Contacts of the helix formed by residues 405 - 417 (chain C) in PDB entry 4K9N
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 PHE 405 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52C GLY* 5.1 6.7 - - - -
55C ASP* 3.7 28.9 - - + -
56C GLY* 5.0 2.0 - - - -
59C GLN* 3.9 19.5 - - - -
84C ASN* 3.7 29.4 - - + +
373C LEU* 4.3 3.8 - - + -
374C ASN 5.4 0.2 - - - -
375C GLU* 3.1 7.1 + - - +
396C TYR* 4.0 23.1 - + + -
397C PHE* 4.0 9.9 - - - -
398C CYS* 3.6 32.1 - - + -
403C LEU 3.4 0.8 + - - -
404C GLY* 1.3 78.8 - - - +
406C ALA* 1.3 66.6 + - + +
407C LEU 3.3 0.7 - - - -
408C PRO* 3.3 5.6 - - - +
409C ALA* 2.8 54.5 + - + +
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Residues in contact with ALA 406 (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 LEU* 3.8 22.6 - - + +
374C ASN 4.3 3.8 - - - +
375C GLU* 2.9 42.2 + - + +
405C PHE* 1.3 82.8 - - + +
407C LEU* 1.3 58.2 + - - +
410C ALA* 2.8 33.8 + - - +
424C ALA* 4.2 0.6 - - + +
426C ILE* 4.1 12.8 - - + -
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Residues in contact with LEU 407 (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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375C GLU* 5.2 1.4 + - - -
404C GLY* 5.0 1.5 - - - -
405C PHE 4.8 0.2 - - - +
406C ALA* 1.3 81.3 - - - +
408C PRO* 1.3 71.1 - - + +
410C ALA 3.5 4.2 + - - -
411C ILE* 3.5 13.5 + - + +
426C ILE* 3.6 23.1 - - + +
430C SER 6.1 0.4 - - - +
431C ALA* 3.8 29.6 - - + +
434C SER* 3.9 10.1 - - - +
435C ILE* 4.3 13.7 - - + -
437C ALA* 3.7 23.6 - - + -
438C LEU* 3.9 22.2 - - + +
450C PHE* 3.7 29.6 - - + -
452C ILE* 5.3 4.9 - - + -
518C LEU* 5.8 0.9 - - + -
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Residues in contact with PRO 408 (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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48C ALA 4.4 0.4 - - - +
49C CYS* 3.7 27.1 - - - +
52C GLY* 4.1 9.2 - - - -
53C ILE* 3.3 20.4 - - + +
404C GLY 3.1 26.2 - - - +
405C PHE 3.3 10.1 - - - +
407C LEU* 1.3 93.3 - - + +
409C ALA* 1.3 62.5 + - - +
411C ILE* 3.0 12.9 + - + +
412C GLY 3.2 8.7 + - - -
434C SER* 3.6 16.6 - - - +
437C ALA* 3.9 16.8 - - + -
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Residues in contact with ALA 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C GLY 3.2 16.3 + - - +
56C GLY* 3.6 6.6 - - - -
373C LEU* 3.7 11.2 - - + -
405C PHE* 2.8 56.7 + - + +
408C PRO* 1.3 74.1 - - - +
410C ALA* 1.3 57.7 + - - +
412C GLY* 3.1 2.3 + - - +
413C VAL* 2.8 32.2 + - - +
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Residues in contact with ALA 410 (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 LEU* 3.6 21.9 - - + +
406C ALA 2.8 19.5 + - - +
407C LEU 3.7 5.4 - - - +
408C PRO 3.1 0.2 - - - -
409C ALA* 1.3 76.7 - - - +
411C ILE* 1.3 57.0 + - - +
413C VAL* 4.4 0.4 - - - -
414C GLN* 3.0 22.7 + - - +
422C VAL* 3.6 5.4 - - + +
424C ALA* 3.7 18.2 - - + -
448C THR* 3.3 30.6 + - + -
450C PHE* 4.4 0.4 - - + -
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Residues in contact with ILE 411 (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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53C ILE* 4.3 8.5 - - + -
407C LEU* 3.5 17.0 - - + +
408C PRO* 3.0 8.4 + - + +
