Contacts of the helix formed by residues 404 - 423 (chain E) in PDB entry 4P0S
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 ASP 404 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369E GLU* 3.9 11.2 - - - -
370E GLU* 4.4 2.5 - - + +
402E THR* 3.3 2.8 - - - +
403E ALA* 1.4 83.5 - - - +
405E ILE* 1.3 64.7 + - + +
406E LYS* 3.1 21.0 + - - +
407E GLU* 3.3 14.8 + - - +
408E SER* 2.8 27.0 + - - -
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Residues in contact with ILE 405 (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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285E PRO* 5.2 14.1 - - + +
286E GLU 5.6 0.9 - - - -
287E LEU* 4.6 27.4 - - + +
290E GLU* 5.9 3.6 - - + -
334E ARG* 3.9 17.5 - - - +
336E ARG* 5.2 4.0 - - - +
369E GLU* 2.9 31.9 - - - +
404E ASP* 1.3 75.3 - - - +
406E LYS* 1.3 51.4 + - - +
408E SER* 3.0 9.9 + - - -
409E ALA* 2.6 35.7 + - + +
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Residues in contact with LYS 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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290E GLU* 3.6 28.6 + - + +
293E ARG* 2.8 40.5 - - - +
294E LEU* 4.8 3.2 - - + +
404E ASP* 3.1 14.4 + - - +
405E ILE* 1.3 76.2 - - - +
407E GLU* 1.3 63.1 + - + +
409E ALA* 3.3 5.4 + - - +
410E ALA* 2.9 27.8 + - + +
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Residues in contact with GLU 407 (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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400E LYS* 6.0 2.3 - - - -
402E THR* 3.9 17.6 + - + +
403E ALA* 4.0 16.3 + - + +
404E ASP* 3.3 11.1 + - - +
406E LYS* 1.3 81.4 - - + +
408E SER* 1.3 52.4 + - - +
410E ALA* 3.2 7.3 - - - +
411E TYR* 2.4 42.0 + - + +
370F PHE* 3.5 29.7 - - - -
405F ARG* 2.8 41.1 + - - +
409F GLU* 5.1 0.2 - - - +
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Residues in contact with SER 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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287E LEU* 5.6 0.9 - - - -
334E ARG* 5.8 4.2 - - - +
367E LEU* 4.4 20.3 - - - +
369E GLU* 4.1 12.7 + - - +
402E THR* 3.2 16.1 - - - +
404E ASP 2.8 20.2 + - - -
405E ILE* 3.0 20.2 - - - -
407E GLU* 1.3 74.7 - - - +
409E ALA* 1.3 64.9 + - - +
411E TYR* 3.9 5.4 - - - +
412E LEU* 3.0 30.9 + - - +
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Residues in contact with ALA 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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287E LEU* 3.9 19.7 - - + +
290E GLU* 3.6 29.8 - - + -
291E LEU* 4.1 16.8 - - + +
294E LEU* 4.2 7.2 - - + -
405E ILE* 2.6 19.2 + - + +
406E LYS 3.3 4.2 + - - +
408E SER* 1.3 72.5 - - - +
410E ALA* 1.3 59.5 + - - +
412E LEU* 3.2 4.7 + - - +
413E ALA* 2.9 27.7 + - - +
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Residues in contact with ALA 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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294E LEU* 4.1 14.7 - - + +
406E LYS* 2.9 21.4 + - + +
407E GLU* 3.3 8.7 - - - +
409E ALA* 1.3 76.2 - - - +
411E TYR* 1.3 64.8 + - - +
413E ALA* 3.1 8.6 + - - +
414E LEU* 2.9 33.2 + - + +
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Residues in contact with TYR 411 (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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332E VAL* 5.8 0.7 - - + -
365E VAL* 4.4 9.9 - - + +
367E LEU* 3.9 27.6 - - + -
398E PHE* 3.6 15.1 - + - -
400E LYS* 3.4 50.8 - - + +
402E THR* 5.0 4.3 - - - +
407E GLU* 2.4 31.3 + - + +
408E SER* 3.9 4.0 - - - +
410E ALA* 1.3 66.5 - - - +
412E LEU* 1.3 67.3 + - + +
414E LEU* 3.1 6.1 + - + +
415E LEU* 2.9 55.0 + - + +
409F GLU* 4.5 8.7 - - + +
412F LEU* 6.3 2.9 - - + -
413F VAL* 5.0 12.6 - - + -
416F GLN* 3.6 18.5 + - - -
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Residues in contact with LEU 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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271E LEU* 4.2 28.9 - - + -
287E LEU* 4.6 10.3 - - + -
291E LEU* 4.4 12.1 - - + -
308E PHE* 3.6 55.6 - - + -
310E TRP* 4.0 4.2 - - + -
332E VAL* 4.7 11.7 - - + -
367E LEU* 4.7 14.8 - - + -
408E SER* 3.0 20.0 + - - +
409E ALA 3.6 4.9 - - - +
411E TYR* 1.3 78.2 - - + +
413E ALA* 1.3 53.5 + - - +
415E LEU* 3.8 8.0 - - + +
416E THR* 2.3 39.9 + - - -
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Residues in contact with ALA 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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291E LEU* 5.4 0.2 - - - +
294E LEU* 4.5 12.1 - - + +
296E VAL* 3.8 27.1 - - + -
409E ALA 2.9 13.3 + - - +
410E ALA* 3.2 13.7 - - - +
412E LEU* 1.3 78.7 - - - +
414E LEU* 1.3 56.5 - - + +
416E THR* 2.8 9.8 + - - -
417E ARG* 2.7 36.6 + - - +
