Contacts of the helix formed by residues 317 - 328 (chain E) in PDB entry 3CQ6
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 317 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315E PHE* 3.8 4.4 - - - +
316E SER* 1.3 77.7 - - - +
318E GLN* 1.3 67.7 + - - +
319E HIS* 3.3 18.8 + - - +
320E ALA* 3.3 29.2 + - + +
321E ALA* 3.2 16.3 + - - +
366E LEU 2.9 14.9 + - - +
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Residues in contact with GLN 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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315E PHE* 3.8 16.7 - - + +
316E SER 5.3 2.0 + - - +
317E ASP* 1.3 76.5 + - - +
319E HIS* 1.3 61.6 + - - +
321E ALA* 3.5 3.2 - - - +
322E TRP* 2.8 27.7 + - - +
334E ASP* 2.8 33.3 - - - +
336E GLY* 4.7 2.0 - - - -
337E ILE 3.6 11.2 + - - +
338E ALA* 3.5 18.2 - - - +
339E GLY 3.1 25.0 - - - +
340E HIS 3.5 22.7 - - - +
341E LEU* 3.4 10.9 - - + +
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Residues in contact with HIS 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLU* 3.6 47.9 + - + +
286A VAL* 5.4 1.5 - - + +
317E ASP* 3.3 12.4 + - - +
318E GLN* 1.3 78.7 + - - +
320E ALA* 1.3 67.6 + - - +
322E TRP* 3.2 36.4 + + - +
323E GLN* 2.9 29.5 + - + +
334E ASP* 3.4 23.6 - - + +
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Residues in contact with ALA 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A PRO* 3.6 21.9 - - + +
317E ASP* 3.3 33.0 + - + +
319E HIS* 1.3 81.3 + - - +
321E ALA* 1.3 56.0 + - - +
323E GLN* 3.3 5.9 + - - +
324E ALA* 3.0 24.4 + - - +
366E LEU* 3.9 13.9 - - + +
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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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315E PHE* 3.5 47.1 - - + -
317E ASP 3.2 5.0 + - - +
318E GLN 3.5 8.1 - - - +
319E HIS 3.2 0.2 - - - -
320E ALA* 1.3 75.3 - - - +
322E TRP* 1.3 65.4 + - - +
324E ALA* 3.1 3.5 + - - +
325E PHE* 2.9 29.2 + - + -
341E LEU* 3.9 3.1 - - + -
361E ILE* 4.7 2.9 - - + -
366E LEU* 3.5 16.9 - - + +
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Residues in contact with TRP 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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286A VAL* 3.7 20.9 - - + -
24E PRO* 3.8 30.5 - - + +
318E GLN 2.8 21.4 + - - +
319E HIS* 3.4 34.5 - + - +
321E ALA* 1.3 72.0 - - - +
323E GLN* 1.3 95.8 + - - +
325E PHE* 3.0 9.2 + - + +
326E LEU* 2.9 37.4 + - + +
330E VAL 4.8 0.2 - - - +
331E LEU* 3.8 19.4 - - + +
332E ILE* 3.0 39.4 + - + +
333E ARG* 4.1 1.3 - - - +
334E ASP* 3.8 24.7 - - + +
341E LEU* 3.7 14.0 - - + +
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Residues in contact with GLN 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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203A PHE 5.5 1.6 - - - +
205A PRO* 4.3 10.5 - - + -
282A GLU* 4.8 0.7 - - - +
285A SER* 3.6 41.5 + - - +
286A VAL* 3.8 8.5 - - - +
288A ARG* 4.0 3.6 - - - +
289A VAL* 4.0 1.0 - - - +
319E HIS* 2.9 22.5 + - + +
320E ALA* 3.6 9.2 - - - +
322E TRP* 1.3 96.4 - - + +
324E ALA* 1.3 51.5 - - - +
326E LEU* 3.0 15.8 + - - +
327E ASP* 2.7 68.6 + - - +
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Residues in contact with ALA 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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205A PRO* 3.8 13.1 - - + +
320E ALA 3.0 13.3 + - - +
321E ALA 3.1 8.7 + - - +
323E GLN* 1.3 77.0 - - - +
325E PHE* 1.3 62.9 + - - +
327E ASP* 3.5 3.0 + - - +
328E ARG* 2.9 45.4 + - - +
361E ILE* 3.7 12.1 - - + -
364E LEU* 4.6 3.6 - - + -
366E LEU* 3.7 20.0 - - + -
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Residues in contact with PHE 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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300E TYR* 4.4 3.8 - - - -
312E PHE* 4.1 13.2 - + - -
315E PHE* 4.4 4.5 - + - -
321E ALA 2.9 29.5 + - - -
322E TRP 3.4 6.1 - - - +
324E ALA* 1.3 75.3 - - - +
326E LEU* 1.3 61.8 + - - +
328E ARG* 3.0 16.9 + - - +
329E GLY 3.4 0.3 + - - -
330E VAL* 3.1 31.1 + - + +
332E ILE* 3.6 29.2 - - + +
341E LEU* 4.1 10.1 - - + -
354E PHE* 3.7 28.7 - + - -
357E ALA* 3.9 10.3 - - + -
358E ALA* 3.7 37.9 - - + -
361E ILE* 3.5 26.9 - - + +
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Residues in contact with LEU 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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286A VAL* 4.7 4.3 - - + -
289A VAL* 3.8 44.6 - - + +
26E LEU* 4.4 9.4 - - + -
28E VAL* 4.7 6.1 - - + -
322E TRP* 2.9 43.5 + - + +
323E GLN* 3.0 20.2 + - - +
325E PHE* 1.3 77.1 - - - +
327E ASP* 1.3 54.8 + - - +
329E GLY* 2.8 24.4 + - - -
330E VAL 3.3 7.0 - - - +
331E LEU* 3.6 35.2 - - + +
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Residues in contact with ASP 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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204A SER* 4.9 0.7 - - - -
205A PRO* 3.5 28.6 - - - +
288A ARG* 3.0 28.0 + - - +
289A VAL* 5.6 0.2 - - - -
304A PRO* 5.4 7.4 - - - +
305A SER 4.8 5.5 - - - +
306A GLU* 4.1 28.7 - - + +
323E GLN* 2.7 46.2 + - - +
324E ALA* 3.7 7.7 - - - +
326E LEU* 1.3 72.2 - - - +
328E ARG* 1.3 65.4 + - + +
329E GLY 3.5 2.3 + - - -
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Residues in contact with ARG 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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205A PRO* 6.0 0.4 - - - +
206A SER* 4.6 9.3 + - - -
306A GLU* 5.1 8.3 + - - -
324E ALA* 2.9 38.3 + - - +
325E PHE 3.0 9.3 + - - +
327E ASP* 1.3 85.0 + - - +
329E GLY* 1.3 58.8 + - - +
330E VAL* 3.4 8.7 + - - +
357E ALA* 4.0 29.6 - - + +
360E GLU* 3.0 36.7 + - - +
361E ILE* 4.1 12.7 - - - +
364E LEU* 4.0 22.4 - - - +
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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