Contacts of the helix formed by residues 428 - 439 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410E GLN* 3.4 33.7 - - + +
424E TYR* 2.9 63.6 + + + +
425E ALA 3.1 15.8 + - - +
426E LYS 3.6 0.2 - - - -
427E THR* 1.3 103.7 + - - +
429E LYS* 1.3 66.2 + - - +
430E GLU* 3.4 1.6 - - - -
431E LEU* 3.4 5.4 + - + +
432E ALA 3.1 11.3 + - - -
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Residues in contact with LYS 429 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399E ASP* 5.7 2.0 - - - +
427E THR 4.3 0.2 - - - -
428E HIS* 1.3 68.0 - - - +
430E GLU* 1.3 79.4 + - - +
432E ALA* 2.9 18.7 + - - +
433E ARG* 3.0 25.9 + - + +
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Residues in contact with GLU 430 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397E HIS* 2.9 28.9 + - - -
399E ASP* 5.6 1.3 - - - -
403E ALA* 3.6 29.4 - - + +
406E ARG* 3.4 39.1 + - + +
407E ALA* 3.7 10.6 - - - +
410E GLN* 3.1 20.7 + - - +
428E HIS* 4.0 1.0 - - - -
429E LYS* 1.3 82.1 + - - +
431E LEU* 1.3 65.7 + - - +
433E ARG* 3.6 1.5 + - - -
434E ALA* 3.4 4.2 + - - +
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Residues in contact with LEU 431 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372E PRO* 5.8 3.3 - - + +
407E ALA* 4.3 8.3 - - - +
410E GLN* 2.8 28.6 - - + +
411E ALA* 5.6 6.5 - - + +
421E LEU 5.3 1.3 - - - +
424E TYR* 5.1 5.6 - - + -
425E ALA* 3.8 19.5 - - + +
428E HIS* 3.6 9.2 - - + +
429E LYS 3.2 0.4 - - - -
430E GLU* 1.3 71.2 - - - +
432E ALA* 1.3 69.6 + - - +
434E ALA* 3.1 14.0 + - - +
435E LEU* 3.1 16.2 + - + +
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Residues in contact with ALA 432 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425E ALA* 3.6 28.9 - - + +
428E HIS 3.1 4.1 + - - +
429E LYS* 2.9 13.5 + - - +
431E LEU* 1.3 81.3 - - - +
433E ARG* 1.3 67.2 + - + +
434E ALA 3.0 0.3 + - - -
435E LEU* 3.1 13.4 + - - +
436E GLU* 3.1 13.8 + - - +
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Residues in contact with ARG 433 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397E HIS* 3.6 8.7 - - + +
398E PRO* 3.2 43.2 + - + +
399E ASP* 3.1 38.2 + - - +
429E LYS* 3.0 24.3 + - + +
432E ALA* 1.3 75.4 - - - +
434E ALA* 1.3 65.3 + - - +
436E GLU* 3.6 13.0 + - - +
437E LYS* 3.4 13.7 + - - +
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Residues in contact with ALA 434 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372E PRO* 4.0 28.9 - - + -
373E GLY 6.0 0.4 - - - +
397E HIS* 3.8 18.5 + - + -
398E PRO* 4.4 2.5 - - - -
407E ALA* 4.7 0.7 - - + -
430E GLU 3.4 10.0 + - - +
431E LEU* 3.1 12.6 + - - +
432E ALA 3.0 0.2 + - - -
433E ARG* 1.3 76.5 - - - +
435E LEU* 1.3 67.8 + - - +
437E LYS* 2.9 13.2 + - - +
438E TRP* 3.0 27.3 + - + -
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Residues in contact with LEU 435 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371E HIS* 6.4 0.2 - - - -
372E PRO* 5.3 3.1 - - + -
373E GLY* 4.0 13.0 - - - +
421E LEU* 3.8 14.6 - - + +
422E ASP* 3.5 20.6 - - - +
425E ALA* 3.7 30.3 - - + -
431E LEU* 3.1 7.8 + - + +
432E ALA* 3.1 7.4 + - - +
434E ALA* 1.3 78.3 - - + +
436E GLU* 1.3 54.3 + - - +
437E LYS 2.5 11.6 + - - -
438E TRP* 5.5 0.2 - - - -
439E GLY* 2.3 60.6 + - - +
440E HIS* 3.6 20.4 - - + +
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Residues in contact with GLU 436 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432E ALA 3.1 9.4 + - - +
433E ARG* 3.7 19.5 - - - +
435E LEU* 1.3 77.9 - - - +
437E LYS* 1.3 60.3 + - - +
439E GLY 4.8 0.2 + - - -
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Residues in contact with LYS 437 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396E GLY* 2.3 42.5 + - - +
398E PRO* 4.2 18.7 - - + +
433E ARG 3.4 8.2 + - - +
434E ALA 2.9 9.1 + - - +
435E LEU 2.5 6.4 + - - -
436E GLU* 1.3 78.2 - - - +
438E TRP* 1.3 89.1 + - + +
56I THR* 4.1 3.7 + - - -
57I THR* 3.6 23.0 + - - -
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Residues in contact with TRP 438 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371E HIS* 3.6 34.0 + + + +
372E PRO* 4.3 2.9 - - + -
392E GLY 3.5 22.7 - - - -
393E GLY* 3.7 19.5 - - - -
396E GLY* 3.6 15.5 - - - -
397E HIS* 3.1 31.2 - + + -
434E ALA* 3.0 38.0 + - + +
435E LEU 2.9 2.0 + - - -
437E LYS* 1.3 96.1 - - + +
439E GLY* 1.3 58.4 + - - +
440E HIS 2.8 10.6 + - - -
441E VAL* 3.1 24.4 + - + +
55I TRP* 3.6 31.5 - + - -
56I THR* 3.6 14.7 + - - -
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Residues in contact with GLY 439 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371E HIS* 3.7 1.1 - - - -
373E GLY* 3.4 9.5 - - - -
435E LEU* 2.3 57.9 + - - +
436E GLU 4.4 0.8 + - - -
437E LYS 3.5 0.6 - - - -
438E TRP* 1.3 63.4 - - - +
440E HIS* 1.3 70.1 + - - -
441E VAL* 5.5 0.9 - - - -
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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