Contacts of the helix formed by residues 324 - 330 (chain B) in PDB entry 5OO2
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 PHE 324 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320B THR 4.4 1.3 - - - -
321B ALA* 3.0 28.2 + - + +
322B ALA 3.0 1.6 - - - -
323B GLN* 1.3 76.3 - - + +
325B ALA* 1.3 64.6 + - - +
326B PRO* 3.2 4.5 - - - -
327B LEU* 2.8 28.6 + - + +
328B LEU* 3.8 1.6 + - - +
340B LEU* 3.6 32.5 - - + -
343B LEU* 3.9 9.4 - - + -
344B LEU* 3.4 52.5 - - + -
349B PHE* 3.5 55.4 - + - -
360B ILE* 4.7 2.0 - - + -
388B PHE* 3.6 22.0 - + + -
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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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253B VAL* 3.6 33.7 - - + +
254B PHE* 3.9 17.3 - - - -
257B ALA* 3.4 24.4 - - + +
294B VAL* 4.4 0.7 - - + -
305B ALA* 4.2 1.3 - - + -
321B ALA 4.3 0.6 + - - -
322B ALA 3.0 17.4 + - - +
324B PHE* 1.3 74.5 - - - +
326B PRO* 1.3 68.6 - - + +
328B LEU* 2.9 16.7 + - - +
329B CYS 3.6 0.9 + - - -
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Residues in contact with PRO 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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294B VAL* 3.8 17.0 - - + -
295B VAL* 5.0 3.1 - - + -
298B THR* 3.6 28.3 - - + -
303B GLY 3.7 9.4 - - - +
305B ALA* 3.5 5.8 - - + -
323B GLN 3.3 11.9 - - - +
324B PHE* 3.2 7.0 - - - -
325B ALA* 1.3 93.8 - - + +
327B LEU* 1.3 55.4 + - - +
329B CYS* 4.1 3.4 - - - -
330B GLY* 2.9 32.7 + - - +
332B LEU* 3.5 27.3 - - + +
337B GLU* 4.2 2.1 - - - +
340B LEU* 3.9 2.5 - - + -
395B ARG* 4.0 1.0 + - - -
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Residues in contact with LEU 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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324B PHE* 2.8 34.9 + - + +
326B PRO* 1.3 78.1 - - - +
328B LEU* 1.3 59.6 + - - +
337B GLU* 3.7 20.2 - - + +
340B LEU* 3.6 27.1 - - + -
341B LEU* 3.9 27.8 - - + -
344B LEU* 3.9 22.0 - - + -
388B PHE* 5.1 0.7 - - + -
392B PHE* 3.9 21.8 - - + -
395B ARG* 2.9 33.1 + - - +
397B TRP* 4.0 13.4 - - + -
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Residues in contact with LEU 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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254B PHE* 3.6 34.5 - - + -
257B ALA* 4.5 7.6 - - + -
258B ILE* 4.2 18.6 - - + +
261B VAL* 3.2 18.7 - - + +
324B PHE 4.3 4.9 - - - +
325B ALA* 2.9 12.9 + - - +
327B LEU* 1.3 81.8 - - - +
329B CYS* 1.3 60.8 + - - +
330B GLY 3.8 0.2 + - - -
387B LEU* 4.4 4.3 - - + +
388B PHE* 3.7 36.8 - - + +
391B CYS* 3.6 42.1 - - + +
392B PHE* 4.7 1.8 - - + -
395B ARG* 3.9 10.2 - - - -
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Residues in contact with CYS 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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257B ALA* 3.7 34.8 - - - +
260B SER* 3.6 21.0 + - - +
261B VAL* 3.6 8.0 - - + +
291B ARG* 3.3 31.9 + - - -
294B VAL* 3.8 27.4 - - - -
325B ALA 3.9 3.1 - - - -
326B PRO 4.0 1.6 - - - -
328B LEU* 1.3 79.2 - - - +
330B GLY* 1.3 72.0 + - - +
395B ARG* 4.8 2.4 - - - -
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Residues in contact with GLY 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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291B ARG* 3.3 12.7 - - - +
295B VAL* 4.1 5.4 - - - +
326B PRO* 2.9 16.6 + - - +
328B LEU 3.5 2.4 - - - -
329B CYS* 1.3 90.9 - - - +
331B GLY* 1.3 61.2 + - - -
332B LEU 3.6 3.0 + - - -
337B GLU* 4.8 0.7 - - - -
395B ARG* 3.6 28.6 - - - +
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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