Contacts of the helix formed by residues 403 - 420 (chain E) in PDB entry 6DWZ
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 VAL 403 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353E ASN* 6.1 0.2 - - - +
356E ILE* 3.6 29.4 - - + -
401E GLY 3.6 6.2 + - - +
402E ASP* 1.3 71.2 - - - +
404E ALA* 1.3 66.2 + - - +
405E ASP* 3.4 23.1 - - + +
406E ILE* 2.8 38.4 + - + +
407E ALA 3.3 1.0 + - - -
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Residues in contact with ALA 404 (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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283E GLU* 5.5 0.4 - - - -
402E ASP 3.3 5.8 + - - -
403E VAL* 1.3 73.9 - - - +
405E ASP* 1.3 68.2 + - - +
407E ALA* 3.1 6.6 + - - +
408E LYS* 2.8 24.1 + - - +
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Residues in contact with ASP 405 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281E THR* 4.3 1.4 - - - +
283E GLU* 2.9 39.9 + - - +
284E LEU* 4.2 24.1 - - + +
353E ASN* 5.3 4.9 + - - -
356E ILE* 4.9 7.1 - - + +
403E VAL* 3.4 21.1 - - + +
404E ALA* 1.3 72.9 + - - +
406E ILE* 1.3 55.2 + - - +
408E LYS* 2.8 24.9 + - - +
409E LEU* 3.1 12.0 + - - +
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Residues in contact with ILE 406 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284E LEU* 4.6 10.5 - - + +
356E ILE* 4.2 12.1 - - + -
359E THR* 3.5 35.0 - - + +
363E ILE* 5.3 7.0 - - + -
401E GLY 5.2 0.7 - - - +
402E ASP* 3.6 28.5 - - + +
403E VAL* 2.8 51.2 + - + +
405E ASP* 1.3 75.2 - - - +
407E ALA* 1.3 59.1 + - - +
409E LEU* 3.3 5.1 + - - +
410E LYS* 3.1 32.9 + - + +
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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
----------------------------------------------------------
398E PRO* 6.1 3.4 - - + -
399E ASP 4.7 5.8 - - - +
402E ASP* 3.7 28.9 - - + +
403E VAL 3.3 1.2 + - - -
404E ALA* 3.1 10.2 + - - +
406E ILE* 1.3 77.2 - - - +
408E LYS* 1.3 60.3 + - - +
410E LYS* 3.8 11.1 - - + +
411E VAL* 3.2 32.5 + - + +
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Residues in contact with LYS 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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280E GLU 4.0 12.1 + - - +
281E THR* 4.0 16.0 - - + +
282E PRO* 4.3 7.7 - - - +
283E GLU* 3.2 27.1 + - - +
404E ALA 2.8 10.5 + - - +
405E ASP* 2.8 11.5 + - - +
407E ALA* 1.3 76.6 - - - +
409E LEU* 1.3 61.3 + - - +
411E VAL* 3.3 7.1 + - + +
412E ASN* 2.8 55.5 + - - +
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Residues in contact with LEU 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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277E SER 3.3 29.8 - - - +
278E PHE* 4.0 34.5 - - + -
281E THR* 3.6 17.5 + - - +
284E LEU* 3.8 23.8 - - + -
360E MET* 5.0 1.1 - - + -
363E ILE* 5.4 8.7 - - + -
405E ASP 3.1 5.3 + - - -
406E ILE* 3.5 8.7 - - - +
408E LYS* 1.3 74.6 - - - +
410E LYS* 1.3 67.4 + - + +
412E ASN* 2.8 3.1 + - - +
413E ILE* 2.7 51.7 + - + +
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Residues in contact with LYS 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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363E ILE* 4.4 22.7 - - + -
394E GLU 5.4 0.4 + - - -
395E ILE 3.1 21.7 + - - -
396E CYS* 3.4 36.6 - - + +
397E SER* 3.1 22.3 + - - +
398E PRO* 4.6 4.7 - - + -
399E ASP* 4.1 8.7 - - - +
402E ASP* 3.2 28.1 + - - +
406E ILE* 3.1 22.3 + - + +
407E ALA* 3.8 8.5 - - - +
408E LYS 3.3 0.2 - - - -
409E LEU* 1.3 77.2 - - + +
411E VAL* 1.3 61.4 + - + +
413E ILE* 3.4 4.3 + - - +
414E ILE* 3.0 29.1 + - + +
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Residues in contact with VAL 411 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398E PRO* 5.1 11.9 - - + -
407E ALA* 3.2 21.0 + - + +
408E LYS* 3.8 8.3 - - + +
409E LEU 3.1 0.6 - - - -
410E LYS* 1.3 81.9 - - + +
412E ASN* 1.3 64.4 + - - +
414E ILE* 3.2 27.4 - - + +
415E LYS* 3.2 25.4 + - - +
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Residues in contact with ASN 412 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277E SER* 3.5 9.9 - - - +
