Contacts of the helix formed by residues 340 - 352 (chain O) in PDB entry 6CNB
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 GLU 340 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338O ASP* 2.9 18.1 + - - +
339O LEU* 1.3 76.0 - - - +
341O GLU* 1.3 63.3 + - + +
343O LYS* 2.9 40.1 + - - +
344O SER* 3.6 5.8 + - - +
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Residues in contact with GLU 341 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238O ARG* 5.3 2.2 - - - +
242O LYS* 3.4 28.5 + - - +
243O MET* 6.0 2.7 - - + -
246O LYS* 3.2 31.2 + - - -
335O LEU* 4.6 13.5 - - - +
336O LEU 4.9 0.5 - - - +
337O GLN* 4.7 1.7 + - - -
338O ASP* 2.9 29.8 + - + +
340O GLU* 1.3 76.2 - - + +
342O ALA* 1.3 62.2 + - - +
344O SER* 2.6 37.8 + - - +
345O PHE* 2.9 20.4 + - - +
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Residues in contact with ALA 342 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ARG* 5.8 0.4 - - - -
158A GLY* 6.1 1.6 - - - -
337O GLN* 3.5 30.7 - - + +
338O ASP 2.5 31.6 + - - +
339O LEU* 5.0 2.0 - - + -
341O GLU* 1.3 78.8 + - - +
343O LYS* 1.3 55.4 + - - +
345O PHE* 3.2 7.5 + - - +
346O GLN* 2.9 28.1 + - - +
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Residues in contact with LYS 343 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A PRO* 5.6 7.0 - - + +
339O LEU 2.4 33.6 + - - +
340O GLU* 2.9 24.2 + - - +
342O ALA* 1.3 78.0 - - - +
344O SER* 1.3 55.4 + - - +
346O GLN* 4.3 6.1 - - - +
347O ASP* 2.9 38.1 + - - +
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Residues in contact with SER 344 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340O GLU* 4.3 4.2 + - - +
341O GLU* 2.6 36.4 + - - +
343O LYS* 1.3 74.9 - - - +
345O PHE* 1.3 53.1 + - - -
347O ASP* 2.8 23.7 + - - +
348O GLU* 3.2 17.3 - - - +
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Residues in contact with PHE 345 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246O LYS* 5.0 10.8 - - - -
328O ASP 4.2 6.1 - - - -
329O PRO* 3.3 32.1 - - + -
331O THR* 3.5 22.7 - - - -
332O GLN* 3.5 34.3 - - + -
335O LEU* 6.1 4.3 - - + -
337O GLN* 4.3 5.4 - - - +
341O GLU* 2.9 17.6 + - - +
342O ALA* 3.3 14.4 - - - +
343O LYS 3.0 0.2 - - - -
344O SER* 1.3 76.5 - - - +
346O GLN* 1.3 69.8 + - + +
348O GLU* 3.2 18.4 - - - +
349O ALA* 2.9 29.9 + - + +
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Residues in contact with GLN 346 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342O ALA 2.9 15.4 + - - +
343O LYS* 3.9 5.8 - - - +
345O PHE* 1.3 81.0 - - + +
347O ASP* 1.3 61.3 + - - +
349O ALA* 2.9 20.1 + - - +
350O GLU* 2.8 44.3 + - + +
485O PRO* 4.9 8.8 - - - +
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Residues in contact with ASP 347 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343O LYS* 2.9 22.1 + - + +
344O SER* 2.8 26.1 + - - +
346O GLN* 1.3 73.9 - - - +
348O GLU* 1.3 85.7 + - - +
350O GLU* 3.0 28.6 + - + +
351O LEU* 3.3 14.9 + - - +
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Residues in contact with GLU 348 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246O LYS* 5.1 12.9 + - - +
344O SER 3.2 20.6 - - - +
345O PHE* 3.2 19.5 - - - +
346O GLN 3.2 0.2 - - - -
347O ASP* 1.3 88.1 + - - +
349O ALA* 1.3 61.8 + - - +
350O GLU 3.4 0.2 + - - -
351O LEU* 3.4 16.7 + - + +
352O VAL* 3.2 24.5 + - + +
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Residues in contact with ALA 349 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328O ASP* 4.4 15.9 - - + +
345O PHE* 2.9 19.1 + - + +
346O GLN* 2.9 26.4 + - - +
348O GLU* 1.3 76.7 - - - +
350O GLU* 1.3 51.1 + - - +
352O VAL* 3.2 14.5 - - - +
481O SER* 2.5 32.7 + - - +
485O PRO* 4.5 8.2 - - + +
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Residues in contact with GLU 350 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346O GLN* 2.8 41.8 + - + +
347O ASP* 3.0 23.1 + - + +
349O ALA* 1.3 69.4 - - - +
351O LEU* 1.3 53.7 + - + +
354O GLU* 4.4 2.9 - - - +
481O SER* 2.7 35.4 + - - -
482O LYS* 3.3 33.6 + - + +
485O PRO* 4.8 8.6 - - - +
486O VAL* 4.8 7.9 - - - +
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Residues in contact with LEU 351 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347O ASP* 3.3 11.0 + - - +
348O GLU* 3.6 20.9 - - + +
349O ALA 3.3 0.2 - - - -
350O GLU* 1.3 76.7 - - + +
352O VAL* 1.3 71.3 + - - +
353O GLU 3.4 0.2 - - - -
354O GLU* 3.0 19.9 + - + +
355O LYS* 3.7 11.7 + - + +
481O SER* 3.0 7.4 - - - -
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Residues in contact with VAL 352 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324O PRO* 5.0 3.8 - - + -
327O ARG* 6.1 0.7 - - - +
328O ASP* 4.3 20.0 - - + +
348O GLU* 3.2 16.2 + - + +
349O ALA* 3.2 24.5 - - - +
351O LEU* 1.3 82.4 - - - +
353O GLU* 1.3 83.1 + - + +
357O PRO* 3.1 23.0 - - + +
481O SER* 2.5 11.2 + - - +
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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