Contacts of the helix formed by residues 428 - 439 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410I GLN* 2.9 35.7 - - + +
424I TYR* 2.5 79.5 + + - +
425I ALA 3.0 13.3 + - - +
426I LYS 3.5 0.4 - - - -
427I THR* 1.3 99.6 + - + +
429I LYS* 1.3 67.2 + - - +
430I GLU* 3.4 2.0 - - - -
431I LEU* 3.8 3.8 - - + +
432I ALA* 3.0 18.2 + - - +
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Residues in contact with LYS 429 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399I ASP* 5.0 2.0 - - - +
427I THR 4.2 0.8 + - - -
428I HIS* 1.3 70.9 - - - +
430I GLU* 1.3 66.2 + - - +
432I ALA* 3.0 7.4 + - - +
433I ARG* 2.7 44.9 + - + +
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Residues in contact with GLU 430 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397I HIS* 2.9 27.8 + - - -
399I ASP* 4.7 2.9 - - - +
403I ALA* 3.5 33.0 - - + +
406I ARG* 2.9 38.8 + - + +
407I ALA* 3.6 8.7 - - - +
410I GLN* 3.1 22.6 - - - +
428I HIS* 4.6 0.5 - - - -
429I LYS* 1.3 86.1 + - - +
431I LEU* 1.3 63.7 + - - +
434I ALA* 3.0 9.4 + - - +
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Residues in contact with LEU 431 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372I PRO* 3.9 26.9 - - + -
407I ALA* 3.8 9.2 - - - +
410I GLN* 3.1 26.4 - - + +
411I ALA* 4.2 12.1 - - + -
421I LEU* 3.8 33.9 - - + +
424I TYR* 3.8 27.4 - - + -
425I ALA* 3.9 7.0 - - + -
428I HIS* 3.8 4.7 - - + +
429I LYS 3.3 0.2 - - - -
430I GLU* 1.3 78.1 - - - +
432I ALA* 1.3 58.7 + - - +
434I ALA* 3.1 4.4 + - - +
435I LEU* 2.8 46.0 + - + +
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Residues in contact with ALA 432 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425I ALA* 3.5 26.2 - - + +
428I HIS 3.0 14.8 + - - +
429I LYS* 3.4 11.2 - - - +
431I LEU* 1.3 77.3 - - - +
433I ARG* 1.3 56.9 + - + +
435I LEU* 3.2 5.1 + - - +
436I GLU* 2.8 30.8 + - - +
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Residues in contact with ARG 433 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397I HIS* 3.6 8.1 - - + +
398I PRO* 3.6 31.1 + - + +
399I ASP* 2.7 43.8 + - - +
429I LYS* 2.7 28.2 + - + +
430I GLU 3.5 4.3 - - - +
432I ALA* 1.3 72.4 - - + +
434I ALA* 1.3 62.6 + - - +
436I GLU* 3.2 33.3 + - - +
437I LYS* 3.2 20.8 + - - +
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Residues in contact with ALA 434 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371I HIS* 6.2 0.2 - - - -
372I PRO* 3.9 29.4 - - + -
397I HIS* 3.7 20.5 + - + -
398I PRO* 4.8 0.4 - - - -
407I ALA* 4.2 2.0 - - + -
430I GLU 3.0 13.5 + - - +
431I LEU 3.4 9.4 - - - +
433I ARG* 1.3 76.8 - - - +
435I LEU* 1.3 56.9 + - - +
437I LYS* 2.9 6.0 + - - -
438I TRP* 2.9 44.0 + - + -
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Residues in contact with LEU 435 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372I PRO* 5.2 0.2 - - + -
373I GLY* 3.8 20.6 - - - +
421I LEU* 3.6 19.5 - - + +
422I ASP* 4.2 10.5 - - - +
425I ALA* 3.6 31.0 - - + -
431I LEU* 2.8 32.9 + - + +
432I ALA* 3.6 4.7 - - - +
434I ALA* 1.3 73.4 - - - +
436I GLU* 1.3 58.8 - - - +
439I GLY* 2.6 51.4 + - - +
440I HIS* 4.3 11.4 - - + +
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Residues in contact with GLU 436 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432I ALA 2.8 13.7 + - - +
433I ARG* 3.3 37.1 + - - +
434I ALA 3.1 0.2 - - - -
435I LEU* 1.3 77.6 - - - +
437I LYS* 1.3 61.8 + - + +
439I GLY 4.9 0.2 + - - -
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Residues in contact with LYS 437 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E PHE* 4.6 12.2 + - - +
56E THR* 3.8 3.4 - - - -
57E THR* 3.3 35.4 + - - -
58E LEU 5.7 0.8 - - - -
396I GLY 2.2 36.1 + - - +
397I HIS 4.6 0.2 - - - -
398I PRO* 3.9 21.3 - - + +
433I ARG 3.2 10.0 + - - +
434I ALA 2.9 8.0 + - - +
436I GLU* 1.3 80.5 - - + +
438I TRP* 1.3 87.5 + - + +
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Residues in contact with TRP 438 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E PHE 4.9 5.8 - - - -
55E TRP* 3.4 30.4 - + - -
56E THR* 3.1 20.8 + - - -
371I HIS* 3.5 31.2 - - + +
372I PRO* 4.0 6.3 - - + -
392I GLY 3.6 11.7 - - - -
393I GLY* 3.6 26.2 - - - -
396I GLY* 3.4 22.9 - - - -
397I HIS* 3.5 27.1 - + - -
434I ALA* 2.9 37.9 + - + +
437I LYS* 1.3 97.4 - - + +
439I GLY* 1.3 66.4 + - - +
440I HIS 3.1 1.4 + - - -
441I VAL* 3.0 35.9 + - + +
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Residues in contact with GLY 439 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371I HIS* 3.3 4.7 + - - -
373I GLY* 3.2 22.9 - - - -
435I LEU* 2.6 40.8 + - - +
436I GLU 4.9 0.2 + - - -
437I LYS 3.8 0.4 - - - -
438I TRP* 1.3 69.4 - - - +
440I HIS* 1.3 68.5 + - - -
441I VAL* 5.1 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