Contacts of the helix formed by residues 395 - 411 (chain B) in PDB entry 3E8R
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 LEU 395 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393B THR 5.8 0.4 - - - +
394B ILE* 1.3 77.5 - - - +
396B THR* 1.3 65.5 + - - +
397B LYS* 4.0 34.1 - - + +
398B GLU* 2.8 44.2 + - - +
399B ALA* 2.9 11.3 + - - +
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Residues in contact with THR 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B TYR* 4.3 32.1 - - + +
254B LEU* 5.6 0.2 - - + -
257B ARG* 3.0 37.5 - - - +
394B ILE 3.6 2.0 + - - -
395B LEU* 1.3 73.5 - - - +
397B LYS* 1.3 64.3 + - - +
399B ALA* 3.2 2.6 + - - +
400B ASP* 3.0 22.3 + - - +
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Residues in contact with LYS 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395B LEU* 3.1 31.0 - - + +
396B THR* 1.3 78.9 - - - +
398B GLU* 1.3 73.3 + - + +
400B ASP* 3.5 11.8 - - - +
401B LEU* 3.3 25.5 + - - +
442B GLY 3.7 23.6 - - - +
443B ASP* 3.7 23.7 + - - +
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Residues in contact with GLU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B ILE* 3.5 16.2 - - + +
395B LEU* 2.8 48.3 + - + +
397B LYS* 1.3 90.6 - - + +
399B ALA* 1.3 64.1 + - - +
401B LEU* 3.2 13.4 + - + +
402B VAL* 3.0 25.3 + - - +
441B SER* 5.9 0.5 - - - -
442B GLY 5.2 3.6 + - - +
486B 615 3.4 46.7 - - + -
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Residues in contact with ALA 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B TYR* 3.4 25.1 - - - +
254B LEU* 3.8 13.7 - - + -
385B THR* 4.6 2.6 - - + +
387B THR* 3.9 19.1 - - + -
394B ILE* 3.6 10.8 - - + +
395B LEU 2.9 10.5 + - - +
396B THR 3.6 6.5 - - - +
398B GLU* 1.3 75.6 - - - +
400B ASP* 1.3 62.6 + - - +
402B VAL* 3.2 4.8 + - - +
403B THR* 3.0 28.9 + - - -
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Residues in contact with ASP 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B LEU* 3.5 14.3 - - - +
257B ARG* 2.6 58.2 + - + +
258B VAL* 3.8 12.7 - - + +
261B ILE* 5.9 6.3 - - + -
396B THR* 3.0 17.4 + - - +
397B LYS* 3.5 12.6 - - - +
399B ALA* 1.3 75.9 - - - +
401B LEU* 1.3 54.2 + - + +
404B THR* 2.6 40.1 + - - +
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Residues in contact with LEU 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B LYS 3.3 14.1 + - - +
398B GLU* 3.2 12.4 + - + +
400B ASP* 1.3 77.7 - - + +
402B VAL* 1.3 65.1 + - - +
404B THR* 3.4 5.4 + - - +
405B HIS* 2.9 25.3 + - - +
434B VAL* 3.8 3.1 - - + +
442B GLY* 3.5 40.2 - - - +
447B ASN* 3.3 30.3 - - + +
448B LYS* 3.5 25.1 - - + +
486B 615 3.5 33.8 - - + +
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Residues in contact with VAL 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LEU* 3.9 40.6 - - + +
385B THR* 3.7 26.2 - - + +
394B ILE* 4.6 2.7 - - + -
398B GLU 3.0 16.0 + - - +
399B ALA* 3.2 5.8 + - - +
401B LEU* 1.3 74.6 - - - +
403B THR* 1.3 59.1 + - - +
405B HIS* 3.1 2.9 + - - +
406B GLU* 2.8 49.1 + - + +
486B 615 3.9 33.2 - - + -
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Residues in contact with THR 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B LEU* 3.9 25.0 - - + +
255B ILE* 4.5 4.5 - - + -
258B VAL* 4.4 4.5 - - + -
336B HIS* 4.1 11.4 - - + +
338B PHE* 3.5 20.8 - - + -
385B THR* 3.0 24.2 + - - +
399B ALA 3.0 16.8 + - - -
400B ASP 4.1 2.2 - - - -
402B VAL* 1.3 77.2 - - - +
404B THR* 1.3 61.6 + - - +
406B GLU* 3.9 1.7 - - - +
407B LEU* 2.9 42.2 + - + +
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Residues in contact with THR 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B VAL* 3.5 22.7 - - + +
261B ILE* 4.3 15.0 - - + +
262B TYR* 2.9 27.7 + - + -
400B ASP 2.6 24.4 + - - -
401B LEU* 3.6 5.8 - - - -
403B THR* 1.3 75.7 - - - +