410C ALA* 1.3 75.2 - - - +
412C GLY* 1.3 58.6 + - - +
414C GLN 3.4 0.5 + - - -
415C LEU* 3.0 27.5 + - - +
437C ALA* 3.1 40.4 - - + +
438C LEU 4.3 0.2 - - - +
440C THR* 4.3 15.7 - - + -
441C ALA* 3.8 17.9 - - + -
446C ILE* 3.6 30.7 - - + +
448C THR* 3.7 7.0 - - - +
450C PHE* 3.8 20.9 - - + -
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Residues in contact with GLY 412 (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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53C ILE* 3.3 33.8 - - - +
57C TYR* 3.5 14.1 - - - -
408C PRO 3.2 7.3 + - - -
409C ALA 3.1 4.9 + - - -
411C ILE* 1.3 74.5 - - - +
413C VAL* 1.3 64.4 + - - +
415C LEU* 3.3 6.9 + - - +
416C ALA* 2.9 23.6 + - - +
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Residues in contact with VAL 413 (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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56C GLY* 3.5 24.4 - - - +
60C ALA* 4.1 11.7 - - + -
371C ILE* 3.7 38.4 - - + -
373C LEU* 4.4 5.4 - - + -
396C TYR* 4.0 24.9 - - + -
409C ALA 2.8 24.8 + - - +
410C ALA* 3.9 6.3 - - - +
412C GLY* 1.3 73.0 - - - +
414C GLN* 1.3 58.3 + - - +
416C ALA* 3.0 4.9 + - - +
417C GLU* 2.9 26.7 + - - +
422C VAL* 3.8 9.0 - - + -
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Residues in contact with GLN 414 (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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410C ALA 3.0 10.2 + - - +
412C GLY 3.3 0.2 - - - -
413C VAL* 1.3 77.3 - - - +
415C LEU* 1.3 61.3 + - - +
417C GLU 3.0 29.7 + - - -
418C PRO* 3.5 16.1 + - + +
420C ARG 2.8 24.3 + - - +
421C GLN* 3.4 13.9 + - - +
422C VAL* 2.9 30.3 + - + +
446C ILE* 3.5 20.0 - - + -
447C PRO* 3.8 19.0 - - + +
448C THR* 3.2 28.7 - - - +
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Residues in contact with LEU 415 (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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21C PHE* 4.0 28.5 - - + -
40C ARG* 3.6 29.9 + - - +
42C ILE* 4.1 21.8 - - + -
53C ILE* 5.3 1.1 - - + -
57C TYR* 4.0 17.6 - - + -
411C ILE 3.0 15.3 + - - +
412C GLY* 3.5 10.1 - - - +
413C VAL 3.3 0.2 - - - -
414C GLN* 1.3 75.9 - - - +
416C ALA* 1.3 60.2 + - - +
417C GLU 3.6 0.2 + - - -
418C PRO* 3.8 11.1 - - - +
444C TYR* 5.7 1.3 - - + +
446C ILE* 3.8 30.6 - - + +
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Residues in contact with ALA 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C TYR* 3.8 27.1 - - + +
60C ALA* 3.6 24.5 - - + -
61C SER* 4.2 10.6 - - - +
412C GLY 2.9 12.9 + - - +
413C VAL 3.0 8.5 + - - +
415C LEU* 1.3 76.3 - - - +
417C GLU* 1.3 66.4 + - + +
418C PRO* 3.5 7.7 - - - +
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Residues in contact with GLU 417 (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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60C ALA* 4.2 24.8 - - + +
62C ARG* 5.4 3.3 + - - -
371C ILE* 4.0 26.7 - - + -
413C VAL 2.9 13.3 + - - +
414C GLN* 3.0 20.3 + - - -
415C LEU 3.3 0.2 - - - -
416C ALA* 1.3 84.8 - - - +
418C PRO* 1.3 62.1 - - - +
419C GLU* 3.0 8.8 + - - +
420C ARG* 3.1 35.2 + - + +
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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