Contacts of the helix formed by residues 391 - 407 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379D GLY 4.2 6.5 - - - -
380D VAL* 4.5 12.8 - - + +
389D GLY 3.9 2.2 + - - -
390D LEU* 1.3 74.3 - - - +
392D HIS* 1.3 58.2 + - - +
393D GLU* 3.7 16.2 + - - +
394D ALA* 3.2 23.2 + - - +
395D ALA* 2.8 33.2 + - - +
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Residues in contact with HIS 392 (chain D).
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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248D THR 5.1 1.1 + - - -
249D ARG* 3.7 6.1 - - - -
251D ASP* 3.1 37.5 + - - +
378D LYS* 3.4 61.1 + - + +
379D GLY* 3.9 13.6 + - - +
391D ASP* 1.3 75.8 + - - +
393D GLU* 1.3 65.8 + - + +
395D ALA* 3.7 4.3 - - - +
396D PHE* 2.8 52.8 + + + +
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Residues in contact with GLU 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391D ASP* 3.5 11.3 + - - +
392D HIS* 1.3 89.2 - - + +
394D ALA* 1.3 59.0 + - - +
396D PHE* 3.7 5.6 + - - +
397D ASN* 2.8 39.4 + - - +
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Residues in contact with ALA 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390D LEU* 4.0 23.8 - - + -
391D ASP* 3.2 23.0 + - - +
392D HIS 3.4 0.2 - - - -
393D GLU* 1.3 78.6 - - - +
395D ALA* 1.3 53.6 + - - +
397D ASN* 3.3 6.1 + - - +
398D ALA* 2.8 38.1 + - - +
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Residues in contact with ALA 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D ASP* 3.7 18.0 - - + -
381D LEU* 3.4 35.9 - - + -
390D LEU* 4.0 7.6 - - + +
391D ASP 2.8 22.4 + - - +
392D HIS* 3.8 0.9 - - - +
394D ALA* 1.3 70.3 - - - +
396D PHE* 1.3 65.5 + - - +
398D ALA* 4.4 4.3 - - - -
399D ILE* 3.2 30.5 + - - +
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Residues in contact with PHE 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D GLU* 4.1 20.4 - - + -
229D GLY* 4.7 3.4 - - - -
230D VAL* 4.2 16.2 - - + -
248D THR 3.7 13.5 - - - -
250D PRO* 3.4 39.8 - - + +
251D ASP* 3.8 11.6 - - + +
392D HIS* 2.8 37.6 + + + +
393D GLU* 3.7 6.7 - - - +
395D ALA* 1.3 73.7 - - - +
397D ASN* 1.3 70.5 + - - +
399D ILE* 4.4 0.2 - - - -
400D ALA* 3.1 28.8 + - - +
411D ARG* 3.8 21.5 - - + -
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Residues in contact with ASN 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393D GLU* 2.8 27.0 + - - +
394D ALA* 3.8 4.1 - - - +
396D PHE* 1.3 86.6 - - - +
398D ALA* 1.3 58.2 + - - +
400D ALA 3.2 0.2 + - - -
401D ASP* 2.8 45.4 + - - +
411D ARG* 3.3 26.6 + - - +
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Residues in contact with ALA 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387D PHE* 3.7 26.0 - - + -
390D LEU* 4.0 14.4 - - + -
394D ALA 2.8 21.9 + - - +
395D ALA 4.1 1.6 - - - +
397D ASN* 1.3 73.7 - - - +
399D ILE* 1.3 57.4 + - - +
401D ASP* 4.2 4.3 - - - +
402D LYS* 3.2 26.5 + - - +
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Residues in contact with ILE 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D PRO* 3.3 33.0 - - + +
251D ASP* 3.6 16.4 - - - +
253D PHE* 4.2 14.4 - - + -
254D MET* 4.6 9.6 - - + -
313D LEU* 4.3 6.5 - - + -
381D LEU* 4.5 6.5 - - + -
387D PHE* 3.5 43.7 - - + -
395D ALA 3.2 17.0 + - - +
396D PHE 4.5 0.2 - - - +
398D ALA* 1.3 74.1 - - - +
400D ALA* 1.3 66.2 + - - +
402D LYS* 3.4 1.2 + - - +
403D LEU* 3.1 41.8 + - + +
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Residues in contact with ALA 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D VAL* 4.0 32.0 - - + +
250D PRO* 5.1 1.7 - - + +
396D PHE* 3.1 20.8 + - + +
397D ASN 3.2 4.2 + - - +
399D ILE* 1.3 78.0 - - - +
401D ASP* 1.3 53.8 + - - +
403D LEU* 3.6 4.3 + - - +
404D THR* 2.6 36.5 + - - -
411D ARG* 3.7 25.8 - - + +
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Residues in contact with ASP 401 (chain D).
