Contacts of the helix formed by residues 342 - 353 (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 342 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338D VAL 3.3 5.3 + - - +
339D PRO 3.5 1.6 - - - +
341D HIS* 1.3 80.8 - - - +
343D GLN* 1.3 56.1 + - - +
344D ARG* 3.8 14.9 + - - +
345D ASP* 3.0 42.1 + - - +
346D TYR* 2.7 34.8 + - - +
374D ALA* 3.7 6.7 - - - +
376D THR* 6.1 2.2 - - - +
902D VRT 4.1 21.5 + - + +
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Residues in contact with GLN 343 (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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342D ASP* 1.3 75.4 + - - +
344D ARG* 1.3 59.2 + - + +
346D TYR* 3.6 18.0 - - - +
347D GLU* 3.0 62.4 + - - +
372D GLN 4.8 1.8 + - - -
373D GLN* 3.8 16.6 - - - +
374D ALA* 3.5 24.8 + - - +
376D THR* 5.4 7.0 + - - +
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Residues in contact with ARG 344 (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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296D ALA* 5.9 3.5 - - - +
300D LYS* 3.6 37.0 - - + +
325D PHE* 3.9 47.9 + - + +
327D LEU* 6.2 0.2 - - - +
342D ASP* 3.4 13.5 + - - +
343D GLN* 1.3 77.2 - - + +
345D ASP* 1.3 62.8 + - - +
347D GLU* 5.5 0.2 - - - +
348D PHE* 3.3 23.9 + - - +
902D VRT 3.2 37.4 + - - -
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Residues in contact with ASP 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258D TYR* 3.2 17.8 + - - +
260D ALA* 5.5 0.3 - - - +
325D PHE* 4.5 14.4 - - - -
335D VAL* 5.4 4.2 - - - +
337D ALA* 3.5 20.6 - - + +
338D VAL 3.2 7.2 + - - -
339D PRO* 3.6 19.5 - - + +
342D ASP* 3.0 24.5 + - - +
344D ARG* 1.3 76.6 - - - +
346D TYR* 1.3 59.4 + - - +
348D PHE* 4.4 0.2 - - - -
349D ALA* 3.0 28.6 + - - +
902D VRT 2.8 29.7 + - - -
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Residues in contact with TYR 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339D PRO* 3.4 21.9 - - - +
342D ASP 2.7 20.2 + - - +
343D GLN* 3.6 24.2 - - - +
344D ARG 3.4 0.2 - - - -
345D ASP* 1.3 73.8 - - - +
347D GLU* 1.3 58.2 + - + +
349D ALA* 3.2 3.1 + - - +
350D SER* 2.8 53.5 + - - -
356D ILE* 4.1 23.5 - - + +
370D LEU* 3.3 15.4 + - + -
371D SER 2.8 35.5 + - - -
372D GLN 3.2 19.9 - - - -
373D GLN* 3.6 13.2 - - - -
374D ALA* 3.8 12.8 - - + -
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Residues in contact with GLU 347 (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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300D LYS* 3.2 33.6 - - + -
343D GLN* 3.0 46.0 + - - +
344D ARG* 5.5 0.2 - - - +
346D TYR* 1.3 76.2 - - + +
348D PHE* 1.3 63.2 + - - +
350D SER* 3.8 7.6 - - - -
351D LYS* 3.2 30.8 + - + +
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Residues in contact with PHE 348 (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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258D TYR* 3.2 31.4 - + - +
260D ALA* 5.8 0.9 - - + -
300D LYS* 3.9 21.2 - - + +
301D LYS 3.9 20.9 - - - -
302D GLY* 4.0 1.8 - - - -
321D TRP* 3.8 41.5 - + + -
322D ALA 4.0 11.4 - - - -
323D ALA* 4.2 4.7 - - + -
325D PHE* 3.8 26.5 - + + -
344D ARG 3.3 18.6 + - - +
345D ASP 3.9 0.2 - - - +
346D TYR 3.3 0.2 - - - -
347D GLU* 1.3 78.6 - - - +
349D ALA* 1.3 61.5 + - - +
351D LYS* 3.5 1.3 + - - -
352D TYR* 3.1 46.2 + + - +
354D LEU* 3.9 12.8 - - + -
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Residues in contact with ALA 349 (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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258D TYR* 4.1 2.5 - - + -
339D PRO* 3.8 23.3 - - + -
345D ASP 3.0 20.6 + - - +
346D TYR 3.6 3.4 - - - +
348D PHE* 1.3 74.1 - - - +
350D SER* 1.3 61.1 + - - +
353D GLY* 3.0 8.7 + - - -
354D LEU* 2.9 57.0 + - + +
356D ILE* 4.2 6.8 - - + +
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Residues in contact with SER 350 (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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346D TYR* 2.8 51.4 + - - -
347D GLU* 3.8 8.5 - - - -
348D PHE 3.3 0.2 - - - -
349D ALA* 1.3 75.5 - - - +
351D LYS* 1.3 64.4 + - - +
353D GLY* 3.7 6.2 + - - -
356D ILE* 5.1 7.5 - - - +
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Residues in contact with LYS 351 (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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299D GLU* 4.7 16.2 - - - +
300D LYS 5.8 1.6 - - - +
347D GLU* 3.2 17.9 + - + +
348D PHE* 4.0 3.1 - - - +
349D ALA 3.5 0.2 - - - -
350D SER* 1.3 83.3 - - - +
352D TYR* 1.3 75.0 + - + +
353D GLY 3.7 0.5 + - - -
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Residues in contact with TYR 352 (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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300D LYS 3.6 19.7 - - - -
301D LYS* 3.4 11.3 - - - +
302D GLY 2.9 41.5 + - - -
321D TRP* 3.5 35.4 - + + -
348D PHE* 3.1 36.2 + + - +
349D ALA 4.0 0.2 - - - -
351D LYS* 1.3 85.6 - - + +
353D GLY* 1.3 61.2 + - - +
354D LEU* 3.5 13.1 + - + +
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Residues in contact with GLY 353 (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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349D ALA 3.0 8.8 + - - -
350D SER 3.7 4.6 + - - -
351D LYS 3.4 4.4 + - - -
352D TYR* 1.3 79.0 - - - +
354D LEU* 1.3 64.5 + - - +
355D ASN* 5.1 2.8 + - - -
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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