Contacts of the helix formed by residues 310 - 334 (chain E) in PDB entry 3DUF
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 SER 310 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307E GLY 5.7 0.3 + - - -
308E LEU 5.5 0.3 - - - -
309E TRP* 1.3 86.4 + - - +
311E GLU* 1.3 65.3 + - - +
312E GLU* 3.7 28.3 + - - -
313E GLU* 3.3 17.6 + - - +
314E GLU* 3.2 20.1 + - - +
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Residues in contact with GLU 311 (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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304E GLU* 6.0 2.0 - - - +
310E SER* 1.3 70.8 - - - +
312E GLU* 1.3 67.6 + - - +
314E GLU* 3.2 8.8 + - - +
315E ASN* 2.7 36.7 + - - +
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Residues in contact with GLU 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310E SER* 3.7 18.8 + - - -
311E GLU* 1.3 84.1 + - - +
313E GLU* 1.3 57.2 + - + +
315E ASN* 3.2 13.2 + - - +
316E ASN* 2.8 44.3 + - - +
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Residues in contact with GLU 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E LYS* 3.1 32.4 - - - +
51E ARG* 4.9 8.5 - - - +
308E LEU 3.3 4.9 - - - +
309E TRP* 2.9 40.4 - - + -
310E SER* 3.3 24.9 + - - +
312E GLU* 1.3 83.6 - - + +
314E GLU* 1.3 59.6 + - - +
316E ASN* 3.5 11.3 + - - +
317E VAL* 3.0 28.2 + - + +
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Residues in contact with GLU 314 (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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50E MET* 4.8 0.2 - - - +
54E VAL* 4.1 16.9 - - + +
300E ARG* 3.3 41.8 + - - -
309E TRP* 3.4 34.3 + - + +
310E SER 3.2 8.2 + - - +
311E GLU* 3.2 10.8 + - - +
313E GLU* 1.3 74.3 - - - +
315E ASN* 1.3 62.5 + - - +
317E VAL* 3.2 3.5 + - - +
318E ILE* 2.9 52.3 + - + +
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Residues in contact with ASN 315 (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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311E GLU* 2.7 28.7 + - - +
312E GLU* 3.2 12.2 + - - +
314E GLU* 1.3 78.7 - - - +
316E ASN* 1.3 54.0 + - - +
318E ILE* 3.1 13.8 + - - +
319E GLU* 2.7 45.0 + - + +
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Residues in contact with ASN 316 (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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312E GLU* 2.8 34.5 + - - +
313E GLU* 3.8 10.8 - - - +
314E GLU 3.3 0.2 - - - -
315E ASN* 1.3 76.7 - - - +
317E VAL* 1.3 62.6 + - + +
319E GLU* 4.2 4.8 - - - +
320E GLN* 3.2 25.3 + - - +
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Residues in contact with VAL 317 (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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51E ARG* 3.6 50.5 - - + +
54E VAL* 4.2 16.8 - - + -
55E TYR* 4.4 11.7 - - + +
309E TRP* 3.9 21.3 - - + -
313E GLU* 3.0 19.3 - - + +
314E GLU* 3.4 7.6 - - - +
315E ASN 3.1 0.4 - - - -
316E ASN* 1.3 77.7 - - + +
318E ILE* 1.3 57.6 + - - +
320E GLN* 3.4 10.1 + - - +
321E ALA* 3.1 25.6 + - - +
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Residues in contact with ILE 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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54E VAL* 3.8 11.7 - - + -
58E ILE* 3.2 30.1 - - + -
314E GLU* 2.9 44.5 + - + +
315E ASN* 3.5 14.1 - - - +
317E VAL* 1.3 73.4 - - - +
319E GLU* 1.3 71.1 + - - +
320E GLN 3.1 1.6 - - - -
321E ALA* 3.1 11.8 + - - +
322E LYS* 3.2 35.5 + - - +
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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
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315E ASN* 2.7 28.0 + - + +
316E ASN* 4.5 4.7 - - - +
318E ILE* 1.3 78.1 - - - +
320E GLN* 1.3 60.7 + - - +
322E LYS* 4.0 22.8 + - - +
323E GLU* 3.2 27.4 + - - +
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Residues in contact with GLN 320 (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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51E ARG* 5.0 14.5 - - - +
55E TYR* 4.3 14.9 - - + -
316E ASN 3.2 20.0 + - - +
317E VAL* 3.5 8.3 + - - +
318E ILE 3.1 0.2 - - - -
319E GLU* 1.3 75.5 - - - +
321E ALA* 1.3 60.1 + - - +
323E GLU* 3.8 5.5 - - - +
324E GLU* 2.9 60.2 + - + +
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Residues in contact with ALA 321 (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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55E TYR* 3.9 30.5 - - + +
58E ILE* 3.6 29.6 - - + -
317E VAL 3.1 13.8 + - - +
318E ILE 3.1 10.1 + - - +
320E GLN* 1.3 75.5 - - - +
322E LYS* 1.3 59.9 + - - +
324E GLU* 3.9 1.2 - - - +
325E ILE* 2.8 37.5 + - + +
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Residues in contact with LYS 322 (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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58E ILE* 4.2 17.7 - - + -
61E GLN* 6.1 0.7 - - - -
62E ARG* 4.6 17.7 - - - +
318E ILE* 3.2 34.1 + - - +
319E GLU* 4.2 22.0 + - - +
321E ALA* 1.3 76.5 - - - +
323E GLU* 1.3 60.8 + - - +
325E ILE* 3.8 6.8 - - - +
326E LYS* 3.1 25.6 + - - +
