Contacts of the helix formed by residues 413 - 430 (chain C) in PDB entry 3FKS
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 ASP 413 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411C ASP 3.9 2.2 + - - +
412C LEU* 1.3 72.8 - - - +
414C ALA* 1.3 60.7 + - - +
415C SER* 3.4 21.4 + - - -
416C THR* 2.7 27.9 + - - +
417C LYS* 3.0 31.0 + - - +
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Residues in contact with ALA 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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413C ASP* 1.3 77.6 - - - +
415C SER* 1.3 62.2 - - - +
416C THR 3.2 2.1 + - - -
417C LYS* 5.0 2.0 - - - -
418C GLN* 3.8 22.0 + - - +
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Residues in contact with SER 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C ASP* 3.4 12.7 + - - -
414C ALA* 1.3 79.2 - - - +
416C THR* 1.3 63.1 + - - +
418C GLN* 5.1 0.7 - - - -
419C THR* 4.0 19.1 + - - +
454D GLU* 5.9 4.0 - - - +
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Residues in contact with THR 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C VAL* 4.8 9.1 - - + +
405C PHE* 6.6 0.2 - - + -
412C LEU* 3.4 20.0 - - - +
413C ASP* 2.7 48.4 + - - +
414C ALA 3.2 0.2 - - - -
415C SER* 1.3 86.5 - - - +
417C LYS* 1.3 63.1 + - - +
418C GLN 3.5 1.1 - - - -
419C THR* 3.2 8.0 + - - -
420C LEU* 3.2 25.6 + - - +
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Residues in contact with LYS 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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412C LEU* 3.6 30.3 - - + +
413C ASP 3.0 19.6 + - - +
414C ALA* 4.8 2.2 - - - +
416C THR* 1.3 77.1 + - - +
418C GLN* 1.3 66.7 + - - +
420C LEU* 3.5 1.2 + - - +
421C VAL* 3.3 43.1 + - + +
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Residues in contact with GLN 418 (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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395C PHE* 6.5 0.2 - - + -
414C ALA 3.8 16.9 + - - +
415C SER 5.6 0.2 - - - -
416C THR 3.5 0.2 - - - -
417C LYS* 1.3 81.3 - - - +
419C THR* 1.3 67.2 + - + +
421C VAL* 4.1 3.1 - - - +
422C ARG* 3.3 44.2 + - - +
456C ASP* 3.7 15.6 - - - +
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Residues in contact with THR 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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395C PHE* 3.6 36.0 - - + -
399C TYR* 4.2 6.6 - - - -
402C VAL* 4.3 17.6 - - - +
415C SER 4.0 15.4 + - - +
416C THR* 3.2 16.4 + - - -
418C GLN* 1.3 81.7 - - + +
420C LEU* 1.3 60.3 + - - +
422C ARG* 4.8 0.2 - - - -
423C GLY* 2.6 34.2 + - - +
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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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399C TYR* 4.2 13.1 - - + -
402C VAL* 4.3 14.6 - - + -
403C ALA* 6.1 0.2 - - - -
406C ALA* 3.9 28.3 - - + -
412C LEU* 3.6 32.3 - - + -
416C THR 3.2 14.0 + - - +
417C LYS 4.0 3.1 - - - +
418C GLN 3.4 0.2 - - - -
419C THR* 1.3 81.4 + - - +
421C VAL* 1.3 68.1 + - + +
424C GLU* 3.3 35.6 + - + +
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Residues in contact with VAL 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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412C LEU* 6.1 0.2 - - + -
417C LYS* 3.3 46.5 + - + +
418C GLN* 4.1 3.8 - - - +
419C THR 3.3 0.4 - - - -
420C LEU* 1.3 83.7 - - + +
422C ARG* 1.3 64.7 + - - +
424C GLU* 4.1 1.6 - - - +
425C ARG* 3.3 49.9 + - - +
456C ASP* 4.2 27.8 - - + +
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Residues in contact with ARG 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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395C PHE* 4.1 22.4 - - - -
418C GLN* 3.3 37.0 + - - +
419C THR 4.3 1.1 - - - +
421C VAL* 1.3 79.4 - - - +
423C GLY* 1.3 57.1 + - - +
425C ARG* 3.3 5.3 + - - +
426C LEU* 3.0 38.6 + - + +
450C GLY 2.7 39.3 + - - +
451C VAL* 2.7 27.6 + - - +
452C ASN 4.3 2.6 + - - -
453C GLY* 3.4 23.3 - - - +
456C ASP* 3.5 26.5 + - - +
