Contacts of the helix formed by residues 321 - 332 (chain A) in PDB entry 3COG
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A ILE* 4.4 0.2 - - - +
320A GLY* 1.3 80.0 - - - +
322A LEU* 1.3 66.8 + - - +
323A GLN* 3.4 16.6 + - - +
324A HIS* 2.9 31.0 + - + +
325A ALA 3.2 8.1 + - - -
371A ASP* 5.7 0.2 - - - -
372A THR* 3.4 15.6 - - - +
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Residues in contact with LEU 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A THR* 1.3 74.5 - - - +
323A GLN* 1.3 56.3 + - - +
325A ALA* 3.1 4.2 + - - +
326A GLU* 2.8 49.2 + - - +
350A LEU* 3.5 31.9 - - + -
353A ILE* 3.9 13.9 - - + -
371A ASP* 3.5 47.7 + - + +
372A THR* 3.9 2.8 - - - +
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Residues in contact with GLN 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A THR* 3.1 13.7 + - - +
322A LEU* 1.3 79.2 - - - +
324A HIS* 1.3 67.7 + - + +
326A GLU* 3.3 9.3 + - - +
327A ILE* 2.8 53.2 + - + +
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Residues in contact with HIS 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A ILE* 3.9 5.8 - - + -
319A LYS 3.7 13.2 - - - +
320A GLY* 3.4 9.3 - - - -
321A THR* 2.9 42.2 + - + +
323A GLN* 1.3 85.9 + - + +
325A ALA* 1.3 61.0 + - - +
327A ILE* 4.6 4.0 - - + -
328A PHE* 2.9 31.4 + - - +
397A ALA* 3.2 35.5 - - + +
398A HIS* 3.6 22.7 + + - +
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Residues in contact with ALA 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A ILE* 3.8 22.7 - - + +
321A THR 3.2 3.9 + - - +
322A LEU 3.1 8.9 + - - +
324A HIS* 1.3 79.7 - - - +
326A GLU* 1.3 57.4 + - - +
328A PHE* 3.4 3.1 - - - +
329A LEU* 2.9 35.5 + - - +
350A LEU* 3.9 18.6 - - + -
371A ASP 3.7 20.4 - - - +
372A THR* 4.5 0.2 - - - -
374A ILE* 4.1 9.0 - - + -
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Residues in contact with GLU 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A LEU* 2.8 49.0 + - + +
323A GLN* 3.7 7.4 - - - +
325A ALA* 1.3 73.9 - - - +
327A ILE* 1.3 56.7 + - + +
329A LEU* 3.3 7.5 + - - +
330A LYS* 2.9 30.2 + - - +
350A LEU* 4.3 7.9 - - + -
353A ILE* 3.9 19.6 - - - +
52B PRO* 4.4 22.1 - - + +
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Residues in contact with ILE 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A GLN* 2.8 55.5 + - + +
324A HIS* 3.9 7.6 - - + +
326A GLU* 1.3 70.6 - - + +
328A PHE* 1.3 64.9 + - - +
330A LYS* 3.3 7.0 + - + -
331A ASN* 2.6 46.9 + - - +
396A ALA* 3.7 9.6 - - + +
397A ALA* 3.7 27.6 - - + +
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Residues in contact with PHE 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A LEU* 5.8 0.2 - - + -
316A PHE* 3.7 20.0 - + - -
318A ILE* 3.7 13.0 - - + -
324A HIS 2.9 19.2 + - - +
325A ALA 3.4 2.9 - - - +
327A ILE* 1.3 78.5 - - - +
329A LEU* 1.3 73.2 + - + +
331A ASN 3.1 7.4 + - - -
332A LEU* 3.5 29.5 + - + +
374A ILE* 3.5 23.3 - - + -
376A LEU* 4.8 2.5 - - + -
390A LEU* 3.7 31.6 - - + -
393A ALA* 3.5 38.8 - - + +
394A LEU* 3.7 35.7 - - + -
397A ALA* 3.9 3.1 - - + +
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Residues in contact with LEU 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A ALA 2.9 22.9 + - - +
326A GLU* 3.8 4.0 - - - +
328A PHE* 1.3 92.3 - - + +
330A LYS* 1.3 61.6 + - - +
331A ASN 3.2 0.9 + - - -
332A LEU* 3.4 21.7 + - + +
337A LEU* 4.2 32.3 - - + +
348A ALA* 3.6 31.0 - - + -
349A GLU 4.3 4.9 - - - +
350A LEU* 3.9 35.7 - - + +
374A ILE* 4.5 7.4 - - + -
52B PRO* 3.9 19.1 - - + -
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Residues in contact with LYS 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A GLU 2.9 16.9 + - - +
327A ILE* 3.3 10.3 + - + +
329A LEU* 1.3 76.1 - - - +
331A ASN* 1.3 69.8 + - - +
332A LEU 3.7 5.0 + - - +
337A LEU* 6.4 0.9 - - - -
50B GLY 5.2 11.4 - - - +
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Residues in contact with ASN 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A ILE* 2.6 46.0 + - - +
328A PHE 3.1 5.1 + - - +
330A LYS* 1.3 89.0 + - - +
332A LEU* 1.3 63.8 + - - +
333A LYS* 3.4 10.7 + - - +
392A GLN* 2.8 26.9 + - - +
393A ALA* 4.0 10.1 - - - -
396A ALA* 3.4 25.1 - - + +
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Residues in contact with LEU 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A PHE* 3.5 34.3 + - + +
329A LEU* 3.4 19.5 + - + +
330A LYS 4.1 5.5 - - - +
331A ASN* 1.3 78.5 - - - +
333A LYS* 1.3 59.8 + - - +
334A LEU 3.7 0.2 - - - -
335A PHE* 3.7 24.0 - - + +
336A THR 5.9 1.3 - - - -
337A LEU* 5.9 1.3 - - + +
348A ALA* 3.7 30.5 - - + -
389A ASP* 3.5 25.8 - - - +
390A LEU* 4.2 11.0 - - + -
392A GLN* 4.0 0.4 - - - +
393A ALA* 3.6 18.8 - - + -
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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