Contacts of the helix formed by residues 315 - 326 (chain E) in PDB entry 3ZNI
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 PRO 315 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241E GLN* 6.1 8.3 - - + +
313E ASN 4.7 1.3 - - - +
314E LYS* 1.3 90.4 - - + +
316E LEU* 1.3 65.5 + - - +
317E PHE* 3.4 34.1 - - + -
318E GLN* 3.3 12.0 + - + +
319E ALA* 3.3 19.1 + - - +
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Residues in contact with LEU 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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239E LEU 5.3 0.7 - - - +
253E LEU* 3.9 20.6 - - + -
285E PHE* 3.8 26.7 - - + -
295E TRP* 3.5 62.2 - - + +
297E ILE* 3.9 28.7 - - + -
311E PRO* 4.9 2.7 - - + -
314E LYS 3.2 6.1 + - - -
315E PRO* 1.3 71.1 - - - +
317E PHE* 1.3 63.9 + - - +
319E ALA* 3.1 7.3 + - + +
320E LEU* 2.9 36.1 + - + +
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Residues in contact with PHE 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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241E GLN 5.8 2.2 - - - -
242E PRO* 5.9 0.9 - - + -
253E LEU* 4.6 6.3 - - + +
315E PRO* 3.4 30.5 - - + -
316E LEU* 1.3 78.5 - - - +
318E GLN* 1.3 78.1 + - + +
320E LEU* 3.4 2.9 + - - +
321E ILE* 3.0 46.0 + - + +
341E LEU* 4.5 28.3 - - + +
343E GLY 5.7 1.8 - - - -
345E CYS* 3.4 54.7 - - + -
346E GLU* 4.4 21.5 - - + -
347E PRO* 4.7 8.3 - - + -
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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 PRO* 3.3 21.9 + - + +
316E LEU 3.2 0.4 - - - -
317E PHE* 1.3 99.4 - - + +
319E ALA* 1.3 60.8 + - - +
321E ILE* 3.3 17.1 + - - +
322E ASP* 2.9 67.4 + - - +
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Residues in contact with ALA 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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297E ILE* 4.2 19.1 - - + -
311E PRO* 4.3 12.1 - - + -
314E LYS* 6.1 0.7 - - + -
315E PRO 3.3 10.4 + - - +
316E LEU* 3.1 9.1 + - - +
318E GLN* 1.3 78.2 - - - +
320E LEU* 1.3 58.0 + - - +
322E ASP* 3.9 6.0 - - - +
323E GLY 3.0 22.5 + - - -
329E TYR* 3.4 13.3 - - + -
10F GLU* 3.9 20.8 - - - +
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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
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253E LEU* 4.3 2.2 - - + -
257E HIS* 4.2 5.6 - - - +
283E TYR* 3.7 30.5 - - + +
285E PHE* 3.9 28.0 - - + -
297E ILE* 4.4 12.3 - - + -
316E LEU* 2.9 38.1 + - + +
317E PHE 3.7 4.9 - - - +
318E GLN 3.2 0.2 - - - -
319E ALA* 1.3 75.6 - - - +
321E ILE* 1.3 64.2 + - - +
323E GLY 4.0 0.2 - - - -
324E SER* 3.0 26.3 + - - -
329E TYR* 4.0 17.3 - - + +
341E LEU* 3.8 28.5 - - + -
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Residues in contact with ILE 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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317E PHE* 3.0 36.7 + - + +
318E GLN* 3.3 21.5 + - - +
320E LEU* 1.3 76.6 - - + +
322E ASP* 1.3 59.5 + - - +
324E SER* 3.3 6.1 + - - -
325E ARG* 2.9 36.4 + - + +
340E ASP* 5.3 0.9 - - - +
341E LEU* 3.8 33.9 - - + +
342E THR* 3.8 27.4 - - + +
343E GLY 4.9 0.9 - - - +
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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
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318E GLN* 2.9 50.4 + - - +
319E ALA* 3.9 5.7 - - - +
321E ILE* 1.3 77.7 - - - +
323E GLY* 1.3 58.1 + - - +
325E ARG* 3.2 28.6 + - - +
326E GLU* 3.0 35.9 + - + +
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Residues in contact with GLY 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 ALA 3.0 11.4 + - - -
322E ASP* 1.3 76.5 - - - +
324E SER* 1.3 58.2 + - - +
326E GLU* 3.4 1.1 + - - -
327E GLY 3.1 3.5 + - - -
328E PHE* 2.7 42.1 + - - -
329E TYR* 3.0 30.0 + - - -
11F PRO* 5.5 2.2 - - - -
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Residues in contact with SER 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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320E LEU 3.0 20.9 + - - -
321E ILE* 3.5 6.3 - - - -
322E ASP 3.2 0.2 - - - -
323E GLY* 1.3 74.3 - - - +
325E ARG* 1.3 65.5 + - - +
327E GLY 3.1 9.4 + - - -
329E TYR* 3.3 19.5 + - - +
330E LEU* 3.6 15.6 - - - +
338E ASN* 3.4 19.1 + - - -
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Residues in contact with ARG 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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321E ILE* 2.9 22.8 + - + +
322E ASP* 3.2 37.6 + - - +
324E SER* 1.3 77.1 - - - +
326E GLU* 1.3 90.9 + - - +
327E GLY 3.4 1.0 + - - -
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Residues in contact with GLU 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 ASP* 3.0 19.9 + - + +
323E GLY 3.4 0.4 + - - +
324E SER 3.1 0.2 - - - -
325E ARG* 1.3 108.7 + - - +
327E GLY* 1.3 61.6 + - - +
328E PHE* 3.3 36.9 + - + -
11F PRO 6.1 0.2 - - - +
12F ALA* 4.8 11.6 - - - -
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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