Contacts of the helix formed by residues 393 - 408 (chain B) in PDB entry 3X0Y
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 PRO 393 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389B SER 5.3 0.4 - - - +
390B LEU* 4.8 2.0 - - - +
391B HIS 4.9 0.2 - - - +
392B ASP* 1.3 88.0 - - + +
394B VAL* 1.3 65.1 - - - +
395B SER* 3.1 14.8 + - - +
396B TYR* 3.2 31.6 + - + +
397B LYS* 3.7 9.9 + - - +
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Residues in contact with VAL 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B LYS* 4.8 3.4 - - + -
350B ALA* 3.7 35.9 - - + +
353B THR* 4.2 28.5 - - + +
389B SER 5.0 5.0 + - - +
392B ASP 3.3 6.2 + - - +
393B PRO* 1.3 69.1 - - - +
395B SER* 1.3 61.5 + - - +
396B TYR 3.2 0.4 - - - -
397B LYS* 3.3 12.1 + - + +
398B ILE* 3.0 36.0 + - + +
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Residues in contact with SER 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B PRO* 4.0 8.8 - - - +
394B VAL* 1.3 83.5 - - - +
396B TYR* 1.3 78.7 + - - +
398B ILE* 3.5 6.1 + - - +
399B ALA* 2.9 25.5 + - - +
300C ARG* 4.0 24.8 + - - +
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Residues in contact with TYR 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B PRO* 3.2 27.6 + - + +
395B SER* 1.3 89.3 + - - +
397B LYS* 1.3 64.3 + - - +
399B ALA* 3.7 18.3 - - + +
400B ASP* 3.0 38.8 + - - +
403B LYS* 5.1 8.5 - - - -
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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
----------------------------------------------------------
255B GLN* 3.2 27.8 - - - -
342B MET* 4.5 2.0 - - + -
346B SER* 3.6 44.4 + - - +
349B LYS* 3.9 20.2 - - + -
350B ALA* 5.0 0.4 - - + -
392B ASP* 3.3 18.1 + - - +
393B PRO 3.7 8.0 + - - +
394B VAL* 3.3 17.0 + - + +
396B TYR* 1.3 78.3 - - - +
398B ILE* 1.3 61.5 + - - +
400B ASP* 3.3 8.0 + - - +
401B VAL* 3.2 26.7 + - - +
416B THR* 2.6 29.9 + - - -
417B SER* 4.4 8.7 - - - +
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Residues in contact with ILE 398 (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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350B ALA* 3.8 11.7 - - + -
394B VAL* 3.0 31.1 + - + +
395B SER* 3.6 7.6 - - - +
397B LYS* 1.3 77.0 - - - +
399B ALA* 1.3 61.7 + - - +
401B VAL* 3.2 5.0 + - - +
402B GLY 3.0 17.7 + - - -
299C ILE 4.6 0.3 - - - +
300C ARG* 3.7 53.8 - - + +
303C GLY* 3.7 4.1 - - - -
304C GLU* 4.1 22.0 - - + +
307C ILE* 3.8 21.5 - - + -
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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
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395B SER 2.9 17.6 + - - +
396B TYR* 3.8 25.6 - - + +
397B LYS 3.3 0.2 - - - -
398B ILE* 1.3 79.0 - - - +
400B ASP* 1.3 57.1 + - - +
402B GLY 3.2 1.0 + - - -
403B LYS* 2.8 41.7 + - - +
296C PRO 6.0 0.4 - - - +
299C ILE* 3.4 20.8 - - + +
300C ARG* 5.1 4.5 - - + +
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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
----------------------------------------------------------
343B VAL* 4.7 4.2 - - - +
346B SER* 4.6 10.1 + - - +
396B TYR* 3.0 27.1 + - - +
397B LYS* 3.7 9.3 + - - +
398B ILE 3.3 0.2 - - - -
399B ALA* 1.3 73.9 - - - +
401B VAL* 1.3 66.5 + - - +
403B LYS* 3.9 16.9 + - - +
404B HIS* 3.1 22.9 + - - +
409B GLN 4.6 1.9 - - - +
410B TYR 6.0 0.2 - - - -
411B PRO* 3.7 38.8 - - + +
417B SER* 3.8 16.3 - - - -
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Residues in contact with VAL 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B VAL* 3.6 37.9 - - + +