280E GLU* 3.2 46.8 + - - +
281E THR* 3.3 13.4 + - - +
408E LYS* 2.8 30.9 + - - +
409E LEU* 2.8 4.6 + - - +
411E VAL* 1.3 75.6 - - - +
413E ILE* 1.3 53.7 - - - +
415E LYS* 3.1 25.9 + - - +
416E ASN* 2.0 37.6 + - - -
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Residues in contact with ILE 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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273E VAL* 4.2 6.2 - - + +
274E LEU* 5.5 9.4 - - + -
277E SER* 3.1 19.6 + - - +
278E PHE* 6.2 0.9 - - + -
363E ILE* 5.2 4.5 - - + -
367E PHE* 4.0 20.0 - - + -
392E VAL* 4.0 8.1 - - + -
396E CYS* 3.4 29.4 - - - -
409E LEU* 2.7 42.7 + - + +
410E LYS* 3.4 7.6 - - - +
412E ASN* 1.3 70.8 - - - +
414E ILE* 1.3 67.4 + - - +
415E LYS 2.7 2.1 + - - -
416E ASN* 2.9 4.5 + - - -
417E VAL* 2.8 40.7 + - + +
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Residues in contact with ILE 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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393E LYS* 4.2 31.4 + - + -
396E CYS* 3.4 35.2 - - + +
397E SER* 5.1 0.9 - - - -
398E PRO* 4.8 10.5 - - + -
410E LYS 3.0 15.7 - - - +
411E VAL* 3.2 30.5 + - + +
413E ILE* 1.3 76.3 - - + +
415E LYS* 1.3 61.9 + - - +
417E VAL* 3.5 18.8 - - + +
418E ARG* 3.5 13.9 + - - +
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Residues in contact with LYS 415 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280E GLU* 5.7 1.6 - - - +
411E VAL* 3.2 28.8 + - - +
412E ASN* 3.1 34.0 + - - +
413E ILE 2.7 4.8 + - - -
414E ILE* 1.3 75.3 - - - +
416E ASN* 1.3 59.0 + - - +
418E ARG* 3.0 37.4 + - - +
419E ILE* 3.0 36.8 + - + +
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Residues in contact with ASN 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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273E VAL* 3.7 8.9 - - + +
276E ASN* 4.3 1.0 - - - +
277E SER* 3.0 24.3 + - - +
280E GLU* 3.6 21.7 + - - +
412E ASN 2.0 34.4 + - - -
413E ILE 2.9 3.6 + - - -
415E LYS* 1.3 71.6 - - - +
417E VAL* 1.3 61.5 + - - +
418E ARG 3.0 1.3 - - - -
419E ILE* 3.4 16.4 - - + +
420E ILE* 2.7 53.2 + - + +
421E TRP 3.1 6.6 + - - -
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Residues in contact with VAL 417 (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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273E VAL* 3.5 11.8 - - + +
389E ILE* 3.7 29.6 - - + -
392E VAL* 3.6 16.6 - - + -
393E LYS* 4.1 15.3 - - + +
413E ILE* 2.8 41.0 + - + +
414E ILE* 3.5 13.5 - - + +
416E ASN* 1.3 75.5 - - - +
418E ARG* 1.3 56.4 + - - +
421E TRP* 3.4 9.6 - - + +
422E GLU* 2.8 39.1 + - - +
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Residues in contact with ARG 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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393E LYS* 5.0 4.9 - - - +
414E ILE 3.5 12.5 + - - +
415E LYS* 3.0 25.5 + - - +
416E ASN 3.0 0.4 - - - -
417E VAL* 1.3 79.7 - - - +
419E ILE* 1.3 83.1 + - + +
420E ILE 3.5 0.2 - - - -
422E GLU* 3.5 26.7 - - - +
423E GLU* 3.2 28.6 + - - +
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Residues in contact with ILE 419 (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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415E LYS* 3.0 38.3 + - + +
416E ASN* 3.3 19.0 + - + +
418E ARG* 1.3 108.1 - - + +
420E ILE* 1.3 64.6 + - + +
423E GLU* 2.8 34.4 - - + +
424E ASN* 4.8 1.4 + - - -
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Residues in contact with ILE 420 (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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249E ARG* 4.0 25.1 - - - +
269E LEU* 3.8 5.4 - - + +
272E ASN* 3.9 10.3 - - + -
273E VAL* 3.6 23.6 - - + +
276E ASN* 3.4 28.7 - - - +
416E ASN* 2.7 43.2 + - + +
419E ILE* 1.3 79.8 - - + +
421E TRP* 1.3 62.9 - - - +
423E GLU 4.2 0.7 - - - -
424E ASN* 2.2 38.2 + - - +
6H A 5.4 2.9 - - - +
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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