Contacts of the helix formed by residues 314 - 332 (chain E) in PDB entry 2OZB
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 GLY 314 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217E PRO* 5.0 3.8 - - - -
218E ASN* 3.2 16.8 - - - -
221E ILE* 3.8 19.2 - - - +
311E SER 3.1 6.8 + - - -
312E THR 3.4 1.4 + - - -
313E GLU* 1.3 78.5 - - - +
315E LYS* 1.3 67.6 + - - +
317E GLY* 3.1 3.5 + - - -
318E TYR* 2.9 29.0 + - - -
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Residues in contact with LYS 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311E SER* 3.2 12.9 + - - +
313E GLU* 3.5 5.1 + - + +
314E GLY* 1.3 75.3 - - - +
316E VAL* 1.3 70.8 + - + +
318E TYR* 4.0 5.9 - - - +
319E GLU* 3.0 61.1 + - + +
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Residues in contact with VAL 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D PRO* 4.0 30.5 - - + -
65D ILE* 6.3 0.2 - - + -
218E ASN* 3.0 18.3 + - + +
301E LEU* 5.2 1.1 - - + -
302E ALA* 4.5 4.5 - - - +
305E VAL* 4.1 21.1 - - + -
311E SER* 3.1 21.4 + - - +
315E LYS* 1.3 82.9 - - + +
317E GLY* 1.3 58.4 + - - +
319E GLU* 3.5 4.3 + - - +
320E LEU* 2.9 54.4 + - + +
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Residues in contact with GLY 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218E ASN* 2.7 43.3 + - - -
221E ILE* 3.8 8.8 - - - +
222E ILE* 3.9 10.3 - - - +
314E GLY 3.6 1.8 - - - -
316E VAL* 1.3 71.0 - - - +
318E TYR* 1.3 58.3 + - - +
320E LEU* 3.3 1.9 + - - +
321E LYS* 2.8 32.6 + - - +
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Residues in contact with TYR 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221E ILE* 3.7 38.3 - - + +
313E GLU 3.6 19.1 - - - -
314E GLY 2.9 29.2 + - - +
315E LYS* 4.0 5.4 - - - +
317E GLY* 1.3 71.9 - - - +
319E GLU* 1.3 65.7 + - + +
321E LYS* 3.4 2.9 + - + +
322E ASP* 3.1 33.0 + - - +
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Residues in contact with GLU 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315E LYS* 3.0 60.6 + - + +
316E VAL* 4.0 3.5 - - - +
318E TYR* 1.3 81.5 - - + +
320E LEU* 1.3 62.1 + - + +
322E ASP* 3.6 9.2 + - - +
323E GLU* 3.2 22.0 + - - +
326E ARG* 4.7 2.6 + - - +
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Residues in contact with LEU 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222E ILE* 4.0 16.8 - - + -
298E LYS* 3.6 50.7 - - + +
301E LEU* 4.4 13.2 - - + -
302E ALA* 4.4 5.4 - - + +
316E VAL* 2.9 43.8 + - + +
317E GLY 3.8 2.7 - - - +
319E GLU* 1.3 74.6 - - + +
321E LYS* 1.3 53.7 + - - +
323E GLU* 3.0 19.9 + - - +
324E ILE* 2.8 40.3 + - + +
31F U 5.5 2.5 - - - +
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Residues in contact with LYS 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221E ILE* 3.4 34.2 + - + +
222E ILE* 3.6 21.9 - - + +
279E ILE* 4.0 15.0 - - + -
317E GLY 2.8 20.1 + - - +
318E TYR* 3.8 4.9 - - + +
320E LEU* 1.3 72.4 - - - +
322E ASP* 1.3 59.6 + - - +
324E ILE* 3.1 11.2 + - - +
325E GLU* 2.8 58.6 + - - +
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Residues in contact with ASP 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318E TYR* 3.1 23.4 + - - +
319E GLU* 3.7 7.6 - - - +
321E LYS* 1.3 78.3 - - - +
323E GLU* 1.3 62.4 + - - +
325E GLU* 3.5 8.2 + - - +
326E ARG* 3.0 55.8 + - - +
501E CA 2.7 26.7 - - - -
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Residues in contact with GLU 323 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294E LEU* 4.9 0.9 - - - +
298E LYS* 3.6 24.5 + - - +
319E GLU 3.2 13.1 + - - +
320E LEU* 3.0 26.6 + - - +
322E ASP* 1.3 73.2 - - - +
324E ILE* 1.3 68.8 + - - +
326E ARG* 3.3 16.9 + - + +
