Contacts of the helix formed by residues 415 - 429 (chain C) in PDB entry 2QLF
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 415 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414C CYS* 1.3 75.7 - - - +
416C CYS* 1.3 63.9 + - - +
417C ALA* 4.0 2.6 + - - +
418C LYS* 3.0 27.6 + - - +
419C MET* 3.0 19.4 + - - +
452C GLY* 4.3 0.4 - - - -
453C LYS* 3.2 32.6 + - - +
454C ASP* 3.0 22.3 + - - -
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Residues in contact with CYS 416 (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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414C CYS 3.9 0.4 + - - -
415C SER* 1.3 70.9 - - - +
417C ALA* 1.3 64.3 + - - +
419C MET* 3.0 22.8 + - - +
420C GLN* 3.1 16.7 + - + +
452C GLY* 3.8 9.1 - - - -
454C ASP* 3.0 18.0 + - + +
455C GLY* 3.4 43.3 - - - -
456C VAL 3.7 17.3 - - - +
457C THR* 4.2 13.3 - - - +
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Residues in contact with ALA 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415C SER* 3.3 4.7 - - - +
416C CYS* 1.3 79.4 - - - +
418C LYS* 1.3 58.1 + - - +
420C GLN* 3.2 9.1 + - - +
421C ASP* 2.8 32.6 + - - +
454C ASP* 3.8 6.4 + - - +
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Residues in contact with LYS 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C TYR* 5.2 8.5 - - + -
414C CYS* 3.6 29.2 - - + -
415C SER* 3.0 29.3 + - - +
417C ALA* 1.3 76.9 - - - +
419C MET* 1.3 57.2 + - - +
421C ASP* 3.8 16.4 + - - +
422C LEU* 2.8 46.3 + - + +
453C LYS* 5.5 0.7 - - - +
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Residues in contact with MET 419 (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 ILE* 3.8 26.9 - - + -
375C ASN* 3.4 20.9 - - - -
414C CYS* 3.6 15.3 - - + -
415C SER 3.0 10.7 + - - +
416C CYS* 3.0 10.8 + - - +
418C LYS* 1.3 77.8 - - - +
420C GLN* 1.3 62.3 + - - +
422C LEU* 3.8 5.0 - - - +
423C LEU* 3.2 29.8 + - - +
441C LEU* 5.4 2.7 - - - -
450C ILE* 4.3 7.2 - - + +
451C TYR 3.6 5.4 - - - +
452C GLY* 3.3 34.8 - - - +
457C THR* 3.9 22.9 - - + -
462C LEU* 4.0 18.4 - - + -
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Residues in contact with GLN 420 (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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416C CYS* 3.1 16.7 + - + +
417C ALA* 3.5 10.5 - - - +
419C MET* 1.3 76.5 - - - +
421C ASP* 1.3 63.7 + - - +
424C LYS* 3.1 24.1 + - - +
457C THR* 2.8 30.6 + - - +
458C PRO 4.3 0.6 + - - -
461C ASP* 3.6 15.5 - - - +
462C LEU* 2.9 33.9 - - - +
465C HIS* 3.2 31.1 + - + +
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Residues in contact with ASP 421 (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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417C ALA 2.8 18.9 + - - +
418C LYS* 3.8 18.3 + - - +
420C GLN* 1.3 74.5 - - - +
422C LEU* 1.3 66.6 + - - +
424C LYS* 3.1 11.8 + - - +
425C LYS* 2.6 64.3 + - - +
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Residues in contact with LEU 422 (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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371C ILE* 3.5 33.3 - - + +
373C ILE* 4.3 11.9 - - + -
411C TYR* 3.3 57.0 + - + +
414C CYS* 4.1 12.1 - - - -
418C LYS* 2.8 30.2 + - + +
419C MET* 3.8 2.7 - - - +
421C ASP* 1.3 76.4 + - - +
423C LEU* 1.3 73.5 + - + +
425C LYS* 3.8 6.0 + - - +
426C ALA* 3.3 18.2 + - - +
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Residues in contact with LEU 423 (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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371C ILE* 4.4 10.3 - - + -
373C ILE* 4.7 8.3 - - + -
419C MET 3.2 10.5 + - - +
422C LEU* 1.3 91.7 - - + +
424C LYS* 1.3 67.2 + - - +
426C ALA* 3.2 2.8 + - - -
427C SER* 3.0 19.2 + - - -
437C PHE* 4.7 1.3 - - + -
439C CYS* 4.0 28.0 - - - -
441C LEU* 5.2 1.6 - - + -
462C LEU* 3.6 48.9 - - + +
465C HIS* 4.1 8.7 - - + -
466C PHE* 3.3 31.8 - - + -
481C PHE* 5.1 4.3 - - + -
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Residues in contact with LYS 424 (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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420C GLN 3.1 19.1 + - - +
421C ASP* 3.1 14.8 + - - +
423C LEU* 1.3 76.7 - - - +
425C LYS* 1.3 68.4 + - + +
427C SER* 2.5 27.0 + - - +
428C GLU* 3.1 33.5 + - + +
465C HIS* 3.6 27.3 - - + +
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Residues in contact with LYS 425 (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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421C ASP* 2.6 51.6 + - - +
422C LEU* 4.0 6.5 - - - +
424C LYS* 1.3 82.7 - - + +
426C ALA* 1.3 61.5 + - - +
428C GLU* 3.0 28.2 + - - +
429C GLU* 3.0 19.8 + - + +
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Residues in contact with ALA 426 (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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369C LYS* 5.8 1.6 - - + -
371C ILE* 3.6 31.2 - - + -
422C LEU 3.3 8.7 + - - +
423C LEU 3.2 10.4 + - - +
425C LYS* 1.3 78.6 - - - +
427C SER* 1.3 56.3 + - - +
429C GLU* 3.2 26.9 + - - +
431C HIS* 2.7 30.9 + - + +
437C PHE* 4.7 3.1 - - + -
466C PHE* 4.2 10.1 - - + -
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Residues in contact with SER 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C LEU 3.0 10.8 + - - -
424C LYS* 2.5 26.5 + - - +
426C ALA* 1.3 76.2 - - - +
428C GLU* 1.3 61.6 + - - +
429C GLU 3.4 2.9 - - - +
465C HIS* 3.1 34.3 + - - +
466C PHE* 3.7 16.7 - - - -
470C ARG 4.3 5.2 + - - +
471C CYS* 3.3 29.9 - - - +
473C THR* 4.9 0.5 + - - -
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Residues in contact with GLU 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C LYS* 3.1 43.9 + - + +
425C LYS* 3.0 24.2 + - - +
427C SER* 1.3 81.4 - - - +
429C GLU* 1.3 68.0 + - - +
470C ARG 5.9 1.3 - - - +
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Residues in contact with GLU 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C LYS* 3.9 27.0 + - - -
371C ILE* 5.6 0.5 - - - +
409C ILE* 6.0 0.5 - - - +
425C LYS* 3.0 17.5 + - + +
426C ALA* 3.2 29.2 + - - +
427C SER 3.9 1.7 - - - +
428C GLU* 1.3 84.5 - - - +
430C ASP* 1.3 66.1 + - - +
431C HIS* 3.5 20.7 + - + +
473C THR* 3.6 6.2 + - - +
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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