346B SER* 3.9 4.0 - - - -
347B GLY* 3.7 18.8 - - - +
397B LYS 3.2 14.1 + - - +
398B ILE 3.2 7.4 + - - +
400B ASP* 1.3 76.2 - - - +
402B GLY* 1.3 53.6 + - - +
404B HIS* 3.2 2.9 + - - +
405B THR* 2.8 37.5 + - - +
303C GLY 4.0 7.0 - - - +
306C THR* 3.4 37.7 - - + -
307C ILE* 4.1 9.4 - - + -
310C GLN* 5.4 2.0 - - - +
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Residues in contact with GLY 402 (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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398B ILE 3.0 10.5 + - - -
399B ALA 3.2 2.2 + - - -
401B VAL* 1.3 78.0 - - - +
403B LYS* 1.3 55.0 + - - +
405B THR* 3.9 1.0 - - - -
406B LEU* 2.9 33.1 + - - +
299C ILE* 3.3 29.2 - - - +
302C TYR* 4.1 4.1 - - - +
303C GLY* 3.4 13.6 - - - -
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Residues in contact with LYS 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B TYR* 5.1 8.1 - - - -
399B ALA* 2.8 35.9 + - - +
400B ASP* 3.9 16.8 + - - +
401B VAL 3.3 0.2 - - - -
402B GLY* 1.3 73.3 - - - +
404B HIS* 1.3 60.3 + - - +
407B ASN* 2.9 36.7 + - - +
408B GLY 3.3 5.2 + - - -
409B GLN* 3.4 34.2 + - + +
299C ILE* 3.8 28.1 - - + +
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Residues in contact with HIS 404 (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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340B GLU* 3.2 34.1 + - - -
343B VAL* 3.7 29.9 - - + +
400B ASP 3.1 13.5 + - - +
401B VAL 3.2 8.0 + - - +
403B LYS* 1.3 74.7 - - - +
405B THR* 1.3 69.8 + - - +
408B GLY* 3.0 25.9 + - - -
409B GLN 3.2 26.4 + - - +
410B TYR* 3.6 20.5 - + - -
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Residues in contact with THR 405 (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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401B VAL* 2.8 22.5 + - - +
402B GLY* 3.9 3.8 - - - -
404B HIS* 1.3 81.9 + - - +
406B LEU* 1.3 60.8 + - - +
408B GLY 4.6 0.3 + - - -
270C LEU* 4.4 12.3 - - + -
274C ARG* 3.0 43.8 + - - +
278C ARG* 4.2 1.7 + - - -
302C TYR* 4.0 26.7 - - + -
306C THR* 2.5 38.2 + - - +
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Residues in contact with LEU 406 (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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279A THR* 3.8 0.2 - - - +
402B GLY 2.9 17.6 + - - +
403B LYS* 4.9 0.2 - - - -
405B THR* 1.3 78.8 - - - +
407B ASN* 1.3 67.8 + - - +
408B GLY 3.7 0.4 - - - -
274C ARG* 4.3 6.3 - - + +
277C THR* 3.7 28.0 - - + -
278C ARG* 2.8 41.6 + - - -
293C THR* 4.0 22.4 - - + +
298C THR* 3.9 17.0 - - + -
299C ILE* 4.4 10.3 - - + -
302C TYR* 3.8 36.1 - - + -
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Residues in contact with ASN 407 (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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279A THR* 3.3 34.2 + - - +
280A GLN* 2.8 25.6 + - - +
403B LYS* 2.9 22.8 + - - +
406B LEU* 1.3 84.8 - - - +
408B GLY* 1.3 59.9 + - - +
409B GLN* 3.6 27.9 - - + +
278C ARG* 5.0 0.4 - - - -
293C THR* 3.2 45.8 + - - +
294C GLU* 6.0 0.8 - - - +
299C ILE* 4.6 6.7 - - - +
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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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280A GLN* 4.4 1.9 + - - -
404B HIS* 3.0 27.7 + - - -
405B THR 4.6 0.4 + - - -
406B LEU 3.7 0.8 - - - -
407B ASN* 1.3 77.4 - - - +
409B GLN* 1.3 61.9 + - - +
410B TYR* 3.9 10.9 + - - -
278C ARG* 5.1 1.8 - - - +
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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