327E LYS* 3.3 54.0 + - - +
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Residues in contact with ILE 324 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222E ILE* 3.9 24.7 - - + -
279E ILE* 4.1 8.3 - - + -
294E LEU* 4.1 18.4 - - + -
295E VAL* 4.1 16.2 - - + -
298E LYS* 3.8 36.6 - - + -
320E LEU* 2.8 24.0 + - + +
321E LYS* 3.5 8.5 - - - +
323E GLU* 1.3 74.1 - - + +
325E GLU* 1.3 57.3 + - - +
327E LYS* 3.1 7.3 + - - +
328E PHE* 3.0 61.8 + - + -
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Residues in contact with GLU 325 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279E ILE* 4.9 6.1 - - + +
321E LYS* 2.8 51.8 + - + +
322E ASP* 4.0 5.7 - - - +
324E ILE* 1.3 80.1 - - + +
326E ARG* 1.3 62.1 + - - +
328E PHE* 3.5 19.6 + - + +
329E ASP* 3.1 29.4 + - - +
333E GLU* 4.4 5.6 - - - +
501E CA 4.0 16.5 - - - -
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Residues in contact with ARG 326 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319E GLU* 4.7 2.8 + - - +
322E ASP* 3.0 50.7 + - - +
323E GLU* 3.7 14.6 - - - +
324E ILE 3.3 0.2 - - - -
325E GLU* 1.3 77.1 - - + +
327E LYS* 1.3 58.2 + - + +
329E ASP* 3.3 10.7 + - - +
330E LYS* 3.0 47.6 + - - +
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Residues in contact with LYS 327 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294E LEU* 3.9 28.5 - - + -
298E LYS* 5.4 1.3 - - - +
323E GLU* 3.3 40.2 + - - +
324E ILE 3.1 8.2 + - - +
326E ARG* 1.3 74.2 - - + +
328E PHE* 1.3 67.0 + - - +
330E LYS* 2.9 17.8 + - + +
331E TRP* 2.9 52.4 + - + +
28F C 5.7 0.4 + - - -
29F A 4.7 15.7 + - - -
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Residues in contact with PHE 328 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279E ILE* 3.6 22.2 - - + -
282E SER* 4.8 2.2 - - - -
283E LEU* 3.4 31.3 - - + +
291E ALA* 3.7 24.5 - - + -
294E LEU* 3.9 9.4 - - + -
295E VAL* 4.0 11.2 - - + -
324E ILE* 3.0 43.4 + - + -
325E GLU* 3.6 17.0 - - + +
327E LYS* 1.3 75.9 - - - +
329E ASP* 1.3 61.5 + - - +
331E TRP* 3.3 27.9 + + - +
332E GLN 3.2 17.3 + - - -
333E GLU* 3.3 34.0 + - + +
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Residues in contact with ASP 329 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325E GLU 3.1 17.3 + - - +
326E ARG* 3.5 12.5 - - - +
327E LYS 3.1 0.2 - - - -
328E PHE* 1.3 77.4 - - - +
330E LYS* 1.3 57.8 + - + +
332E GLN* 2.9 30.0 + - - +
333E GLU* 3.1 29.6 - - - +
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Residues in contact with LYS 330 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326E ARG* 3.0 36.4 + - - +
327E LYS* 2.9 19.9 + - + +
329E ASP* 1.3 77.4 - - + +
331E TRP* 1.3 62.2 + - + +
332E GLN* 2.9 19.6 + - - -
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Residues in contact with TRP 331 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283E LEU* 4.1 11.7 - - + -
287E LEU* 3.8 33.9 - - + +
290E LYS* 3.6 53.1 - - + +
291E ALA* 3.8 20.2 - - + -
294E LEU* 3.7 32.5 - - + -
327E LYS* 2.9 34.1 + - + +
328E PHE* 3.6 26.7 - + - +
330E LYS* 1.3 82.2 - - + +
332E GLN* 1.3 69.0 + - - +
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Residues in contact with GLN 332 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284E PRO* 4.2 1.6 - - - +
287E LEU* 3.2 22.4 - - - +
328E PHE 3.2 2.8 + - - -
329E ASP 2.9 20.3 + - - +
330E LYS* 2.9 24.8 + - - +
331E TRP* 1.3 79.3 + - - +
333E GLU* 1.3 65.2 + - - +
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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
------------------------------------------------------------
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