Contacts of the helix formed by residues 428 - 439 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410H GLN* 3.2 34.3 - - + +
424H TYR* 2.8 67.6 + + - +
425H ALA 2.5 11.9 + - - +
427H THR* 1.3 92.6 - - + +
429H LYS* 1.3 56.0 + - - +
430H GLU* 3.5 1.6 - - - -
431H LEU* 3.3 7.6 + - + -
432H ALA* 2.5 38.0 + - - +
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Residues in contact with LYS 429 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399H ASP* 5.5 3.6 - - - +
427H THR 4.2 0.2 - - - -
428H HIS* 1.3 69.4 - - - +
430H GLU* 1.3 67.3 + - - +
432H ALA* 4.4 3.1 - - - -
433H ARG* 2.3 47.1 + - + +
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Residues in contact with GLU 430 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397H HIS* 3.3 11.0 + - - -
399H ASP* 5.1 4.2 + - - +
403H ALA* 4.0 6.7 - - + +
406H ARG* 3.0 50.1 + - + +
407H ALA* 3.8 15.0 - - - +
410H GLN* 2.8 26.9 - - - +
428H HIS* 5.0 0.5 - - - -
429H LYS* 1.3 83.3 + - - +
431H LEU* 1.3 53.4 + - - +
433H ARG* 3.5 2.9 - - - +
434H ALA* 2.8 36.0 + - - +
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Residues in contact with LEU 431 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372H PRO* 4.4 15.7 - - + +
407H ALA* 3.9 9.6 - - - +
410H GLN* 2.7 26.8 - - + +
411H ALA* 4.0 34.1 - - + +
414H ALA* 4.7 1.8 - - + -
421H LEU* 4.0 8.7 - - + +
424H TYR* 3.5 34.3 - - + -
425H ALA* 3.7 22.2 - - + +
428H HIS* 3.5 4.7 - - + +
429H LYS 3.2 0.4 - - - -
430H GLU* 1.3 70.8 - - - +
432H ALA* 1.3 57.1 + - - +
434H ALA* 2.7 30.1 + - - +
435H LEU* 3.0 17.8 + - + +
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Residues in contact with ALA 432 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425H ALA* 3.2 31.6 - - + +
426H LYS* 5.1 0.7 - - - -
428H HIS 2.5 23.5 + - - +
429H LYS* 3.7 3.4 - - - +
431H LEU* 1.3 74.2 - - - +
433H ARG* 1.3 62.7 + - - +
434H ALA 3.0 1.0 + - - -
435H LEU* 3.1 16.6 + - - +
436H GLU* 3.3 10.4 + - - +
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Residues in contact with ARG 433 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397H HIS* 4.2 3.1 - - + -
398H PRO* 3.5 28.4 - - + +
399H ASP* 4.2 10.8 - - - +
429H LYS* 2.3 38.9 + - + +
430H GLU* 3.5 6.5 - - - +
432H ALA* 1.3 68.6 - - - +
434H ALA* 1.3 59.5 + - - +
436H GLU* 3.4 18.4 - - - +
437H LYS 4.1 1.7 + - - -
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Residues in contact with ALA 434 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372H PRO* 4.0 21.8 - - + -
397H HIS* 4.0 12.6 - - + +
398H PRO* 4.5 3.8 - - - -
407H ALA* 4.0 16.8 - - + -
430H GLU 2.8 12.5 + - - +
431H LEU* 2.7 20.5 + - - +
433H ARG* 1.3 67.4 - - - +
435H LEU* 1.3 64.1 - - - +
436H GLU 2.9 3.2 + - - -
437H LYS* 3.1 12.3 + - - +
438H TRP* 3.4 22.5 + - + -
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Residues in contact with LEU 435 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372H PRO* 4.8 4.0 - - + +
373H GLY* 4.1 15.3 - - - +
421H LEU* 4.1 8.3 - - + +
422H ASP* 4.0 18.8 - - - +
425H ALA* 3.4 31.6 - - + -
431H LEU* 3.0 21.4 + - + +
432H ALA* 3.5 7.2 - - - +
434H ALA* 1.3 75.0 - - + +
436H GLU* 1.3 60.3 + - - +
439H GLY* 2.3 58.2 + - - +
440H HIS* 3.6 15.3 - - + +
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Residues in contact with GLU 436 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432H ALA 3.3 6.8 + - - +
433H ARG* 3.4 15.7 - - - +
434H ALA 2.9 1.0 + - - -
435H LEU* 1.3 81.4 - - - +
437H LYS* 1.3 64.3 + - - +
438H TRP 4.5 0.2 - - - -
439H GLY* 4.1 1.4 + - - -
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Residues in contact with LYS 437 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A THR* 3.7 15.3 + - - -
57A THR* 3.5 26.3 + - - -
396H GLY* 2.3 39.4 + - - +
397H HIS 4.5 6.7 + - - -
398H PRO* 4.8 11.6 - - + +
433H ARG 4.1 3.6 + - - +
434H ALA 3.1 7.5 + - - +
436H GLU* 1.3 80.0 - - - +
438H TRP* 1.3 78.4 + - + +
441H VAL* 5.9 0.2 - - - +
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Residues in contact with TRP 438 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A TRP* 3.6 27.6 - + - -
56A THR* 3.5 18.1 + - - -
371H HIS* 3.7 27.1 - + + +
372H PRO* 3.9 21.1 - - + -
392H GLY 3.7 12.1 - - - -
393H GLY* 3.5 23.6 - - - -
396H GLY* 3.2 24.7 - - - -
397H HIS* 3.3 32.1 - + + -
398H PRO* 4.9 1.6 - - + -
434H ALA* 3.4 31.7 + - + +
436H GLU 4.5 0.7 - - - -
437H LYS* 1.3 93.4 - - + +
439H GLY* 1.3 60.1 + - - +
440H HIS 2.9 9.2 + - - -
441H VAL* 3.0 26.7 + - + +
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Residues in contact with GLY 439 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371H HIS* 4.0 1.9 + - - -
373H GLY* 3.5 16.5 - - - -
435H LEU* 2.3 39.5 + - - +
436H GLU 4.1 0.9 + - - -
438H TRP* 1.3 66.0 - - - +
440H HIS* 1.3 81.6 + - - -
441H VAL* 5.3 0.2 - - - -
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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