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Residues in contact with LEU 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 ALA* 2.9 26.1 + - + +
411E TYR* 3.9 5.2 - - + +
413E ALA* 1.3 77.9 - - + +
415E LEU* 1.3 61.1 + - - +
417E ARG* 3.8 9.7 - - + +
418E GLY 2.9 22.9 + - - -
406F VAL* 4.4 17.5 - - + +
409F GLU* 4.1 14.6 - - + -
410F GLU* 3.9 37.7 - - + +
413F VAL* 3.5 21.2 - - + +
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Residues in contact with LEU 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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310E TRP* 3.7 28.7 - - + -
330E HIS* 5.0 7.0 - - + -
332E VAL* 4.4 13.5 - - + -
365E VAL* 4.9 3.1 - - + -
411E TYR* 2.9 52.2 + - + +
412E LEU* 3.8 9.2 - - + +
414E LEU* 1.3 76.0 - - - +
416E THR* 1.3 64.4 + - - +
418E GLY* 3.1 3.8 + - - -
419E LEU* 3.1 26.2 + - + +
413F VAL* 4.2 17.3 - - + +
416F GLN* 3.0 38.4 - - + +
417F LEU* 4.9 5.7 - - + +
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Residues in contact with THR 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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269E VAL* 4.8 2.4 - - + +
271E LEU* 4.0 18.4 - - + +
296E VAL* 4.9 6.9 - - + +
297E THR* 4.5 14.8 - - - +
310E TRP* 3.0 35.0 + - + +
412E LEU 2.3 23.8 + - - -
413E ALA* 2.8 14.0 + - - -
415E LEU* 1.3 77.6 - - - +
417E ARG* 1.3 59.0 + - - -
419E LEU* 3.0 6.7 + - - +
420E GLN* 3.0 33.8 + - + +
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Residues in contact with ARG 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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413E ALA 2.7 17.9 + - - +
414E LEU* 3.9 11.9 - - + +
416E THR* 1.3 72.8 - - - +
418E GLY* 1.3 63.4 + - - +
420E GLN* 2.6 60.5 + - - +
421E ARG* 3.0 39.3 + - + +
424E GLN* 4.2 16.2 - - - +
410F GLU* 6.6 0.2 - - - -
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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 LEU 2.9 15.5 + - - -
415E LEU 3.1 4.9 + - - -
417E ARG* 1.3 79.0 - - - +
419E LEU* 1.3 49.5 + - - +
421E ARG* 2.9 11.4 + - - +
422E LEU* 2.5 35.0 + - - +
413F VAL* 4.1 14.1 - - - -
414F ASP* 4.9 6.7 - - - +
417F LEU* 4.0 9.3 - - - +
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Residues in contact with LEU 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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269E VAL* 4.2 8.9 - - + +
310E TRP* 3.4 47.3 - - + -
328E LEU* 3.6 29.6 - - + -
330E HIS* 4.5 12.8 - - + +
415E LEU* 3.1 12.9 + - + +
416E THR* 3.0 8.5 + - - +
418E GLY* 1.3 74.2 - - - +
420E GLN* 1.3 69.1 + - - +
422E LEU* 3.1 33.4 + - + +
423E TYR* 3.1 22.2 + - + +
417F LEU* 4.0 17.5 - - + -
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Residues in contact with GLN 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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268E ARG* 6.1 0.6 - - - +
269E VAL* 3.4 40.2 + - + +
297E THR* 3.4 33.2 + - - +
416E THR* 3.0 18.4 + - + +
417E ARG* 2.6 58.7 + - - +
419E LEU* 1.3 79.2 - - - +
421E ARG* 1.3 61.5 - - - +
423E TYR 3.8 0.7 + - - -
424E GLN* 3.3 29.6 + - - +
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Residues in contact with ARG 421 (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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417E ARG* 3.0 34.8 + - + +
418E GLY* 2.9 9.3 + - - +
420E GLN* 1.3 77.3 - - - +
422E LEU* 1.3 65.7 + - - +
423E TYR 3.3 0.4 - - - -
424E GLN* 4.0 18.2 + - - +
329F LYS* 3.8 6.2 - - - +
410F GLU* 4.1 13.4 + - - +
414F ASP* 2.4 47.7 + - - -
418F HIS* 5.0 12.5 + - - -
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Residues in contact with LEU 422 (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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330E HIS* 5.3 0.4 - - + -
418E GLY 2.5 18.6 + - - +
419E LEU* 3.1 18.3 + - + +
421E ARG* 1.3 77.2 - - - +
423E TYR* 1.3 74.0 + - + +
424E GLN 3.6 0.6 - - - +
426E HIS* 3.6 18.4 + - + -
448E ASN* 4.0 14.8 - - - +
449E PRO* 3.7 26.0 - - + +
417F LEU* 3.6 43.3 - - + +
418F HIS* 4.3 27.6 - - + +
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Residues in contact with TYR 423 (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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267E TYR* 2.3 39.7 + - + +
269E VAL* 5.6 4.9 - - + -
328E LEU* 4.0 27.9 - - + +
329E ASP* 4.8 5.0 + - - +
419E LEU* 3.1 21.9 + - + +
420E GLN 4.5 1.1 - - - +
422E LEU* 1.3 97.5 - - + +
424E GLN* 1.3 61.9 + - - +
426E HIS* 3.2 21.1 + - + +
428E LEU* 3.5 31.0 - - + -
448E ASN* 5.4 2.0 + - - -
449E PRO* 4.6 6.9 - - + +
450E LEU* 2.4 46.3 + - - +
451E CYS* 4.6 3.6 - - - -
453E LEU* 4.1 17.1 - - + +
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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