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Residues in contact with GLY 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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395C PHE* 4.1 14.3 - - - -
396C LEU* 4.4 3.7 - - - +
399C TYR* 3.6 25.3 - - - -
419C THR 2.6 24.8 + - - -
422C ARG* 1.3 74.0 - - - +
424C GLU* 1.3 57.5 + - - +
426C LEU* 3.7 7.2 + - - +
427C THR* 3.0 21.7 + - - -
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Residues in contact with GLU 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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399C TYR* 3.6 22.5 + - + +
420C LEU* 3.3 31.7 + - + +
421C VAL* 4.1 3.4 - - - +
422C ARG 3.2 0.4 - - - -
423C GLY* 1.3 76.2 - - - +
425C ARG* 1.3 69.5 + - - +
427C THR* 3.3 18.3 - - - +
428C GLN* 3.7 6.1 + - - +
460C LEU* 3.9 30.8 - - + +
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Residues in contact with ARG 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 VAL* 3.3 35.2 + - - +
422C ARG* 3.3 5.7 + - - +
424C GLU* 1.3 81.6 + - - +
426C LEU* 1.3 63.4 + - - +
427C THR 3.2 0.4 - - - -
428C GLN* 3.6 3.7 + - - +
429C LEU* 3.2 22.2 + - - +
455C LEU* 3.5 27.0 - - + +
456C ASP* 3.5 18.1 + - - +
457C GLY 5.2 0.6 + - - -
458C ILE 2.8 27.1 + - - -
459C GLU* 3.9 3.4 - - - +
460C LEU* 3.4 38.0 - - + +
463C ILE* 3.9 29.1 - - + +
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Residues in contact with LEU 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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392C LEU* 3.9 29.4 - - + -
395C PHE* 4.3 14.4 - - + -
396C LEU* 4.1 12.3 - - + -
422C ARG* 3.0 43.6 + - + +
423C GLY* 3.9 6.3 - - - +
425C ARG* 1.3 75.3 - - - +
427C THR* 1.3 64.2 + - - +
429C LEU* 3.3 26.3 + - + +
430C LEU* 3.1 30.4 + - + +
447C ILE* 5.2 2.5 - - + +
450C GLY* 3.9 21.5 - - - +
451C VAL* 4.5 6.1 - - + +
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Residues in contact with THR 427 (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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363C ILE* 3.8 33.6 - - + +
396C LEU* 4.9 5.8 - - - +
399C TYR* 3.7 18.0 + - + +
423C GLY 3.0 17.4 + - - -
424C GLU* 3.3 11.7 + - - -
425C ARG 3.2 0.4 - - - -
426C LEU* 1.3 78.9 - - - +
428C GLN* 1.3 63.2 + - - +
430C LEU* 3.2 14.7 + - - +
431C LYS* 3.5 15.2 + - - +
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Residues in contact with GLN 428 (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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424C GLU 3.7 6.5 + - - +
425C ARG* 3.6 4.6 + - - +
427C THR* 1.3 80.4 - - - +
429C LEU* 1.3 62.0 + - - +
431C LYS* 2.9 58.5 + - - +
460C LEU* 4.8 12.8 - - + +
463C ILE* 3.6 32.8 - - + +
464C GLY* 4.6 11.6 - - - +
467C GLU* 5.7 0.7 - - - +
376F GLU* 5.6 0.8 + - - -
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Residues in contact with LEU 429 (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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153C LYS* 3.2 25.7 + - + +
425C ARG 3.2 17.4 + - - +
426C LEU* 3.4 30.3 - - + +
427C THR 3.1 0.6 - - - -
428C GLN* 1.3 79.1 - - - +
430C LEU* 1.3 60.7 + - + +
446C LEU* 3.4 50.9 - - + +
447C ILE* 4.7 4.5 - - + -
450C GLY* 4.3 1.6 - - - -
455C LEU* 3.5 27.4 - - + -
463C ILE* 3.9 13.7 - - + +
466C PHE* 5.5 3.8 - - + -
467C GLU* 4.7 5.2 - - + +
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Residues in contact with LEU 430 (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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153C LYS* 3.6 39.9 - - + +
154C ALA* 3.6 27.9 + - + +
157C ALA* 4.4 10.3 - - + -
158C LEU* 4.5 10.1 - - + -
363C ILE* 6.3 0.9 - - - -
364C ARG 4.6 1.7 - - - +
365C PRO* 5.2 2.3 - - - +
392C LEU* 4.1 16.4 - - + -
396C LEU* 3.7 31.0 - - + -
426C LEU* 3.1 18.5 + - + +
427C THR* 3.2 6.2 + - - +
429C LEU* 1.3 79.4 - - + +
431C LYS* 1.3 66.7 + - - +
432C GLN* 3.7 2.4 + - - +
447C ILE* 5.5 7.2 - - + -
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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