Contacts of the helix formed by residues 453 - 468 (chain B) in PDB entry 3QNF
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 SER 453 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449B ARG 3.0 5.6 - - - +
451B TYR 3.9 0.2 + - - -
452B LEU* 1.3 79.1 - - - +
454B ALA* 1.3 64.3 + - - +
455B ASP* 3.8 9.0 - - - -
456B ALA* 3.7 22.4 - - - +
457B PHE* 3.1 17.0 + - - +
579B ARG* 4.9 10.7 - - - +
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Residues in contact with ALA 454 (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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296B TYR* 4.8 0.7 + - - -
449B ARG* 3.6 44.1 + - + +
450B GLU* 5.5 4.0 - - - +
453B SER* 1.3 73.0 - - - +
455B ASP* 1.3 57.8 + - - +
457B PHE* 3.2 4.5 + - - +
458B LYS* 2.8 34.3 + - - +
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Residues in contact with ASP 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B SER* 3.2 6.6 - - - -
454B ALA* 1.3 79.3 + - - +
456B ALA* 1.3 59.7 + - - +
458B LYS* 3.2 17.4 + - - +
459B SER* 2.8 33.6 + - - -
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Residues in contact with ALA 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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452B LEU* 4.0 11.9 - - + -
453B SER* 3.6 27.8 + - - +
454B ALA 3.4 0.4 - - - -
455B ASP* 1.3 76.8 - - - +
457B PHE* 1.3 64.0 + - - +
459B SER* 3.2 8.6 + - - -
460B GLY* 3.0 19.6 + - - -
482B MET* 5.0 0.9 - - - +
485B ILE* 3.6 18.5 - - + +
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Residues in contact with PHE 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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296B TYR* 3.3 22.2 - - - -
378B PHE* 4.2 20.0 - + - -
381B PHE* 3.7 27.4 - + - -
445B LEU* 3.9 35.7 - - + -
448B LEU* 4.2 10.8 - - + -
449B ARG* 3.7 31.0 - - + -
452B LEU* 4.5 6.4 - - + +
453B SER 3.1 15.6 + - - +
454B ALA 3.4 7.2 - - - +
456B ALA* 1.3 77.1 - - - +
458B LYS* 1.3 63.3 + - - +
460B GLY* 3.3 1.4 + - - -
461B ILE* 3.1 22.6 + - + +
482B MET* 3.8 29.7 - - + +
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Residues in contact with LYS 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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295B ASP* 5.4 1.1 - - - +
296B TYR* 3.6 65.0 - - + +
454B ALA 2.8 14.8 + - - +
455B ASP* 3.4 22.2 - - - +
457B PHE* 1.3 76.3 - - - +
459B SER* 1.3 62.7 + - - +
461B ILE* 3.3 4.1 + - - +
462B VAL* 3.0 28.8 + - + +
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Residues in contact with SER 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 ASP* 2.8 16.5 + - - +
456B ALA* 3.2 9.2 + - - -
458B LYS* 1.3 73.1 - - - +
460B GLY* 1.3 66.9 + - - +
462B VAL* 3.1 8.3 + - - +
463B GLN* 2.8 26.8 + - - +
485B ILE* 3.7 15.9 - - - -
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Residues in contact with GLY 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 ALA 3.0 12.3 + - - -
457B PHE 3.3 3.1 + - - -
459B SER* 1.3 76.5 - - - +
461B ILE* 1.3 56.3 + - - +
463B GLN* 3.5 1.9 + - - +
464B TYR* 2.9 31.2 + - - +
481B SER* 3.6 22.3 - - - -
482B MET* 3.8 21.1 - - - -
485B ILE* 3.9 4.6 - - - +
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Residues in contact with ILE 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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296B TYR* 4.8 10.1 - - + -
297B PHE* 4.9 8.3 - - + -
