Contacts of the helix formed by residues 323 - 333 (chain E) in PDB entry 4HHM
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 323 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319E ALA 3.0 16.1 + - - +
320E PHE 3.4 1.0 + - - +
322E ALA* 1.3 74.2 - - - +
324E PRO* 1.3 66.0 - - - +
325E GLU* 2.7 22.3 + - - +
326E VAL* 2.9 25.6 + - + +
327E GLN* 2.9 27.5 + - - +
382E HIS* 2.8 22.5 + - + +
387E ARG* 2.9 25.3 + - - -
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Residues in contact with PRO 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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322E ALA 3.2 9.6 - - - +
323E ASP* 1.3 87.6 - - - +
325E GLU* 1.3 56.8 + - - +
327E GLN* 3.0 21.2 + - - +
328E GLU* 2.8 30.9 + - - +
331E ARG* 4.8 1.7 + - - -
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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
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323E ASP* 2.7 16.0 + - - +
324E PRO* 1.3 75.0 - - - +
326E VAL* 1.3 58.2 + - + +
328E GLU* 3.5 9.8 - - + +
329E ALA* 3.1 23.7 + - - +
374E ARG* 3.6 27.1 + - - +
378E LEU* 4.1 13.7 - - + +
387E ARG* 2.7 34.9 + - - +
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Residues in contact with VAL 326 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320E PHE* 3.3 54.5 - - + +
321E ARG* 5.1 1.6 - - - -
323E ASP* 2.9 34.9 + - + +
325E GLU* 1.3 75.6 - - - +
327E GLN* 1.3 60.3 + - + +
328E GLU 3.0 1.6 - - - -
329E ALA* 2.9 9.5 + - - +
330E LEU* 2.9 34.6 + - + +
375E LEU* 4.5 6.0 - - + +
378E LEU* 4.2 14.4 - - + -
382E HIS* 3.8 11.9 - - + +
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Residues in contact with GLN 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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321E ARG 3.3 19.3 - - - +
322E ALA* 3.0 20.4 - - - +
323E ASP 2.9 16.6 + - - +
324E PRO* 3.5 22.1 - - - +
326E VAL* 1.3 76.0 - - + +
328E GLU* 1.3 61.7 + - - +
330E LEU* 3.2 19.8 + - + +
331E ARG* 3.2 41.9 + - - +
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Residues in contact with GLU 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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324E PRO 2.8 15.8 + - - +
325E GLU* 3.5 11.0 - - + +
327E GLN* 1.3 78.0 - - - +
329E ALA* 1.3 63.7 + - - +
331E ARG* 2.9 38.6 + - - +
332E ALA* 3.0 23.2 + - + +
374E ARG* 5.9 3.1 - - - +
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Residues in contact with ALA 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 10.3 + - - +
326E VAL 2.9 9.7 + - - +
328E GLU* 1.3 79.7 - - - +
330E LEU* 1.3 61.6 + - - +
332E ALA* 3.3 10.6 + - - +
333E ALA* 3.0 24.1 + - - +
371E ALA* 5.0 2.6 - - - +
374E ARG* 3.9 12.8 - - + +
375E LEU* 4.2 21.4 - - + +
378E LEU* 3.8 21.8 - - + -
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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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320E PHE* 5.2 0.2 - - + -
321E ARG* 4.0 31.0 - - - +
326E VAL* 2.9 20.8 + - + +
327E GLN* 3.4 25.6 - - + +
328E GLU 3.1 0.2 - - - -
329E ALA* 1.3 76.8 - - - +
331E ARG* 1.3 62.7 + - + +
333E ALA* 3.1 14.3 + - - +
334E ARG 3.1 9.4 + - - -
335E LEU* 3.1 39.0 + - + +
336E ASP 5.2 0.4 - - - -
375E LEU* 3.7 24.9 - - + -
147F ALA* 4.2 6.7 - - + +
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Residues in contact with ARG 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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324E PRO 4.8 1.8 + - - -
327E GLN* 3.2 30.3 + - - +
328E GLU* 2.9 44.1 + - - +
330E LEU* 1.3 77.2 - - + +
332E ALA* 1.3 63.4 + - - +
334E ARG* 3.0 18.7 + - - +
336E ASP* 3.7 26.3 - - + +
368E ARG* 5.9 0.2 + - - -
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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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328E GLU* 3.0 16.6 + - + +
329E ALA* 3.5 13.2 - - - +
330E LEU 3.2 0.2 - - - -
331E ARG* 1.3 76.9 - - - +
333E ALA* 1.3 50.2 + - - +
334E ARG* 2.8 34.8 + - - +
368E ARG* 4.9 5.2 + - - +
370E MET 4.0 2.0 - - - +
371E ALA* 4.5 14.9 - - + +
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Residues in contact with ALA 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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329E ALA 3.0 16.1 + - - +
330E LEU 3.1 0.6 + - - +
332E ALA* 1.3 74.9 - - - +
334E ARG* 1.3 61.4 + - - +
335E LEU* 3.3 21.1 - - + -
370E MET* 3.2 28.7 - - - +
371E ALA 4.4 3.4 - - - +
372E PHE* 3.8 12.1 - - + -
375E LEU* 4.2 6.7 - - + -
107F ASN* 2.7 30.1 + - - -
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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
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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