Contacts of the helix formed by residues 321 - 332 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320B GLY* 1.3 80.0 - - - +
322B LEU* 1.3 66.2 + - - +
323B GLN* 3.4 19.3 + - - +
324B HIS* 3.0 34.1 + - + +
325B ALA 3.3 8.1 + - - -
371B ASP* 5.5 0.4 - - - -
372B THR* 3.6 14.2 - - - +
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Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B THR* 1.3 74.3 - - - +
323B GLN* 1.3 64.5 + - - +
325B ALA* 3.1 4.3 + - - +
326B GLU* 2.8 61.7 + - - +
350B LEU* 3.8 21.8 - - + -
371B ASP* 3.4 57.2 + - + +
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Residues in contact with GLN 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B THR* 3.1 12.9 + - - +
322B LEU* 1.3 83.6 - - - +
324B HIS* 1.3 67.9 + - - +
326B GLU* 3.2 9.5 + - - +
327B ILE* 2.9 58.0 + - + +
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Residues in contact with HIS 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B ILE* 4.0 7.0 - - + -
319B LYS 3.8 13.0 - - - +
320B GLY* 3.4 9.0 - - - -
321B THR* 3.0 44.9 + - + +
323B GLN* 1.3 86.6 + - - +
325B ALA* 1.3 57.5 + - - +
327B ILE* 3.3 6.6 + - + +
328B PHE* 2.9 30.5 + - - +
397B ALA* 3.3 34.9 + - + +
398B HIS* 3.5 24.7 + + - +
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Residues in contact with ALA 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B ILE* 3.8 20.0 - - + +
321B THR 3.3 3.7 + - - +
322B LEU 3.1 9.5 + - - +
324B HIS* 1.3 77.4 - - - +
326B GLU* 1.3 56.9 + - - +
328B PHE* 3.3 7.2 + - - +
329B LEU* 2.9 35.0 + - - +
350B LEU* 3.9 20.2 - - + -
371B ASP 3.6 22.0 - - - +
372B THR* 4.3 0.4 - - - -
374B ILE* 4.2 6.3 - - + -
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Residues in contact with GLU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B LEU* 2.8 42.9 + - + +
323B GLN* 3.6 12.4 - - + +
325B ALA* 1.3 74.3 - - - +
327B ILE* 1.3 60.4 + - + +
329B LEU* 3.3 7.9 + - + +
330B LYS* 2.9 32.6 + - - +
350B LEU* 4.4 12.2 - - + +
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Residues in contact with ILE 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B GLN* 2.9 52.2 + - + +
324B HIS* 3.8 6.3 - - + +
326B GLU* 1.3 72.1 - - + +
328B PHE* 1.3 67.9 + - - +
330B LYS* 3.4 5.1 + - - +
331B ASN* 2.7 46.2 + - - +
396B ALA* 3.5 24.7 - - + +
397B ALA* 3.6 18.8 - - - +
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Residues in contact with PHE 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B PHE* 3.9 19.7 - + - -
318B ILE* 3.7 13.5 - - + -
324B HIS 2.9 14.5 + - - +
325B ALA 3.3 7.4 - - - +
327B ILE* 1.3 75.2 - - - +
329B LEU* 1.3 69.9 + - + +
331B ASN 3.0 11.1 + - - -
332B LEU* 3.4 39.0 + - + +
374B ILE* 3.9 28.0 - - + -
376B LEU* 4.8 2.0 - - + -
390B LEU* 3.8 29.8 - - + -
393B ALA* 3.5 41.9 - - + +
394B LEU* 3.7 25.6 - - + -
397B ALA* 4.0 1.0 - - + +
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Residues in contact with LEU 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B ALA 2.9 22.0 + - - +
326B GLU* 3.8 6.1 - - + +
328B PHE* 1.3 76.7 - - + +
330B LYS* 1.3 63.6 + - - +
331B ASN 3.2 0.9 + - - -
332B LEU* 3.3 24.9 + - + +
337B LEU* 3.7 28.5 - - + +
348B ALA* 3.9 28.3 - - + -
349B GLU* 4.4 5.8 - - - +
350B LEU* 3.3 47.1 - - + +
374B ILE* 4.1 19.3 - - + -
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Residues in contact with LYS 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B GLU 2.9 19.0 + - - +
327B ILE* 3.8 6.5 - - + +
329B LEU* 1.3 76.6 - - - +
331B ASN* 1.3 66.5 + - - +
332B LEU 3.7 4.3 + - - +
337B LEU* 4.6 6.9 - - - +
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Residues in contact with ASN 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B ILE* 2.7 43.7 + - - +
328B PHE 3.0 6.1 + - - +
330B LYS* 1.3 83.6 - - - +
332B LEU* 1.3 66.8 + - - +
333B LYS* 3.4 16.3 + - - +
392B GLN* 3.2 24.7 + - - +
393B ALA* 4.0 9.2 - - - -
396B ALA* 3.4 26.5 - - + +
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Residues in contact with LEU 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B PHE* 3.4 36.7 + - + +
329B LEU* 3.3 19.7 + - + +
330B LYS 4.2 5.5 - - - +
331B ASN* 1.3 78.3 - - - +
333B LYS* 1.3 59.3 + - - +
335B PHE* 3.9 24.3 - - + +
337B LEU* 4.0 5.7 - - + +
348B ALA* 3.7 30.5 - - + -
389B ASP* 3.6 25.1 - - - +
390B LEU* 4.2 9.2 - - + -
392B GLN* 4.2 0.7 - - - +
393B ALA* 3.7 17.7 - - + -
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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