Contacts of the helix formed by residues 402 - 413 (chain C) in PDB entry 6RKU
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 THR 402 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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467A THR* 4.5 2.5 - - - -
469A LEU* 5.1 4.2 - - - +
400C ALA* 4.2 2.1 - - - +
401C PRO* 1.3 82.5 - - - +
403C PRO* 1.3 70.8 - - + +
404C ALA* 3.5 20.4 - - + +
405C GLU* 3.5 25.4 - - + +
406C ALA* 2.9 27.4 + - - +
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Residues in contact with PRO 403 (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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464A GLN* 5.4 17.9 - - + +
467A THR* 4.2 21.5 - - + +
469A LEU* 5.2 7.9 - - + -
401C PRO 4.1 4.7 - - - +
402C THR* 1.3 90.1 - - + +
404C ALA* 1.3 56.6 + - + +
406C ALA* 3.2 9.5 + - + +
407C LYS* 2.9 28.5 + - - +
459C LEU* 4.4 11.2 - - + +
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Residues in contact with ALA 404 (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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402C THR* 3.3 11.3 - - + +
403C PRO* 1.3 82.1 - - + +
405C GLU* 1.3 59.6 + - + +
407C LYS* 3.2 11.4 + - - +
408C THR* 2.9 31.7 + - - -
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Residues in contact with GLU 405 (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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400C ALA* 5.0 4.5 - - + -
401C PRO* 5.5 4.5 - - + -
402C THR* 3.2 31.6 + - + +
404C ALA* 1.3 78.4 - - + +
406C ALA* 1.3 58.1 + - - +
408C THR* 3.3 12.1 + - - +
409C ALA* 2.9 29.9 + - - +
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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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467A THR* 5.8 2.2 - - + -
396C LEU* 4.0 12.6 - - + +
397C ILE* 5.0 13.9 - - + -
400C ALA* 3.7 23.3 - - + +
402C THR 2.9 13.1 + - - +
403C PRO* 3.4 12.3 - - + +
405C GLU* 1.3 73.9 - - - +
407C LYS* 1.3 60.1 + - - +
409C ALA* 3.3 2.9 + - - +
410C LEU* 2.9 35.7 + - + +
459C LEU* 5.3 7.9 - - + -
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Residues in contact with LYS 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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403C PRO 2.9 12.9 + - - +
404C ALA* 3.2 13.0 + - - +
406C ALA* 1.3 76.6 - - - +
408C THR* 1.3 62.6 + - - +
410C LEU* 3.2 11.9 + - - +
411C VAL* 2.9 32.8 + - + +
452C GLU* 4.3 22.2 + - + +
455C ALA* 3.7 16.2 - - + -
456C GLN* 3.8 43.9 + - - +
459C LEU* 4.3 14.5 - - + +
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Residues in contact with THR 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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404C ALA 2.9 18.0 + - - -
405C GLU* 3.6 15.1 - - - +
407C LYS* 1.3 76.8 - - - +
409C ALA* 1.3 59.2 + - - +
411C VAL* 3.2 8.9 + - + +
412C ALA* 2.9 29.9 + - + +
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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
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396C LEU* 4.0 24.6 - - + +
405C GLU 2.9 17.6 + - - +
406C ALA* 3.7 4.7 - - - +
408C THR* 1.3 76.1 - - - +
410C LEU* 1.3 61.4 + - - +
412C ALA* 3.2 16.1 + - - +
413C ASN* 3.4 23.4 + - - +
415C TRP* 5.6 0.2 - - - -
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Residues in contact with LEU 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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393C ILE* 4.3 20.4 - - + -
396C LEU* 4.0 19.7 - - + -
397C ILE* 5.4 2.2 - - + -
406C ALA* 2.9 23.0 + - + +
407C LYS* 3.2 11.2 + - - +
409C ALA* 1.3 76.1 - - - +
411C VAL* 1.3 62.8 + - - +
413C ASN 3.6 5.0 - - - +
415C TRP* 3.6 49.8 + - + -
450C LEU* 3.7 14.9 - - + +
455C ALA* 4.8 12.6 - - + +
458C ILE* 5.0 14.1 - - + -
459C LEU* 4.4 25.4 - - + -
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Residues in contact with VAL 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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407C LYS* 2.9 23.3 + - + +
408C THR* 3.2 10.7 + - + +
410C LEU* 1.3 78.7 - - - +
412C ALA* 1.3 64.9 + - - +
413C ASN 3.5 3.5 + - - +
441C PHE* 6.2 1.8 - - + -
449C TYR* 5.1 7.3 - - - -
450C LEU* 4.8 21.8 + - + +
451C THR* 4.3 25.8 - - - +
452C GLU* 4.5 13.9 - - + +
455C ALA* 4.3 8.1 - - + -
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Residues in contact with ALA 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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408C THR* 2.9 19.4 + - + +
409C ALA* 3.2 9.8 + - - +
411C VAL* 1.3 80.0 - - - +
413C ASN* 1.3 68.1 + - - +
414C PRO* 3.9 5.0 - - - +
449C TYR* 5.2 4.2 - - - -
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Residues in contact with ASN 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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396C LEU* 4.7 13.9 - - + +
409C ALA* 3.4 18.9 + - - +
410C LEU 3.6 4.8 - - - +
411C VAL 4.0 2.9 - - - +
412C ALA* 1.3 85.0 - - - +
414C PRO* 1.3 77.8 - - + +
415C TRP* 3.5 21.2 + - + -
449C TYR* 4.8 3.9 - - - -
450C LEU* 5.8 0.7 + - - +
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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