Contacts of the helix formed by residues 474 - 483 (chain C) 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 LYS 474 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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367C GLU* 4.9 10.5 - - + -
371C ASP* 3.3 10.1 - - - +
464C TYR* 5.1 0.3 - - - -
473C THR* 1.3 81.5 + - - +
475C ASN* 1.3 68.5 + - - +
476C GLU* 4.2 11.2 - - + +
477C ASP* 2.7 34.0 + - - +
478C LEU 3.9 1.4 + - - -
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Residues in contact with ASN 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370C ASN* 5.8 0.6 - - - +
371C ASP* 2.9 39.9 + - - +
373C TRP* 4.0 19.7 - - + -
374C LEU* 3.9 26.0 - - + -
420C SER* 4.9 6.2 + - - -
474C LYS* 1.3 74.8 - - - +
476C GLU* 1.3 67.7 + - - +
478C LEU* 3.0 17.2 + - - +
479C TRP* 3.0 37.7 + - - +
522C ASN* 4.6 8.1 - - - +
525C THR* 4.9 2.9 + - - -
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Residues in contact with GLU 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474C LYS* 3.1 10.2 + - + -
475C ASN* 1.3 85.0 - - - +
477C ASP* 1.3 58.6 + - - +
479C TRP* 3.2 15.4 + - + +
480C ASP* 2.8 35.4 + - - +
518C LYS* 3.9 22.8 - - + +
522C ASN* 6.1 0.9 - - - +
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Residues in contact with ASP 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464C TYR* 3.7 4.0 - - + -
468C HIS* 4.1 24.4 + - + -
473C THR* 3.5 18.1 - - - -
474C LYS* 2.7 41.7 + - - +
476C GLU* 1.3 75.1 - - - +
478C LEU* 1.3 61.4 + - - +
480C ASP* 3.7 11.8 - - - +
481C SER* 3.1 26.9 + - - -
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Residues in contact with LEU 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360C PHE* 4.1 11.4 - - + -
374C LEU* 3.9 31.2 - - + -
378C PHE* 5.2 0.9 - - + -
445C LEU* 4.5 7.2 - - + -
461C ILE* 3.8 16.6 - - + -
464C TYR* 3.5 41.9 - - + -
474C LYS 3.9 0.2 + - - -
475C ASN 3.0 11.3 + - - +
477C ASP* 1.3 76.1 - - - +
479C TRP* 1.3 81.3 + - + +
481C SER* 3.1 4.9 + - - -
482C MET* 2.8 56.5 + - + +
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Residues in contact with TRP 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373C TRP* 4.0 23.9 - + - -
374C LEU* 4.0 13.9 - - + -
445C LEU* 3.9 18.4 - - + -
448C LEU* 3.7 21.3 - - + -
475C ASN* 3.0 36.9 + - - -
476C GLU* 3.2 12.0 + - - +
478C LEU* 1.3 92.7 - - + +
480C ASP* 1.3 53.3 + - - +
482C MET* 3.5 6.9 - - + +
483C ALA* 2.7 37.9 + - - +
517C VAL* 3.8 9.4 - - + +
518C LYS* 3.6 36.8 - - + +
521C MET* 3.5 47.2 - - + +
522C ASN* 5.1 5.0 + - - -
525C THR* 4.7 1.9 + - + +
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Residues in contact with ASP 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476C GLU* 2.8 26.4 + - - +
477C ASP* 3.7 15.0 - - - +
479C TRP* 1.3 72.7 - - - +
481C SER* 1.3 61.4 + - - +
483C ALA* 3.2 7.9 + - - +
484C SER* 3.1 23.0 + - - -
518C LYS* 3.1 38.2 + - - +
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Residues in contact with SER 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460C GLY* 3.6 13.6 - - - -
463C GLN* 3.1 36.2 + - - +
464C TYR* 3.3 29.2 - - - -
467C LYS* 5.0 0.2 - - - +
468C HIS* 4.4 4.9 - - - -
477C ASP 3.1 13.6 + - - -
478C LEU 3.1 9.4 + - - -
480C ASP* 1.3 74.8 - - - +
482C MET* 1.3 62.4 + - - +
484C SER* 2.6 17.6 + - - -
485C ILE* 3.3 6.4 + - - +
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Residues in contact with MET 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448C LEU* 4.1 9.2 - - + -
452C LEU* 3.6 29.6 - - + +
456C ALA 5.6 0.4 - - - +
457C PHE* 3.8 48.2 - - + +
460C GLY* 3.9 13.5 - - - -
461C ILE* 4.2 6.3 - - + +
478C LEU* 2.8 53.5 + - + +
479C TRP* 3.5 15.9 - - + +
481C SER* 1.3 78.6 - - - +
483C ALA* 1.3 60.4 + - - +
484C SER 3.2 1.1 + - - -
485C ILE* 3.5 15.4 + - - +
517C VAL* 4.1 9.8 - - + +
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Residues in contact with ALA 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479C TRP 2.7 21.5 + - - +
480C ASP* 3.2 7.8 + - - +
482C MET* 1.3 71.9 - - - +
484C SER* 1.3 58.6 + - - +
485C ILE 4.5 3.1 - - - +
515C VAL 3.8 14.0 + - - +
516C ASP* 5.2 1.1 - - - +
517C VAL* 3.7 24.7 - - + +
518C LYS* 5.0 2.2 - - + +
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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