 1.3 59.2 + - + +
458A LYS* 3.4 9.4 + - - +
459A ARG* 3.0 40.2 + - - +
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Residues in contact with LEU 456 (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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453A TYR* 3.1 27.8 + - + +
455A ASP* 1.3 80.1 - - + +
457A PHE* 1.3 56.8 - - - +
459A ARG* 3.4 32.4 + - - +
460A TYR* 2.9 40.3 + - + +
523A PRO* 4.5 2.2 - - + -
524A GLU* 3.9 45.3 - - + +
527A ILE* 3.9 22.7 - - + -
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Residues in contact with PHE 457 (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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452A ALA 3.4 10.1 - - - -
453A TYR* 3.0 27.2 + - + +
454A ASN 3.9 2.5 - - - +
456A LEU* 1.3 75.2 - - - +
458A LYS* 1.3 57.3 + - - +
460A TYR 3.8 0.2 - - - -
461A THR* 2.7 38.5 + - - +
468A GLN* 3.7 18.6 - - + +
471A ALA* 3.8 37.9 - - + -
472A MET* 3.5 13.9 - - + -
475A ALA* 3.8 22.2 - - + -
481A TRP* 3.5 24.5 - + - -
494A LEU* 5.1 1.3 - - + -
495A MET* 4.3 10.8 - - + -
527A ILE* 3.6 41.7 - - + -
531A THR* 4.5 2.5 - - + -
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Residues in contact with LYS 458 (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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454A ASN* 3.0 21.7 + - - +
455A ASP* 3.6 9.6 - - - +
457A PHE* 1.3 77.0 - - - +
459A ARG* 1.3 63.2 + - - +
461A THR* 3.5 3.6 + - - -
462A SER* 3.0 29.5 + - - -
468A GLN* 3.4 23.0 - - - +
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Residues in contact with ARG 459 (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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455A ASP* 3.0 26.3 + - - +
456A LEU* 3.7 20.2 - - - +
458A LYS* 1.3 77.6 - - - +
460A TYR* 1.3 76.1 + - + +
462A SER* 2.9 22.5 + - - +
463A GLY 4.6 0.9 + - - -
524A GLU* 3.0 31.3 + - - -
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Residues in contact with TYR 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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456A LEU* 2.9 31.8 + - + +
457A PHE 4.4 0.2 - - - +
458A LYS 3.3 0.2 - - - -
459A ARG* 1.3 96.1 + - + +
461A THR* 1.3 59.9 + - - +
462A SER 3.7 0.2 - - - -
463A GLY 5.0 0.9 - - - -
464A LYS* 2.8 37.9 + - - +
524A GLU* 2.7 48.1 + - + +
527A ILE* 4.0 17.5 - - + -
528A ASN* 3.5 44.4 + - + +
531A THR* 3.5 16.7 + - + +
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Residues in contact with THR 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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457A PHE 2.7 23.1 + - - +
458A LYS* 3.5 3.8 + - - -
460A TYR* 1.3 80.6 - - - +
462A SER* 1.3 61.4 + - - +
463A GLY 3.2 2.9 - - - -
464A LYS* 2.9 32.8 + - - +
466A ILE* 3.7 28.2 - - + +
468A GLN* 3.5 25.2 + - - +
471A ALA* 3.9 27.8 - - + -
531A THR* 4.1 4.9 - - + -
711A SO4 4.3 5.2 + - - -
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Residues in contact with SER 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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458A LYS* 3.0 19.2 + - - -
459A ARG* 2.9 22.6 + - - -
461A THR* 1.3 77.7 - - - +
463A GLY* 1.3 59.8 + - - +
464A LYS 3.6 2.8 + - - +
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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