360B PHE* 5.7 1.6 - - + -
378B PHE* 4.6 24.0 - - + -
457B PHE* 3.1 15.8 + - + +
458B LYS* 3.7 9.6 - - - +
459B SER 3.2 0.2 - - - -
460B GLY* 1.3 75.0 - - - +
462B VAL* 1.3 60.1 + - + +
464B TYR* 3.2 8.1 + - - +
465B LEU* 2.8 36.8 + - + +
478B LEU* 4.9 8.3 - - + -
482B MET* 4.2 2.9 - - + -
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Residues in contact with VAL 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B TYR 3.5 18.2 - - - +
297B PHE* 3.3 30.1 - - - +
298B SER* 3.9 14.6 - - - +
458B LYS* 3.0 21.7 + - + +
459B SER* 3.1 9.4 + - - +
461B ILE* 1.3 77.5 - - + +
463B GLN* 1.3 64.9 + - - +
465B LEU* 3.2 4.1 + - - +
466B GLN* 2.8 48.7 + - - +
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Residues in contact with GLN 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 SER 2.8 19.4 + - - +
460B GLY* 3.9 4.5 - - - +
462B VAL* 1.3 73.3 - - - +
464B TYR* 1.3 55.9 + - - +
466B GLN* 3.6 9.7 - - - +
467B LYS* 2.7 39.2 + - + +
481B SER* 4.7 9.9 - - - +
484B SER* 6.0 1.3 - - - +
485B ILE* 6.5 0.4 - - + -
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Residues in contact with TYR 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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360B PHE* 3.6 32.0 - + - -
364B VAL* 3.3 26.3 + - + +
365B THR 5.6 0.2 - - - -
374B LEU* 5.0 4.9 - - + +
460B GLY 2.9 19.9 + - - +
461B ILE 3.4 4.0 - - - +
463B GLN* 1.3 75.8 - - - +
465B LEU* 1.3 77.4 + - + +
467B LYS* 4.6 0.7 - - - -
468B HIS* 3.1 36.8 + - - +
473B THR* 2.8 36.3 + - + -
474B LYS 5.1 0.2 - - - -
477B ASP 3.7 9.2 - - - -
478B LEU* 3.6 48.7 - - + -
481B SER* 3.4 17.5 + - - +
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Residues in contact with LEU 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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297B PHE* 3.3 48.7 - - + +
299B ILE* 3.5 17.7 - - + -
359B TRP* 4.0 23.3 - - + +
360B PHE* 4.1 13.7 - - + -
363B LEU* 5.1 1.8 - - + -
364B VAL* 3.5 26.4 - - + +
461B ILE* 2.8 24.2 + - + +
462B VAL 3.8 1.3 - - - +
464B TYR* 1.3 86.3 - - + +
466B GLN* 1.3 59.1 + - - +
469B SER* 2.5 36.6 + - - -
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Residues in contact with GLN 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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298B SER* 4.0 16.2 + - - -
299B ILE* 4.0 16.3 - - + +
462B VAL* 2.8 38.1 + - - +
463B GLN* 3.6 7.8 - - - +
465B LEU* 1.3 78.8 - - - +
467B LYS* 1.3 62.4 + - - +
469B SER* 3.4 15.3 + - - -
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Residues in contact with LYS 467 (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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463B GLN* 2.7 23.6 + - + +
464B TYR* 3.8 0.4 - - - +
466B GLN* 1.3 75.5 - - - +
468B HIS* 1.3 87.9 + - + +
469B SER 3.7 1.0 + - - +
471B LYS* 4.3 13.4 + - - +
481B SER* 5.1 4.9 - - - +
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Residues in contact with HIS 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B VAL* 3.7 11.8 - - + +
464B TYR* 3.1 31.3 + + - +
467B LYS* 1.3 106.9 + - + +
469B SER* 1.3 67.5 + - - +
470B TYR 3.3 0.5 + - - -
471B LYS* 2.9 37.2 + - + +
472B ASN 4.4 6.3 - - - -
473B THR* 3.5 30.5 - - + -
477B ASP* 4.1 30.3 + - + +
481B SER* 4.4 11.0 - - - -
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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