Contacts of the helix formed by residues 406 - 425 (chain C) in PDB entry 2QLR
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 406 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404C SER 3.6 1.8 + - - -
405C ALA* 1.3 74.2 - - - +
407C PRO* 1.4 68.7 - - - +
408C GLU* 3.6 11.3 + - - +
409C GLN* 2.8 52.0 + - - +
410C MET* 3.0 12.6 + - - +
428C GOL 3.5 18.6 + - - -
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Residues in contact with PRO 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C GLN* 5.4 2.7 - - - +
332C ALA* 4.2 28.3 - - + -
405C ALA 4.6 0.7 - - - +
406C SER* 1.4 88.3 - - - +
408C GLU* 1.3 67.1 + - - +
410C MET* 3.8 5.5 + - - +
411C ASP* 3.2 25.8 + - - +
428C GOL 3.7 12.8 - - - +
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Residues in contact with GLU 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C SER* 3.1 10.0 + - - +
407C PRO* 1.3 96.1 - - - +
409C GLN* 1.3 59.6 + - + +
411C ASP* 3.2 8.1 + - - +
412C VAL* 3.0 35.0 + - + +
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Residues in contact with GLN 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C SER 4.5 0.5 - - - +
405C ALA* 3.1 12.8 - - + -
406C SER* 2.8 36.0 + - - +
408C GLU* 1.3 76.6 - - + +
410C MET* 1.3 65.1 + - - +
412C VAL* 3.5 4.0 + - - +
413C ALA 3.0 18.9 + - - -
428C GOL 5.1 0.5 + - - -
33D MET 5.7 0.4 + - - -
34D ILE* 3.1 37.5 - - + +
426D GOL 3.9 26.1 + - - -
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Residues in contact with MET 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C GLN* 3.4 40.4 - - - +
332C ALA* 3.6 14.6 - - + +
333C ILE* 3.4 39.3 - - + -
336C ALA* 4.1 12.3 - - + -
401C SER 5.1 0.4 - - - +
402C PHE* 3.7 17.0 - - + +
405C ALA* 3.9 18.4 - - + +
406C SER 3.0 16.5 + - - +
407C PRO* 4.1 6.5 - - - +
409C GLN* 1.3 74.9 - - - +
411C ASP* 1.3 56.7 + - - +
413C ALA* 4.2 5.6 - - - -
414C PHE* 2.9 42.8 + - + -
36D LEU* 4.7 7.4 - - + -
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Residues in contact with ASP 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C ALA* 4.5 8.3 - - + +
339C LYS* 2.7 34.7 + - - +
340C TRP* 3.3 25.2 + - - +
407C PRO 3.2 16.6 + - - +
408C GLU* 3.4 11.4 - - - +
409C GLN 3.2 0.6 - - - -
410C MET* 1.3 78.9 - - - +
412C VAL* 1.3 62.5 + - - +
415C GLN* 3.0 26.0 + - - +
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Residues in contact with VAL 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C VAL* 5.2 5.4 - - + -
408C GLU* 3.0 19.8 + - + +
409C GLN* 4.3 3.8 - - - +
411C ASP* 1.3 78.9 - - - +
413C ALA* 1.3 65.2 + - - +
415C GLN* 3.6 11.3 - - + +
416C VAL* 3.1 44.3 + - + +
34D ILE* 5.4 9.6 - - + -
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Residues in contact with ALA 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C VAL* 3.8 25.1 - - + +
381C MET* 6.0 3.3 - - - +
409C GLN 3.0 19.8 + - - +
410C MET 3.8 3.4 - - - +
412C VAL* 1.3 77.9 - - - +
414C PHE* 1.3 61.5 + - - +
416C VAL 3.5 0.2 + - - -
417C LEU* 3.1 24.3 + - - +
34D ILE* 3.6 23.2 - - + +
36D LEU* 4.1 19.5 - - + -
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Residues in contact with PHE 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C ILE* 3.5 37.9 - - + -
336C ALA* 3.6 31.6 - - + +
337C ALA* 4.0 12.6 - - + -
340C TRP* 3.8 11.1 - - + +
341C LEU* 3.1 42.3 - - + +
356C LEU* 4.3 7.2 - - + -
358C ILE* 4.9 4.9 - - + -
381C MET* 5.0 4.7 - - + -
400C ALA* 4.8 7.4 - - + -
410C MET* 2.9 31.8 + - + +
413C ALA* 1.3 69.7 - - - +
415C GLN* 1.4 64.8 + - - +
417C LEU* 3.2 14.2 + - + +
418C ALA* 3.0 24.1 + - - +
36D LEU* 4.1 15.0 - - + -
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Residues in contact with GLN 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C TRP* 3.4 51.3 - - + -
411C ASP* 3.0 12.8 + - - +
412C VAL* 3.6 16.8 - - - +
414C PHE* 1.4 74.0 - - - +
416C VAL* 1.3 79.9 + - + +
418C ALA* 3.5 1.6 + - - +
419C GLN* 3.2 27.2 + - - +