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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
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319E GLU* 3.2 21.0 + - - +
320E GLN* 3.8 6.8 - - - +
321E ALA 3.2 0.2 - - - -
322E LYS* 1.3 78.4 - - - +
324E GLU* 1.3 62.3 + - + +
326E LYS* 3.6 15.4 + - - +
327E GLU* 3.4 38.0 + - + +
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Residues in contact with GLU 324 (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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55E TYR* 2.9 32.7 + - - +
115E LEU* 3.9 5.2 - - + +
320E GLN* 2.9 53.7 + - + +
321E ALA 4.1 0.4 - - - +
323E GLU* 1.3 76.7 - - + +
325E ILE* 1.3 63.6 + - - +
327E GLU* 3.6 14.8 + - - +
328E ALA* 3.2 23.2 + - - +
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Residues in contact with ILE 325 (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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55E TYR* 5.0 4.5 - - + +
58E ILE* 5.4 0.2 - - + -
59E LEU* 3.3 33.2 - - + -
62E ARG* 4.3 25.6 - - + +
66E LEU* 4.2 16.8 - - + -
115E LEU* 3.2 27.6 - - + -
119E PHE* 3.9 14.7 - - + -
321E ALA* 2.8 30.7 + - + +
322E LYS* 3.8 7.9 - - - +
323E GLU 3.3 0.2 - - - -
324E GLU* 1.3 75.8 - - - +
326E LYS* 1.3 66.7 + - - +
328E ALA* 3.3 3.0 + - - +
329E ILE* 3.0 22.8 + - + +
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Residues in contact with LYS 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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322E LYS 3.1 15.8 + - - +
323E GLU* 3.8 15.9 - - - +
324E GLU 3.4 0.2 - - - -
325E ILE* 1.3 81.6 - - - +
327E GLU* 1.3 62.1 + - - +
329E ILE* 3.0 30.3 - - + +
330E LYS* 3.4 7.4 + - - +
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Residues in contact with GLU 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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323E GLU* 3.4 30.8 + - + +
324E GLU* 3.9 15.6 - - - +
325E ILE 3.2 0.4 - - - -
326E LYS* 1.3 81.8 - - + +
328E ALA* 1.3 60.7 + - - +
330E LYS* 3.3 6.6 + - - +
331E LYS* 3.0 28.8 + - - +
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Residues in contact with ALA 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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115E LEU* 3.7 28.7 - - + -
116E TYR* 3.5 26.4 - - + +
119E PHE* 3.8 7.9 - - + -
324E GLU 3.2 16.6 + - - +
325E ILE 3.3 4.0 + - - +
327E GLU* 1.3 77.3 - - - +
329E ILE* 1.3 65.0 + - - +
331E LYS* 4.3 1.8 - - - -
332E ALA* 3.2 22.0 + - - +
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Residues in contact with ILE 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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66E LEU* 3.9 30.7 - - + -
71E ARG* 3.5 37.9 - - - +
72E LEU* 5.9 1.1 - - + -
119E PHE* 4.0 13.0 - - + -
123E ARG* 2.9 33.4 - - - +
325E ILE* 3.0 14.3 + - + +
326E LYS* 3.0 22.4 - - + +
327E GLU 3.2 0.2 - - - -
328E ALA* 1.3 77.1 - - - +
330E LYS* 1.3 68.3 + - + +
332E ALA* 3.2 5.3 + - + +
333E ASP* 3.1 21.4 + - - +
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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 LYS 3.4 9.4 + - - +
327E GLU* 3.3 10.7 + - - +
328E ALA 3.3 0.2 - - - -
329E ILE* 1.3 79.6 - - + +
331E LYS* 1.3 61.6 + - - +
332E ALA 3.0 5.9 + - - -
333E ASP* 3.2 21.4 + - + +
334E GLU* 3.2 37.6 + - + +
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Residues in contact with LYS 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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116E TYR* 3.5 50.7 + - + -
327E GLU 3.0 16.7 + - - +
328E ALA* 3.9 6.5 - - - +
329E ILE 3.4 0.2 - - - -
330E LYS* 1.3 77.3 - - - +
332E ALA* 1.3 58.9 + - - +
334E GLU* 3.9 14.3 + - + +
335E THR* 3.4 25.8 + - - +
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Residues in contact with ALA 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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116E TYR* 4.2 11.4 - - - +
119E PHE* 4.5 8.5 - - + -
120E LEU* 3.8 25.4 - - + +
123E ARG* 3.6 20.6 + - - +
328E ALA 3.2 13.1 + - - +
329E ILE* 3.4 12.1 - - - +
330E LYS 3.0 0.6 - - - -
331E LYS* 1.3 76.7 - - - +
333E ASP* 1.3 61.4 + - - +
334E GLU 3.2 1.6 - - - -
335E THR* 2.9 21.9 + - - +
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Residues in contact with ASP 333 (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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71E ARG* 4.4 7.2 + - - -
123E ARG* 2.7 33.7 + - - +
329E ILE* 3.1 22.9 + - - +
330E LYS* 3.2 16.3 + - + +
332E ALA* 1.3 77.9 - - - +
334E GLU* 1.3 65.0 + - + +
335E THR 3.5 7.3 + - - +
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Residues in contact with GLU 334 (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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330E LYS* 3.2 40.9 + - + +
331E LYS* 4.2 14.4 + - + +
332E ALA 3.2 0.2 - - - -
333E ASP* 1.3 77.7 - - + +
335E THR* 1.3 64.9 + - - +
336E PRO* 3.3 6.1 - - - +
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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