Contacts of the helix formed by residues 324 - 333 (chain B) in PDB entry 4OSI
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 324 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318B CYS* 4.3 0.9 - - - -
322B GLY 4.8 4.0 - - - +
323B LEU* 1.3 73.4 - - - +
325B PRO* 1.3 63.7 - - - +
326B GLN* 3.5 16.5 + - - +
327B GLN* 2.7 67.3 + - + +
328B VAL* 3.2 3.8 + - - +
360B GLU* 6.0 0.4 - - - +
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Residues in contact with PRO 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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287B LEU 5.9 3.4 - - - +
289B LEU* 5.9 3.4 - - + -
293B GLN* 5.2 7.2 - - - +
314B LEU* 4.4 15.7 - - + -
318B CYS* 4.0 12.6 - - - -
323B LEU 3.7 4.7 - - - +
324B THR* 1.3 84.0 - - - +
326B GLN* 1.3 56.2 + - - +
328B VAL* 2.6 36.4 + - + +
329B VAL* 2.9 15.8 + - - +
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Residues in contact with GLN 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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293B GLN* 4.9 13.6 - - - +
324B THR* 3.3 12.2 + - - +
325B PRO* 1.3 74.9 - - - +
327B GLN* 1.3 68.2 + - + +
329B VAL* 2.9 9.8 + - - +
330B ALA* 2.9 24.7 + - - +
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Residues in contact with GLN 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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322B GLY 4.6 0.9 - - - +
323B LEU* 3.4 21.0 - - + +
324B THR* 2.7 58.1 + - + +
326B GLN* 1.3 72.7 - - + +
328B VAL* 1.3 59.9 + - - +
330B ALA* 3.3 6.1 + - - +
331B ILE* 2.9 30.4 + - + +
360B GLU* 4.3 24.9 + - - +
363B VAL* 3.1 45.9 - - + +
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Residues in contact with VAL 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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310B VAL* 4.6 12.3 - - + -
314B LEU* 3.5 46.0 - - + -
317B LEU* 4.7 17.0 - - + -
318B CYS* 4.1 10.5 - - - -
323B LEU* 5.0 8.1 - - + +
324B THR 3.2 9.1 + - - +
325B PRO* 2.6 21.3 + - + +
327B GLN* 1.3 71.0 - - - +
329B VAL* 1.3 55.1 + - + +
331B ILE* 3.3 13.7 + - + +
332B ALA* 2.9 24.5 + - - +
341B LEU* 4.1 17.0 - - + +
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Residues in contact with VAL 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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289B LEU* 4.0 22.0 - - + -
293B GLN* 4.0 25.4 - - + +
296B ALA* 4.7 3.6 - - + -
297B ILE* 3.6 28.7 - - + -
310B VAL* 5.6 0.9 - - + -
314B LEU* 5.2 4.0 - - + -
325B PRO 2.9 12.8 + - - +
326B GLN* 2.9 8.7 + - - +
328B VAL* 1.3 75.1 - - + +
330B ALA* 1.3 54.3 + - - +
331B ILE 2.9 1.3 - - - -
332B ALA* 2.5 11.7 + - - +
333B SER* 2.5 51.7 + - - +
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Residues in contact with ALA 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 GLN 2.9 15.1 + - - +
327B GLN* 3.5 13.0 - - - +
329B VAL* 1.3 74.0 - - - +
331B ILE* 1.3 56.9 + - - +
333B SER* 3.6 7.9 + - - -
334B HIS* 2.9 32.1 + - - -
363B VAL* 5.1 2.7 - - + -
367B SER* 3.4 16.1 + - - +
6H T 4.7 13.0 - - - +
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Residues in contact with ILE 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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317B LEU* 6.1 1.6 - - + -
323B LEU* 4.9 7.2 - - + -
327B GLN* 2.9 28.0 + - + +
328B VAL* 3.3 11.7 - - + +
329B VAL 2.9 0.8 - - - -
330B ALA* 1.3 79.6 - - - +
332B ALA* 1.3 59.8 + - - +
333B SER 3.3 0.9 + - - -
334B HIS* 3.5 13.9 + - - +
337B GLY* 4.5 2.1 - - - -
340B ALA* 3.9 30.0 - - + +
341B LEU* 3.3 27.8 - - + +
344B VAL* 4.6 18.8 - - + -
363B VAL* 4.2 19.5 - - + -
366B ALA* 4.2 17.2 - - + +
367B SER* 3.7 15.5 - - - +
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Residues in contact with ALA 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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297B ILE* 3.7 17.3 - - + +
300B HIS* 4.1 2.6 - - - -
306B ALA* 3.9 15.8 - - + +
310B VAL* 3.4 33.4 - - + -
328B VAL 2.9 9.6 + - - +
329B VAL* 2.5 14.4 + - - +
331B ILE* 1.3 71.0 - - - +
333B SER* 1.3 50.3 + - - +
334B HIS 2.8 26.6 + - - +
337B GLY* 4.0 10.2 - - - -
341B LEU* 4.5 5.2 - - + -
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Residues in contact with SER 333 (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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296B ALA* 3.8 22.5 - - - +
297B ILE* 4.0 2.4 - - - +
300B HIS* 2.9 23.2 + - - -
329B VAL* 2.5 45.8 + - - +
330B ALA* 3.8 10.0 + - - -
331B ILE 3.2 2.4 - - - -
332B ALA* 1.3 68.5 - - - +
334B HIS* 1.3 76.3 + - - +
7H A 5.2 7.7 + - - -
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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