405B HIS* 1.3 52.7 + - - +
408B GLY* 2.8 30.3 + - - -
434B VAL* 3.9 18.2 - - + -
448B LYS 4.3 11.0 - - - +
450B PHE* 4.0 15.2 - - + -
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Residues in contact with HIS 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ZN 2.1 36.9 - - - -
401B LEU 2.9 9.9 + - - +
402B VAL 3.4 3.1 - - - +
404B THR* 1.3 76.5 - - - +
406B GLU* 1.3 63.3 + - - +
408B GLY* 3.0 10.9 + - - -
409B HIS* 3.1 12.2 + - - -
415B HIS* 3.5 12.6 - + - -
434B VAL* 2.7 25.1 + - + +
435B MET* 3.4 26.2 - - + +
436B TYR 3.3 22.7 - - - -
486B 615 3.2 50.6 + + - +
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Residues in contact with GLU 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B HIS* 3.9 19.1 - - + -
349B GLY* 3.1 13.3 + - - -
350B LEU 3.3 22.1 - - - +
351B ALA* 3.3 21.9 + - + +
384B LEU 3.6 17.3 - - - +
385B THR* 4.2 1.8 - - - +
402B VAL* 2.8 29.5 + - + +
403B THR 4.1 0.2 - - - +
405B HIS* 1.3 77.9 - - - +
407B LEU* 1.3 60.9 + - - +
409B HIS* 3.1 5.9 + - - -
410B ASN* 3.1 18.4 + - - -
486B 615 2.7 45.2 + - - -
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Residues in contact with LEU 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B LEU* 4.7 11.4 - - + -
255B ILE* 5.0 1.3 - - + -
258B VAL* 4.2 6.5 - - + -
262B TYR* 3.1 19.1 - - + +
277B ILE* 3.5 37.9 - - + -
334B LEU* 3.8 16.8 - - + -
336B HIS* 4.0 20.4 - - + +
403B THR* 2.9 35.4 + - + +
404B THR 3.8 0.2 - - - +
406B GLU* 1.3 75.2 - - - +
408B GLY* 1.3 55.8 + - - +
410B ASN* 3.1 21.5 + - - +
411B PHE* 2.8 37.8 + - + -
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Residues in contact with GLY 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B TYR* 2.9 10.1 + - - -
404B THR 2.8 13.4 + - - -
405B HIS 3.0 7.0 + - - -
407B LEU* 1.3 75.6 - - - +
409B HIS* 1.3 60.8 + - - +
411B PHE* 3.2 11.0 + - - +
412B GLY 3.3 0.5 + - - -
413B ALA* 3.0 25.8 + - - +
435B MET* 4.0 9.9 - - - -
450B PHE* 4.0 11.0 - - - -
458B ILE* 3.9 3.1 - - - +
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Residues in contact with HIS 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ZN 2.1 30.6 - - - -
351B ALA* 4.1 20.9 - - + +
352B TYR 3.7 2.7 - - - +
353B GLY 3.3 12.6 - - - -
354B GLY* 4.3 14.2 - - - +
405B HIS* 3.1 19.1 + - - -
406B GLU* 3.1 16.4 + - - +
408B GLY* 1.3 74.2 - - - +
410B ASN* 1.3 55.1 + - - +
412B GLY* 2.8 25.5 + - - -
413B ALA 2.8 24.8 + - - -
414B GLU* 4.2 6.4 - - - -
415B HIS* 3.4 14.6 - + - -
435B MET* 3.3 13.9 - - + +
486B 615 3.0 17.3 - - - -
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Residues in contact with ASN 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334B LEU* 3.5 35.2 - - + +
335B ALA 5.1 0.5 - - - +
336B HIS* 4.7 0.7 + - - -
351B ALA* 3.7 3.5 - - - +
352B TYR 2.8 31.0 + - - +
353B GLY* 4.8 0.2 - - - -
363B GLY* 3.1 8.0 - - - -
364B VAL* 2.9 25.9 + - - +
382B SER 3.1 30.0 + - - +
383B GLY* 4.5 2.3 + - - -
406B GLU 3.1 12.4 + - - +
407B LEU* 3.1 32.8 + - - +
409B HIS* 1.3 76.2 - - - +
411B PHE* 1.3 57.6 + - - +
412B GLY* 3.3 3.5 + - - -
465B LYS* 4.7 1.9 + - - -
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Residues in contact with PHE 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B CYS* 4.0 20.9 - - + -
262B TYR* 3.9 29.4 - + - -
275B TYR* 5.2 3.6 - - + -
276B GLY 4.3 5.8 - - - -
277B ILE* 4.1 20.0 - - + -
334B LEU* 4.3 7.9 - - + -
364B VAL* 3.7 18.6 - - + -
407B LEU* 2.8 30.4 + - + +
408B GLY* 3.7 7.2 - - - +
409B HIS 3.2 0.4 - - - -
410B ASN* 1.3 73.3 - - + +
412B GLY* 1.3 51.4 + - - +
413B ALA 3.7 0.7 - - - -
458B ILE* 3.6 38.4 - - + +
461B THR* 2.6 36.8 + - + -
462B ILE* 4.1 16.2 - - + -
470B PHE* 3.7 24.5 - + - -
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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