Contacts of the helix formed by residues 321 - 332 (chain D) in PDB entry 3ELP
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 THR 321 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318D ILE* 5.0 0.3 - - - +
320D GLY* 1.3 76.9 - - - +
322D LEU* 1.3 54.8 + - - +
323D GLN* 2.7 22.6 + - - +
324D HIS* 2.5 40.7 + - - +
325D ALA* 3.2 8.7 + - - +
371D ASP* 4.7 6.3 - - - +
372D THR* 4.9 5.6 + - - -
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Residues in contact with LEU 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321D THR* 1.3 74.9 - - - +
323D GLN* 1.3 58.3 - - - +
324D HIS 3.2 0.2 - - - -
325D ALA* 3.9 2.7 - - - -
326D GLU* 2.9 26.6 + - + +
350D LEU* 3.5 30.7 - - + -
352D ALA* 5.1 0.4 - - + -
353D ILE* 4.2 22.9 - - + -
371D ASP* 3.2 50.5 + - + +
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Residues in contact with GLN 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321D THR* 2.7 15.7 + - - +
322D LEU* 1.3 79.1 - - - +
324D HIS* 1.3 70.2 + - + +
326D GLU* 3.2 15.9 - - + +
327D ILE* 3.1 31.3 - - + +
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Residues in contact with HIS 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D ILE* 3.8 6.9 - - + +
319D LYS 4.1 8.1 - - - +
320D GLY* 3.2 21.4 - - - -
321D THR* 2.5 30.7 + - - +
323D GLN* 1.3 86.2 + - + +
325D ALA* 1.3 64.3 + - - +
326D GLU 2.9 1.3 - - - -
327D ILE* 4.3 6.3 - - + -
328D PHE* 2.9 24.9 + - - +
397D ALA* 3.7 19.7 + - - +
398D HIS* 3.0 33.5 + + + +
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Residues in contact with ALA 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D ILE* 3.8 24.8 - - + +
321D THR 3.2 6.5 + - - +
322D LEU 4.0 3.4 - - - +
323D GLN 3.5 0.2 - - - -
324D HIS* 1.3 77.3 - - - +
326D GLU* 1.3 56.0 + - - +
328D PHE* 3.5 4.4 - - - +
329D LEU* 3.0 35.5 + - - +
350D LEU* 3.7 35.9 - - + -
371D ASP 4.0 11.0 - - - +
372D THR* 4.7 0.4 - - - -
374D ILE* 4.3 5.6 - - + -
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Residues in contact with GLU 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322D LEU* 2.9 25.3 + - + +
323D GLN* 3.2 14.8 - - + +
325D ALA* 1.3 76.7 - - - +
327D ILE* 1.3 70.5 + - + +
328D PHE 3.2 0.2 + - - -
329D LEU* 3.9 4.9 - - - +
330D LYS* 3.0 30.0 + - - +
350D LEU* 3.9 4.0 - - - +
353D ILE* 3.0 32.6 - - - +
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Residues in contact with ILE 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323D GLN* 3.1 25.7 + - + +
324D HIS* 3.3 8.9 + - + +
326D GLU* 1.3 78.1 - - + +
328D PHE* 1.3 64.0 + - - +
330D LYS* 3.3 5.6 + - + +
331D ASN* 2.7 47.7 + - - +
396D ALA 3.4 8.7 - - - +
397D ALA* 3.3 29.8 - - - +
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Residues in contact with PHE 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316D PHE* 3.5 29.8 - + - -
318D ILE* 3.6 13.5 - - + -
324D HIS 2.9 16.9 + - - +
325D ALA 3.5 2.0 - - - +
327D ILE* 1.3 74.3 - - - +
329D LEU* 1.3 76.4 + - + +
331D ASN* 2.8 26.9 + - - +
332D LEU* 3.3 35.7 + - + +
374D ILE* 3.3 26.7 - - + -
376D LEU* 5.1 2.5 - - + -
390D LEU* 4.0 25.8 - - + -
393D ALA* 3.5 35.3 - - + +
394D LEU* 3.9 15.0 - - + -
397D ALA* 3.7 3.0 - - + +
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Residues in contact with LEU 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325D ALA 3.0 18.4 + - - +
326D GLU* 3.9 4.5 - - - +
328D PHE* 1.3 90.6 - - + +
330D LYS* 1.3 61.9 + - - +
331D ASN 3.3 0.7 + - - -
332D LEU* 3.5 34.7 + - + +
337D LEU* 3.5 31.3 - - + +
348D ALA* 3.6 17.9 - - + -
349D GLU 4.1 4.5 - - - +
350D LEU* 3.4 39.7 - - + +
354D MET* 3.7 17.5 - - + -
374D ILE* 4.4 7.6 - - + -
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Residues in contact with LYS 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326D GLU* 3.0 20.5 + - - +
327D ILE* 3.8 6.1 - - + +
329D LEU* 1.3 78.1 - - - +
331D ASN* 1.3 61.2 + - - +
332D LEU 4.2 4.1 - - - +
337D LEU* 5.0 7.9 - - + -
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Residues in contact with ASN 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327D ILE* 2.7 42.2 + - - +
328D PHE 2.8 8.5 + - - +
330D LYS* 1.3 79.8 - - - +
332D LEU* 1.3 67.7 + - - +
333D LYS* 3.3 12.7 - - - +
392D GLN* 3.1 24.4 + - - +
393D ALA* 3.5 19.7 - - + -
396D ALA* 3.3 21.3 - - - +
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Residues in contact with LEU 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D PHE* 3.3 36.0 + - + +
329D LEU* 3.5 33.4 + - + +
330D LYS 4.2 4.9 - - - +
331D ASN* 1.3 78.7 - - - +
333D LYS* 1.3 60.8 + - - +
335D PHE* 4.0 21.2 - - + +
337D LEU* 4.1 4.3 - - + -
348D ALA* 3.5 31.9 - - + -
376D LEU* 5.5 0.2 - - + -
389D ASP* 3.6 23.1 - - - +
390D LEU* 4.1 11.0 - - + -
393D ALA* 3.7 7.6 - - + +
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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