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Residues in contact with VAL 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374C ALA 5.4 0.2 - - - +
377C MET* 3.6 44.6 - - + +
379C VAL* 3.8 21.3 - - + -
412C VAL* 3.1 32.3 + - + +
413C ALA 3.9 2.7 - - - +
415C GLN* 1.3 95.3 - - + +
417C LEU* 1.3 58.0 + - - +
419C GLN* 3.5 4.4 + - - +
420C LEU* 3.1 31.4 + - + +
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Residues in contact with LEU 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C LEU* 4.1 23.6 - - + -
358C ILE* 4.9 3.4 - - + -
369C LEU* 3.9 17.5 - - + -
370C ILE* 5.8 1.6 - - + -
374C ALA* 5.6 8.1 - - + -
379C VAL* 4.9 6.0 - - + +
381C MET* 4.2 21.8 - - + -
398C LEU* 3.7 32.5 - - + -
413C ALA 3.1 14.3 + - - +
414C PHE* 3.4 11.7 - - + +
416C VAL* 1.3 73.8 - - - +
418C ALA* 1.3 55.4 + - - +
420C LEU* 3.1 6.4 + - + -
421C ILE* 2.7 64.4 + - + +
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Residues in contact with ALA 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C TRP* 3.3 35.7 - - + +
341C LEU* 3.9 13.6 - - + +
344C LEU* 4.0 5.1 - - + +
414C PHE 3.0 15.5 + - - +
415C GLN* 3.5 4.7 + - - +
417C LEU* 1.3 76.2 - - - +
419C GLN* 1.3 61.5 - - - +
421C ILE* 3.3 4.8 + - - +
422C LYS* 3.0 38.3 + - - +
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Residues in contact with GLN 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415C GLN* 3.2 22.7 + - - +
416C VAL* 3.8 4.9 - - - +
417C LEU 3.1 0.6 - - - -
418C ALA* 1.3 79.8 - - - +
420C LEU* 1.3 58.3 + - + +
422C LYS* 3.5 22.4 + - - +
423C GLU* 2.7 57.9 + - - +
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Residues in contact with LEU 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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369C LEU* 3.6 15.2 - - + +
373C LYS* 3.4 27.4 - - + +
374C ALA* 3.2 45.5 - - + +
377C MET* 3.8 24.0 - - + -
416C VAL* 3.1 22.9 + - + +
417C LEU* 3.1 7.2 + - + +
419C GLN* 1.3 78.3 - - + +
421C ILE* 1.3 62.6 + - - +
423C GLU* 3.3 20.6 + - + +
424C SER* 3.1 24.9 + - - -
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Residues in contact with ILE 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C LEU* 4.5 10.3 - - + -
344C LEU* 4.1 27.6 - - + +
345C ALA* 5.5 2.7 - - + -
358C ILE* 5.6 0.2 - - + -
360C VAL* 3.7 39.3 - - + -
361C LYS 4.8 2.9 - - - +
363C ILE* 4.5 3.7 - - + +
369C LEU* 3.9 23.3 - - + -
417C LEU* 2.7 51.5 + - + +
418C ALA* 3.6 4.3 - - - +
420C LEU* 1.3 71.7 - - - +
422C LYS* 1.3 62.1 + - - +
424C SER* 3.3 5.2 + - - -
425C LEU* 3.2 30.9 + - + +
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Residues in contact with LYS 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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344C LEU* 3.9 31.7 - - + +
418C ALA* 3.0 38.7 + - - +
419C GLN* 3.6 22.3 - - - +
421C ILE* 1.3 75.0 - - - +
423C GLU* 1.3 61.9 + - - +
424C SER 3.2 1.2 + - - -
425C LEU* 3.6 25.4 + - + +
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Residues in contact with GLU 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C LYS* 4.3 11.6 + - - +
419C GLN* 2.7 51.7 + - - +
420C LEU* 3.3 24.1 + - + +
422C LYS* 1.3 76.0 - - - +
424C SER* 1.3 59.4 + - - +
425C LEU 3.4 1.3 - - - -
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Residues in contact with SER 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C GLY 5.5 0.5 - - - +
363C ILE* 3.6 24.5 - - - +
369C LEU* 3.1 25.7 - - - +
373C LYS* 3.5 20.5 + - - +
420C LEU 3.1 7.4 + - - -
421C ILE 3.4 10.1 - - - -
422C LYS 3.2 0.4 - - - -
423C GLU* 1.3 76.0 - - - +
425C LEU* 1.3 62.8 + - - +
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Residues in contact with LEU 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C LEU* 4.7 12.3 - - + -
361C LYS 4.2 5.4 - - - +
362C GLY* 3.9 37.2 - - - +
363C ILE* 4.7 2.7 - - + -
421C ILE* 3.2 19.8 + - + +
422C LYS* 3.7 29.6 - - + +
423C GLU 3.4 2.3 - - - -
424C SER* 1.3 84.4 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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