Contacts of the helix formed by residues 428 - 439 (chain C) in PDB entry 3KDO
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 HIS 428 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410C GLN* 3.4 34.3 - - + +
424C TYR* 2.7 67.7 + + + +
425C ALA 2.6 22.0 + - - +
426C LYS 3.6 0.4 - - - -
427C THR* 1.3 99.4 + - + +
429C LYS* 1.3 66.5 + - - +
430C GLU 3.6 0.4 - - - -
431C LEU* 3.6 5.9 + - + +
432C ALA* 3.0 15.3 + - - +
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Residues in contact with LYS 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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428C HIS* 1.3 67.0 - - - +
430C GLU* 1.3 79.9 + - - +
432C ALA* 2.7 19.8 + - - +
433C ARG* 2.8 25.5 + - + +
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Residues in contact with GLU 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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397C HIS* 2.9 27.5 + - - -
399C ASP* 5.2 2.7 - - - +
403C ALA* 3.4 43.5 - - + +
406C ARG* 2.9 33.6 + - + +
407C ALA* 3.6 7.2 - - + +
410C GLN* 3.0 24.9 - - - +
429C LYS* 1.3 82.8 + - - +
431C LEU* 1.3 62.9 + - - +
433C ARG* 3.4 0.6 + - - -
434C ALA* 2.9 10.7 + - - +
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Residues in contact with LEU 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C PRO* 4.2 13.9 - - + +
407C ALA* 3.9 10.1 - - - +
410C GLN* 2.8 25.5 - - + +
411C ALA* 3.9 33.4 - - + +
414C ALA* 5.1 0.4 - - + -
421C LEU* 3.8 14.6 - - + +
424C TYR* 3.8 22.4 - - + -
425C ALA* 3.7 30.3 - - + +
428C HIS* 3.7 6.3 - - + +
429C LYS 3.1 0.2 - - - -
430C GLU* 1.3 72.7 - - - +
432C ALA* 1.3 66.3 + - - +
434C ALA* 2.9 4.7 + - - +
435C LEU* 2.9 38.1 + - + +
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Residues in contact with ALA 432 (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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425C ALA* 4.1 21.9 - - + +
426C LYS* 6.0 0.4 - - - -
428C HIS 3.0 11.4 + - - +
429C LYS* 2.7 16.6 + - - +
431C LEU* 1.3 74.8 - - - +
433C ARG* 1.3 60.1 + - + +
434C ALA 3.1 0.5 + - - -
435C LEU* 3.1 6.7 + - - +
436C GLU* 2.9 28.6 + - - +
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Residues in contact with ARG 433 (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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397C HIS* 4.2 0.7 - - + -
398C PRO* 3.2 38.6 + - + +
399C ASP* 2.6 41.1 + - - +
429C LYS* 2.8 28.7 + - + +
430C GLU 4.0 3.4 - - - +
432C ALA* 1.3 74.8 - - + +
434C ALA* 1.3 61.0 + - - +
436C GLU* 2.9 37.0 + - - +
437C LYS* 3.5 11.8 + - - +
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Residues in contact with ALA 434 (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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372C PRO* 3.8 29.4 - - + -
397C HIS* 3.8 19.3 + - + -
398C PRO* 4.4 1.1 - - - -
407C ALA* 4.1 2.9 - - + -
430C GLU 2.9 13.6 + - - +
431C LEU 2.9 10.9 + - - +
433C ARG* 1.3 74.4 - - - +
435C LEU* 1.3 65.6 + - - +
436C GLU 3.1 1.6 - - - -
437C LYS* 3.0 11.8 + - - -
438C TRP* 3.1 26.2 + - + +
439C GLY 4.0 0.3 + - - -
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Residues in contact with LEU 435 (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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372C PRO* 4.6 1.1 - - + -
373C GLY* 3.7 21.1 - - - +
421C LEU* 4.0 14.1 - - + +
422C ASP* 3.8 21.1 - - - +
425C ALA* 3.9 27.6 - - + -
431C LEU* 2.9 26.0 + - + +
432C ALA* 3.6 6.7 - - - +
434C ALA* 1.3 76.7 - - - +
436C GLU* 1.3 57.3 + - - +
439C GLY* 2.6 52.9 + - - +
440C HIS* 4.0 12.3 - - + +
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Residues in contact with GLU 436 (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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432C ALA 2.9 12.5 + - - +
433C ARG* 2.9 39.8 + - - +
434C ALA 3.1 0.2 - - - -
435C LEU* 1.3 78.8 - - - +
437C LYS* 1.3 59.6 + - - +
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Residues in contact with LYS 437 (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 GLY 2.7 29.8 + - - +
397C HIS 4.9 1.0 - - - -
398C PRO* 4.6 18.2 - - + +
433C ARG 3.5 8.0 + - - +
434C ALA 3.0 7.9 + - - +
436C GLU* 1.3 82.7 - - - +
438C TRP* 1.3 90.6 + - + +
56F THR* 3.9 3.3 + - - -
57F THR* 2.9 34.2 + - - -
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Residues in contact with TRP 438 (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 HIS* 3.5 35.0 - + + +
372C PRO* 3.8 11.7 - - + -
392C GLY 3.7 10.5 - - - -
393C GLY* 3.5 26.9 - - - -
396C GLY* 3.3 24.5 - - - -
397C HIS* 3.5 26.0 - + - -
398C PRO* 5.0 0.9 - - + -
434C ALA* 3.1 32.4 + - + +
437C LYS* 1.3 96.2 - - + +
439C GLY* 1.3 66.8 + - - +
440C HIS 3.0 4.0 + - - -
441C VAL* 3.0 27.4 + - + +
55F TRP* 3.5 27.6 - + - -
56F THR* 3.3 19.4 + - - -
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Residues in contact with GLY 439 (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 HIS* 3.6 1.4 + - - -
373C GLY* 3.3 22.3 - - - -
435C LEU* 2.6 43.1 + - - +
436C GLU 4.9 0.2 + - - -
437C LYS 3.6 0.8 - - - -
438C TRP* 1.3 70.8 - - - +
440C HIS* 1.3 68.0 + - - -
441C VAL* 5.4 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