Contacts of the helix formed by residues 400 - 418 (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 GLY 400 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395E LEU 4.1 2.0 - - - -
397E HIS* 3.1 20.6 + - - +
398E PRO 3.1 2.8 + - - -
399E ASP* 1.3 80.7 - - - +
401E PRO* 1.3 77.7 - - - +
402E ALA* 3.4 2.0 - - - -
403E ALA* 3.2 10.9 + - - +
404E GLY 3.3 8.8 + - - -
59I TYR* 5.1 6.3 - - - -
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Residues in contact with PRO 401 (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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176E LEU* 3.9 16.2 - - + -
179E ASP* 6.1 1.8 - - + -
180E LEU* 3.5 26.5 - - + +
394E THR 3.6 13.5 - - - +
395E LEU* 3.7 31.8 - - + +
400E GLY* 1.3 80.6 - - - -
402E ALA* 1.3 67.9 + - - +
404E GLY* 2.7 14.4 + - - -
405E ALA 2.9 11.3 + - - -
59I TYR* 4.4 16.2 - - + -
61I TRP* 5.7 3.4 - - + -
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Residues in contact with ALA 402 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179E ASP* 4.8 12.4 - - + +
180E LEU* 4.2 5.5 - - - +
183E ASN* 3.7 28.3 - - - +
399E ASP 5.7 1.3 - - - +
400E GLY 3.4 0.8 - - - -
401E PRO* 1.3 79.5 - - - +
403E ALA* 1.3 64.9 + - - +
405E ALA* 3.3 4.3 + - - +
406E ARG* 3.3 33.8 + - - +
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Residues in contact with ALA 403 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397E HIS* 3.6 12.3 - - + +
399E ASP* 3.5 32.5 + - + +
400E GLY 3.2 10.8 + - - +
401E PRO 3.1 0.6 - - - -
402E ALA* 1.3 78.5 - - - +
404E GLY* 1.3 52.2 + - - +
406E ARG* 3.1 28.5 + - - +
407E ALA* 2.8 33.4 + - - +
430E GLU* 3.6 9.0 - - + +
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Residues in contact with GLY 404 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372E PRO* 6.2 0.4 - - - -
393E GLY 5.4 1.3 - - - -
394E THR* 3.8 15.0 - - - -
397E HIS* 3.4 23.7 - - - -
400E GLY 3.3 4.6 + - - -
401E PRO 2.7 13.3 + - - -
403E ALA* 1.3 74.1 - - - +
405E ALA* 1.3 52.8 + - - -
407E ALA* 2.8 4.9 + - - +
408E VAL* 2.7 41.4 + - - +
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Residues in contact with ALA 405 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158E TYR* 3.3 19.7 - - + +
180E LEU* 3.9 24.2 - - + +
183E ASN* 3.4 23.8 - - + +
185E ALA* 4.4 5.6 - - + +
394E THR* 4.0 2.2 - - - +
401E PRO 2.9 9.5 + - - +
402E ALA 3.6 8.3 - - - +
404E GLY* 1.3 73.8 - - - +
406E ARG* 1.3 62.2 + - - +
408E VAL* 3.5 2.6 + - - +
409E ARG* 3.1 27.9 + - - +
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Residues in contact with ARG 406 (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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183E ASN* 2.7 54.6 + - + +
402E ALA* 3.3 21.7 + - - +
403E ALA* 3.1 30.9 + - - +
405E ALA* 1.3 72.5 - - - +
407E ALA* 1.3 64.8 + - - +
409E ARG* 3.5 4.9 + - - +
410E GLN* 3.0 30.6 + - - +
430E GLU* 3.4 28.7 + - + +
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Residues in contact with ALA 407 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372E PRO* 4.6 11.7 - - + -
397E HIS* 4.1 4.5 - - + -
403E ALA 2.8 13.8 + - - +
404E GLY* 2.8 18.8 + - - +
406E ARG* 1.3 76.4 - - - +
408E VAL* 1.3 49.0 + - - +
410E GLN* 2.8 10.6 - - - +
411E ALA* 2.7 37.2 + - - +
430E GLU* 3.7 32.3 - - - +
431E LEU* 4.0 4.6 - - - +
434E ALA* 4.7 0.2 - - + -
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Residues in contact with VAL 408 (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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158E TYR* 3.4 50.9 - - + +
372E PRO* 4.1 13.2 - - + -
375E ILE* 4.9 4.5 - - + -
388E LEU* 5.8 0.9 - - + -
390E LEU* 3.7 29.6 - - + -
393E GLY 4.5 2.9 - - - +
394E THR* 3.9 6.3 - - - +
404E GLY 2.7 19.3 + - - +
405E ALA 3.8 0.2 - - - +
407E ALA* 1.3 72.2 - - - +
409E ARG* 1.3 53.7 + - - +
411E ALA* 3.0 9.4 + - - +
412E ILE* 2.7 49.5 + - + +
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Residues in contact with ARG 409 (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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155E ARG* 3.6 47.2 - - - +
158E TYR* 4.0 12.3 - - + -
183E ASN 4.4 0.7 - - - +
184E GLY* 2.7 59.3 + - - +
186E ASP* 4.2 0.4 + - - -
222E GLU* 4.1 22.4 + - - -
405E ALA 3.1 18.8 + - - +
