Contacts of the helix formed by residues 326 - 337 (chain E) in PDB entry 2P1N
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 326 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302E GLN* 5.4 3.9 - - - +
303E SER* 3.9 20.7 + - - +
323E ASP 3.8 4.7 - - - +
324E TYR 2.9 16.9 + - - +
325E ILE* 1.3 75.1 - - - +
327E ASP* 1.3 64.9 + - - +
328E ALA* 3.3 6.8 - - + +
329E GLY 2.9 11.1 + - - +
330E LEU* 3.0 11.8 + - - +
357E VAL* 3.7 9.6 - - + +
358E ALA* 2.7 55.0 + - + +
359E LEU* 3.8 8.1 - - - -
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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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326E GLU* 1.3 73.1 - - + +
328E ALA* 1.3 62.0 + - - +
330E LEU* 3.0 13.0 + - - +
331E GLU* 3.1 13.0 + - - +
358E ALA* 2.9 12.9 + - + +
359E LEU* 3.6 2.3 - - - +
360E THR* 2.6 52.7 + - - +
362E GLN* 3.4 13.0 - - + +
363E GLY* 3.0 32.0 + - - +
366E SER* 5.2 0.9 + - - -
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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
----------------------------------------------------------
303E SER* 5.3 2.9 - - - +
307E VAL* 5.1 0.9 - - - -
326E GLU* 3.1 6.4 + - + +
327E ASP* 1.3 77.7 - - - +
329E GLY* 1.3 61.9 + - - +
331E GLU* 3.3 20.6 - - - +
332E VAL* 3.2 25.3 + - - +
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Residues in contact with GLY 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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303E SER* 3.9 12.2 + - - -
307E VAL* 3.7 23.2 - - - +
310E LEU* 5.1 2.6 - - - +
325E ILE* 3.4 18.4 - - - +
326E GLU 2.9 8.6 + - - -
328E ALA* 1.3 81.6 - - - +
330E LEU* 1.3 60.1 + - - +
332E VAL* 3.2 6.6 + - - +
333E LEU* 3.2 16.1 + - - +
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Residues in contact with LEU 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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319E LEU* 5.6 0.7 - - + -
321E VAL* 5.4 0.9 - - + -
325E ILE* 3.7 25.1 - - + -
326E GLU 3.0 6.2 + - - +
327E ASP 3.0 7.5 + - - +
329E GLY* 1.3 73.8 - - - +
331E GLU* 1.3 61.0 + - - +
332E VAL 3.1 0.2 - - - -
333E LEU* 3.2 27.7 - - + +
334E ALA* 2.9 27.0 + - - +
343E LEU* 3.9 22.0 - - + -
345E VAL* 4.5 2.5 - - + -
359E LEU* 3.8 25.4 - - + -
363E GLY* 3.4 39.0 - - - +
366E SER* 4.5 1.5 - - - -
367E VAL* 3.5 4.0 - - + +
379E TYR* 3.9 12.1 - - + +
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Residues in contact with GLU 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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327E ASP 3.1 10.1 + - - +
328E ALA* 3.3 23.0 - - - +
330E LEU* 1.3 76.9 - - - +
332E VAL* 1.3 65.5 + - + +
334E ALA* 3.3 3.7 + - - +
335E SER* 3.2 21.5 + - - -
366E SER* 4.0 24.7 - - - +
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Residues in contact with VAL 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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307E VAL* 3.9 26.7 - - + +
310E LEU* 5.4 3.4 - - + -
311E CYS* 3.9 26.2 - - - +
328E ALA 3.2 13.4 + - - +
329E GLY 3.2 7.1 + - - +
330E LEU 3.1 0.4 - - - -
331E GLU* 1.3 76.4 - - + +
333E LEU* 1.3 68.9 + - - +
335E SER* 2.9 14.6 + - - +
336E THR* 2.8 31.3 + - + +
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Residues in contact with LEU 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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310E LEU* 4.3 16.1 - - + +
316E LEU* 4.9 2.9 - - + -
319E LEU* 3.7 28.3 - - + -
329E GLY 3.2 5.7 + - - +
330E LEU* 3.2 31.6 - - + +
332E VAL* 1.3 80.4 - - - +
334E ALA* 1.3 62.6 + - - +
335E SER 3.0 0.3 + - - -
336E THR* 4.2 4.0 - - - -
337E CYS* 3.0 52.6 + - + +
340E LEU* 3.8 24.7 - - + -
343E LEU* 4.3 4.0 - - + -
367E VAL* 3.5 22.9 - - + -
371E CYS* 4.6 0.6 - - - -
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Residues in contact with ALA 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 LEU 2.9 16.7 + - - +
331E GLU* 3.6 7.4 - - + +
332E VAL 3.1 0.6 - - - -
333E LEU* 1.3 76.3 - - - +
335E SER* 1.3 59.6 + - - +
337E CYS 4.5 0.5 + - - -
338E LYS* 2.9 24.6 + - - -
366E SER* 3.6 29.2 - - - +
367E VAL* 3.8 9.9 - - - -
370E GLY* 3.3 12.3 - - - +
371E CYS* 3.8 14.7 - - - -
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Residues in contact with SER 335 (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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331E GLU 3.2 13.2 + - - -
332E VAL* 2.9 6.7 + - - +
333E LEU 2.9 1.8 - - - -
334E ALA* 1.3 85.1 - - - +
336E THR* 1.3 64.5 + - - +
337E CYS 3.7 0.2 - - - -
338E LYS* 3.3 20.8 - - - +
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Residues in contact with THR 336 (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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310E LEU* 4.6 5.3 + - - +
311E CYS* 4.5 34.3 + - + +
313E CYS 5.8 0.2 - - - -
314E PRO* 4.0 18.0 - - - +
332E VAL* 2.8 24.9 + - + +
333E LEU* 3.9 3.6 + - - -
335E SER* 1.3 85.6 + - - +
337E CYS* 1.3 65.2 + - - +
338E LYS* 3.7 6.8 + - - +
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Residues in contact with CYS 337 (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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310E LEU* 4.7 7.9 - - - -
313E CYS 3.3 24.5 - - - -
314E PRO 4.5 4.9 - - - -
316E LEU* 4.0 19.7 - - + +
333E LEU* 3.0 40.4 + - + +
334E ALA 4.5 0.2 + - - -
335E SER 3.7 1.4 - - - -
336E THR* 1.3 85.0 - - - +
338E LYS* 1.3 61.3 + - - +
339E ASP 3.0 6.6 + - - +
340E LEU* 3.2 26.9 + - + +
371E CYS* 3.8 9.9 - - - -
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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