Contacts of the helix formed by residues 391 - 407 (chain A) in PDB entry 5ON2
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 391 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379A GLY 4.1 7.0 - - - -
380A VAL* 4.6 10.5 - - + +
389A GLY 3.8 1.8 + - - -
390A LEU* 1.3 72.0 - - - +
392A HIS* 1.3 54.1 + - - +
393A GLU* 3.1 13.7 + - - +
394A ALA* 2.9 34.7 + - - +
395A ALA* 2.7 35.0 + - - +
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Residues in contact with HIS 392 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A THR 5.2 1.6 - - - -
249A ARG* 4.2 12.6 - - - -
251A ASP* 3.5 22.4 + - - +
378A LYS* 3.7 54.1 + - + +
379A GLY* 3.7 14.5 + - - +
391A ASP* 1.3 73.4 - - - +
393A GLU* 1.3 76.9 + - + +
395A ALA* 4.0 4.4 - - - +
396A PHE* 3.0 45.2 + + + +
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Residues in contact with GLU 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A ASP* 3.1 8.6 + - - +
392A HIS* 1.3 93.3 + - + +
394A ALA* 1.3 61.1 + - - +
396A PHE* 3.7 4.7 + - - +
397A ASN* 3.3 33.7 + - - +
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Residues in contact with ALA 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A LEU* 4.0 26.7 - - + -
391A ASP* 2.9 23.7 + - - +
393A GLU* 1.3 74.1 - - - +
395A ALA* 1.3 54.4 + - - +
397A ASN* 3.3 6.0 + - - +
398A ALA* 2.7 39.3 + - + +
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Residues in contact with ALA 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ASP* 3.5 20.9 + - + -
381A LEU* 3.4 34.1 - - + -
387A PHE* 6.0 0.2 - - - -
390A LEU* 4.2 7.3 - - + +
391A ASP 2.7 24.2 + - - +
392A HIS 4.0 1.1 - - - +
394A ALA* 1.3 70.4 - - - +
396A PHE* 1.3 64.7 + - - +
398A ALA* 4.4 5.6 - - - -
399A ILE* 3.5 28.5 + - - +
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Residues in contact with PHE 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A GLU* 4.0 23.8 - - + -
229A GLY* 4.2 10.8 - - - -
230A VAL* 4.6 5.6 - - + -
248A THR 3.6 12.6 - - - -
250A PRO* 3.3 45.9 - - + +
251A ASP* 4.3 3.0 - - - +
392A HIS* 3.0 34.5 + + + +
393A GLU* 3.8 6.7 - - - +
395A ALA* 1.3 77.8 - - - +
397A ASN* 1.3 71.1 + - - +
400A ALA* 3.2 26.2 + - - +
411A ARG* 3.9 17.9 - - + -
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Residues in contact with ASN 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A GLU* 3.3 22.7 + - - +
394A ALA* 3.3 5.7 + - - +
396A PHE* 1.3 90.9 - - - +
398A ALA* 1.3 55.2 + - - +
400A ALA 3.3 0.2 + - - -
401A ASP* 2.7 50.2 + - - +
411A ARG* 3.5 17.4 + - - +
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Residues in contact with ALA 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387A PHE* 3.9 26.3 - - + -
390A LEU* 4.0 14.1 - - + -
394A ALA 2.7 23.0 + - - +
395A ALA 4.3 2.2 - - - +
397A ASN* 1.3 73.0 - - - +
399A ILE* 1.3 57.1 + - - +
401A ASP* 3.8 6.2 - - - +
402A LYS* 3.0 28.2 + - - +
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Residues in contact with ILE 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A PRO* 3.2 37.2 - - + +
251A ASP* 3.7 15.3 - - - +
253A PHE* 4.0 18.4 - - + -
254A MET* 4.7 7.4 - - + -
313A LEU* 4.2 6.3 - - + -
381A LEU* 4.6 7.0 - - + -
