Contacts of the helix formed by residues 454 - 466 (chain B) in PDB entry 3QGT
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 454 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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435B ARG* 2.6 63.9 + - - +
436B HIS* 6.2 0.2 - - - -
452B GLY 3.6 4.2 + - - +
453B VAL* 1.3 71.3 - - - +
455B GLN* 1.3 60.8 + - - +
456B LEU 3.5 0.5 + - - -
457B LYS* 3.1 41.7 + - + +
458B ASN* 2.9 26.9 + - - +
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Residues in contact with GLN 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477A TRP* 5.0 0.3 + - - -
479A VAL* 3.5 36.2 - - + +
433B GLN 2.7 28.5 + - - +
434B TRP* 3.0 8.5 + - - +
437B PHE* 3.6 7.8 - - + -
453B VAL* 3.0 11.0 + - + +
454B ASP* 1.3 70.8 - - - +
456B LEU* 1.3 54.2 - - - +
458B ASN* 3.1 10.1 + - - +
459B ILE* 2.7 37.8 + - - +
473B LEU 4.0 6.4 - - - +
474B LEU* 3.4 18.4 - - + +
475B CYS 2.7 49.6 + - - +
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Residues in contact with LEU 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B ILE* 4.0 32.3 - - + +
434B TRP* 3.0 17.3 + - + +
435B ARG* 3.7 35.4 - - - +
455B GLN* 1.3 75.5 - - - +
457B LYS* 1.3 63.5 + - - +
459B ILE* 3.1 31.3 - - + +
460B ILE* 3.3 21.1 + - + +
474B LEU* 3.9 8.8 - - + +
528B PHE* 4.2 24.9 - - + -
532B ILE* 4.3 3.6 - - + -
583B ILE* 4.1 22.2 - - + -
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Residues in contact with LYS 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435B ARG* 4.8 5.1 - - - +
454B ASP* 3.1 38.8 + - + +
456B LEU* 1.3 80.1 - - - +
458B ASN* 1.3 68.5 + - - +
460B ILE* 3.5 7.9 + - - +
461B ASN* 3.1 47.5 + - - +
583B ILE* 6.3 0.7 - - - -
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Residues in contact with ASN 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B VAL* 3.4 30.9 - - - +
454B ASP* 2.9 14.2 + - - +
455B GLN* 3.1 9.1 + - - +
457B LYS* 1.3 90.0 + - - +
459B ILE* 1.3 67.0 + - + +
461B ASN* 3.2 8.4 + - - +
462B LEU* 3.0 32.7 + - + +
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Residues in contact with ILE 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455B GLN 2.7 20.6 + - - +
456B LEU* 3.1 25.8 - - + +
458B ASN* 1.3 73.2 - - + +
460B ILE* 1.3 74.5 + - + +
462B LEU* 3.3 6.6 + - + +
463B ILE* 2.9 38.4 + - + +
472B ILE* 3.6 21.3 - - + +
473B LEU 3.1 37.2 - - - +
474B LEU* 4.2 10.5 - - + +
496B PHE* 3.9 25.1 - - + -
532B ILE* 4.2 14.6 - - + -
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Residues in contact with ILE 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456B LEU* 3.3 20.3 + - + +
457B LYS* 3.7 7.2 - - - +
458B ASN 3.2 0.4 - - - -
459B ILE* 1.3 89.0 - - + +
461B ASN* 1.3 64.1 + - - +
463B ILE* 3.4 3.7 + - - +
464B LYS* 3.2 42.7 + - + +
532B ILE* 4.2 15.9 - - + -
535B VAL* 4.3 10.8 - - + -
536B CYS* 3.9 21.3 - - - -
583B ILE* 3.6 39.3 - - + +
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Residues in contact with ASN 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457B LYS* 3.1 44.6 + - - +
458B ASN* 3.2 9.2 + - - +
460B ILE* 1.3 77.1 - - - +
462B LEU* 1.3 61.5 + - - +
464B LYS* 4.5 11.4 + - - +
465B ASN* 2.9 49.7 + - - +
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Residues in contact with LEU 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458B ASN* 3.0 24.6 + - + +
459B ILE* 3.6 9.6 - - + +
461B ASN* 1.3 74.8 - - + +
463B ILE* 1.3 60.1 + - - +
466B ASP* 2.7 60.2 + - + +
469B SER* 4.5 8.1 - - - +
471B ARG* 4.1 17.7 - - + +
472B ILE* 3.8 27.4 - - + -
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Residues in contact with ILE 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459B ILE* 2.9 25.9 + - + +
460B ILE* 3.7 5.4 - - - +
462B LEU* 1.3 76.0 - - - +
464B LYS* 1.3 60.5 + - - +
467B PRO* 3.6 20.7 - - - +
472B ILE* 3.8 22.2 - - + -
496B PHE* 4.2 13.7 - - + -
498B VAL* 4.0 8.2 - - + +
503B LEU* 4.0 16.2 - - + -
532B ILE* 3.5 30.5 - - + -
536B CYS* 3.7 13.9 - - + -
538B LEU* 3.4 32.9 - - + +
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Residues in contact with LYS 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B ILE* 3.2 34.5 + - + +
461B ASN* 3.8 12.3 + - - +
462B LEU 3.2 0.8 - - - -
463B ILE* 1.3 78.1 - - - +
465B ASN* 1.3 70.4 + - - +
467B PRO* 4.2 4.6 - - - +
535B VAL 3.3 26.7 + - - -
536B CYS* 4.0 20.9 - - + +
537B ASN* 6.1 1.3 - - - +
581B LYS 5.2 4.0 + - - -
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Residues in contact with ASN 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461B ASN* 2.9 41.3 + - - +
464B LYS* 1.3 83.3 - - - +
466B ASP* 1.3 62.4 + - + +
467B PRO* 3.5 6.2 - - - +
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Residues in contact with ASP 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A ASP 5.6 0.5 - - - +
462B LEU* 2.7 36.9 + - + +
465B ASN* 1.3 78.3 - - + +
467B PRO* 1.3 59.8 - - - +
468B THR* 3.2 13.3 + - - -
469B SER* 2.9 39.7 + - - -
472B ILE* 4.1 1.2 - - - +
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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