406E ARG* 3.8 6.3 - - - +
408E VAL* 1.3 77.6 - - - +
410E GLN* 1.3 58.0 + - - +
412E ILE* 3.1 12.4 + - - +
413E ASP* 2.8 36.4 + - - +
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Residues in contact with GLN 410 (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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406E ARG* 3.0 13.7 + - - +
407E ALA* 2.8 20.2 - - - +
409E ARG* 1.3 76.6 - - - +
411E ALA* 1.3 59.9 + - - +
412E ILE 3.1 0.2 - - - -
413E ASP* 3.1 12.2 + - - +
414E ALA* 2.9 22.7 + - - +
424E TYR* 3.3 29.4 - - + +
428E HIS* 3.4 30.0 - - + +
430E GLU* 3.1 22.2 + - - +
431E LEU* 2.8 41.5 - - + +
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Residues in contact with ALA 411 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372E PRO* 4.1 22.9 - - + +
375E ILE* 4.3 10.4 - - + +
407E ALA 2.7 18.0 + - - +
408E VAL* 3.3 14.8 - - - +
410E GLN* 1.3 73.8 - - + +
412E ILE* 1.3 58.3 + - - +
414E ALA* 3.5 9.5 - - - +
415E ILE* 3.1 29.0 + - - +
421E LEU* 6.3 2.5 - - + -
424E TYR* 5.3 1.8 - - - -
431E LEU* 5.6 7.2 - - + -
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Residues in contact with ILE 412 (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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155E ARG* 4.4 13.2 - - + +
156E PRO* 4.3 26.0 - - + +
158E TYR* 4.0 26.2 - - + -
375E ILE* 4.4 11.0 - - + -
379E ILE* 5.2 2.9 - - + -
388E LEU* 4.4 16.2 - - + -
408E VAL* 2.7 28.5 + - + +
409E ARG* 3.3 18.2 - - - +
411E ALA* 1.3 75.2 - - - +
413E ASP* 1.3 63.8 + - - +
414E ALA 3.1 1.1 - - - -
415E ILE* 3.1 7.5 + - - +
416E MET* 2.8 47.4 + - + +
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Residues in contact with ASP 413 (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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155E ARG* 5.5 3.6 - - - -
409E ARG* 2.8 21.5 + - - +
410E GLN* 3.1 14.0 + - - +
412E ILE* 1.3 82.0 - - - +
414E ALA* 1.3 52.6 + - - +
416E MET* 3.6 8.6 - - - +
417E GLN* 2.7 38.2 + - - +
424E TYR* 4.0 16.9 + - - +
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Residues in contact with ALA 414 (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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410E GLN 2.9 12.3 + - - +
411E ALA* 3.5 13.9 - - - +
412E ILE 3.1 0.2 - - - -
413E ASP* 1.3 74.7 - - - +
415E ILE* 1.3 58.1 + - + +
417E GLN* 3.2 1.5 + - - -
418E GLY* 2.7 31.0 + - - -
419E ILE 2.9 32.1 + - - +
420E PRO 4.8 2.2 - - - +
421E LEU* 5.0 5.4 - - + -
424E TYR* 3.9 24.7 - - + -
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Residues in contact with ILE 415 (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 6.0 0.4 - - - +
375E ILE* 4.4 7.9 - - + +
376E GLN* 3.9 33.4 - - + +
379E ILE* 3.5 49.8 - - + -
380E GLU 5.6 0.2 - - - +
411E ALA 3.1 17.0 - - - +
412E ILE* 3.1 7.1 + - - +
414E ALA* 1.3 77.9 - - + +
416E MET* 1.3 65.1 + - + +
418E GLY* 3.4 10.4 + - - -
421E LEU* 6.3 4.3 - - + +
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Residues in contact with MET 416 (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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154E ASP* 4.3 12.1 - - + -
155E ARG* 3.7 39.3 - - + +
156E PRO* 4.2 9.9 - - - -
379E ILE* 6.1 1.8 - - - -
384E THR* 4.5 16.4 - - + -
412E ILE* 2.8 36.7 + - + +
413E ASP* 3.7 9.4 - - - +
415E ILE* 1.3 80.0 - - + +
417E GLN* 1.3 59.4 + - - +
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Residues in contact with GLN 417 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413E ASP 2.7 19.4 + - - +
414E ALA 4.0 0.7 - - - +
416E MET* 1.3 75.9 - - - +
418E GLY* 1.3 62.2 + - - +
419E ILE* 3.5 30.2 + - + +
424E TYR* 5.6 1.3 - - + -
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Residues in contact with GLY 418 (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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414E ALA 2.7 9.6 + - - -
415E ILE* 3.4 7.7 + - - -
416E MET 3.4 3.8 - - - -
417E GLN* 1.3 78.5 - - - +
419E ILE* 1.3 57.0 + - - +
420E PRO* 3.2 11.9 - - - +
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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
------------------------------------------------------------
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