387A PHE* 3.7 36.1 - - + -
395A ALA 3.5 17.5 + - - +
397A ASN 3.5 0.2 - - - -
398A ALA* 1.3 74.1 - - - +
400A ALA* 1.3 60.1 + - - +
402A LYS* 3.7 6.2 - - - +
403A LEU* 3.1 46.5 + - + +
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Residues in contact with ALA 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A VAL* 4.2 23.7 - - + +
250A PRO* 5.2 1.2 - - - +
396A PHE 3.2 21.5 + - - +
397A ASN 3.3 0.6 + - - +
398A ALA 3.3 0.6 - - - -
399A ILE* 1.3 74.9 - - - +
401A ASP* 1.3 57.1 + - - +
403A LEU* 3.4 5.3 + - - +
404A THR* 2.7 38.1 + - - -
409A GLY 5.6 0.3 - - - -
411A ARG* 3.3 33.2 - - + +
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Residues in contact with ASP 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A ASN* 2.7 34.5 + - - +
398A ALA* 3.9 6.0 - - - +
400A ALA* 1.3 68.5 - - - +
402A LYS* 1.3 59.8 + - - +
404A THR* 3.9 6.3 + - - -
405A ALA* 2.9 30.0 + - - +
411A ARG* 2.8 22.2 + - - -
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Residues in contact with LYS 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A LEU* 3.9 25.4 - - + -
386A GLU* 3.0 34.2 + - - +
387A PHE* 4.0 10.3 - - + -
398A ALA 3.0 18.8 + - - +
399A ILE* 3.7 9.4 - - - +
400A ALA 3.3 0.2 - - - -
401A ASP* 1.3 77.0 - - - +
403A LEU* 1.3 53.0 + - - +
405A ALA* 3.2 7.7 + - + +
406A MET* 2.8 53.0 + - + +
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Residues in contact with LEU 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A VAL* 4.7 7.2 - - + -
232A ILE* 4.0 31.9 - - + -
250A PRO* 5.8 0.4 - - + -
253A PHE* 4.2 18.8 - - + -
312A PRO* 4.3 10.5 - - + -
313A LEU* 4.4 12.8 - - + -
399A ILE* 3.1 41.0 + - + +
400A ALA* 4.1 2.9 - - - +
402A LYS* 1.3 75.8 - - + +
404A THR* 1.3 59.4 + - - +
406A MET* 4.4 5.6 - - - -
407A GLY 3.1 4.2 + - - -
408A VAL* 3.1 50.0 + - + +
409A GLY* 3.3 19.4 + - - -
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Residues in contact with THR 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A ALA* 2.7 24.4 + - - +
401A ASP* 3.9 7.5 + - - -
403A LEU* 1.3 76.7 - - - +
405A ALA* 1.3 61.8 + - - +
407A GLY* 3.4 11.6 + - - -
409A GLY 3.5 16.4 + - - +
410A GLU* 4.5 9.1 - - + -
411A ARG* 5.0 8.5 + - - +
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Residues in contact with ALA 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A ASP 2.9 20.6 + - - +
402A LYS* 3.2 8.7 + - + +
404A THR* 1.3 75.2 - - - +
406A MET* 1.3 64.0 + - + +
407A GLY* 4.5 0.5 - - - -
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Residues in contact with MET 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A PRO* 3.8 39.3 - - + +
313A LEU* 3.7 25.1 - - + -
402A LYS* 2.8 38.3 + - + +
403A LEU* 4.2 4.9 - - + +
405A ALA* 1.3 73.5 - - + +
407A GLY* 1.3 60.5 + - - +
408A VAL* 4.1 19.8 - - + +
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Residues in contact with GLY 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A LEU 3.1 7.0 + - - -
404A THR* 3.4 9.8 + - - -
405A ALA 3.3 3.4 - - - -
406A MET* 1.3 79.5 - - - +
408A VAL* 1.3 67.2 + - - +
409A GLY 3.8 2.7 - - - -
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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