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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397D ASN* 2.8 25.1 + - - +
398D ALA* 4.2 4.7 - - - +
400D ALA* 1.3 70.7 - - - +
402D LYS* 1.3 59.4 + - - +
404D THR* 3.7 6.8 - - - -
405D ALA* 2.8 30.5 + - - +
411D ARG* 2.8 34.0 + - - -
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Residues in contact with LYS 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313D LEU* 3.6 27.6 - - + -
386D GLU* 3.7 30.4 + - - +
387D PHE* 4.2 8.3 - - + -
398D ALA 3.2 19.7 + - - +
399D ILE* 3.6 9.0 - - - +
400D ALA 3.3 0.2 - - - -
401D ASP* 1.3 77.4 - - - +
403D LEU* 1.3 56.7 + - - +
405D ALA* 3.3 7.6 + - + +
406D MET* 2.9 47.3 + - + +
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Residues in contact with LEU 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D VAL* 4.9 9.2 - - + -
231D GLU 5.5 0.2 - - - +
232D ILE* 4.0 33.7 - - + -
250D PRO* 5.5 0.9 - - + -
253D PHE* 4.2 8.7 - - + -
312D PRO* 3.9 29.4 - - + -
313D LEU* 4.4 13.7 - - + -
399D ILE* 3.1 37.8 + - + +
400D ALA* 4.1 3.6 - - - +
402D LYS* 1.3 72.9 - - - +
404D THR* 1.3 61.1 + - - +
406D MET* 3.9 4.9 - - - -
407D GLY 3.0 20.3 + - - -
408D VAL* 3.0 34.5 + - + +
409D GLY* 3.6 9.7 - - - +
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Residues in contact with THR 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400D ALA* 2.6 24.2 + - - +
401D ASP* 3.7 7.8 - - - -
403D LEU* 1.3 74.1 - - - +
405D ALA* 1.3 64.3 + - - +
407D GLY* 3.2 13.6 + - - -
409D GLY 3.4 16.9 + - - +
410D GLU* 4.2 14.3 - - + -
411D ARG* 4.9 8.3 + - - -
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Residues in contact with ALA 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401D ASP 2.8 19.0 + - - +
402D LYS* 3.3 10.1 + - + +
404D THR* 1.3 77.8 - - - +
406D MET* 1.3 62.8 + - + +
407D GLY* 3.5 0.5 + - - -
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Residues in contact with MET 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312D PRO* 3.9 27.6 - - + +
313D LEU* 4.1 23.6 - - - -
402D LYS* 2.9 34.7 + - + +
403D LEU* 4.0 3.1 - - - +
405D ALA* 1.3 75.5 - - + +
407D GLY* 1.3 61.2 + - - +
408D VAL* 4.0 24.2 - - + +
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Residues in contact with GLY 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403D LEU 3.0 5.4 + - - -
404D THR* 3.2 15.7 + - - -
405D ALA 4.4 0.2 - - - -
406D MET* 1.3 79.6 - - - +
408D VAL* 1.3 66.1 + - - +
409D GLY 3.7 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
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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