Contacts of the helix formed by residues 321 - 332 (chain B) in PDB entry 4OL0
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 LEU 321 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310B ILE* 4.1 14.4 - - + -
314B PRO* 4.3 12.6 - - + -
315B GLY* 4.1 12.8 - - - +
319B GLY 3.6 14.6 - - - +
320B ASP* 1.3 72.9 + - - +
322B ARG* 1.3 62.2 + - - +
323B THR* 3.0 4.5 - - - +
324B LEU* 3.4 25.8 + - + +
325B GLU* 3.1 19.5 + - - +
364B ILE* 4.1 18.4 - - + -
365B PHE* 4.6 4.0 - - + -
368B TYR* 3.5 38.3 + - + +
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Residues in contact with ARG 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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270B PHE* 4.6 2.4 - - - -
271B GLN* 5.9 1.6 - - - +
274B LEU* 3.6 44.4 - - + +
320B ASP* 2.6 36.9 + - + +
321B LEU* 1.3 75.4 - - - +
323B THR* 1.3 55.8 + - + +
325B GLU* 3.1 13.5 - - + +
326B LEU* 2.8 38.6 + - + +
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Residues in contact with THR 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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270B PHE* 3.4 41.1 - - + -
274B LEU* 5.2 1.8 - - + -
302B LEU* 3.7 15.5 - - + -
303B CYS* 3.4 26.1 - - - -
306B PHE* 5.6 0.4 - - + -
310B ILE* 3.3 24.9 - - + +
320B ASP 3.2 12.2 + - - +
321B LEU* 4.3 0.2 - - - -
322B ARG* 1.3 73.5 - - - +
324B LEU* 1.3 70.9 + - - +
326B LEU* 3.0 14.1 + - - +
327B LEU 2.9 23.7 + - - -
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Residues in contact with LEU 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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303B CYS* 5.0 0.2 - - - -
310B ILE* 4.5 5.4 - - + -
321B LEU* 3.4 24.6 + - + +
323B THR* 1.3 87.6 + - - +
325B GLU* 1.3 57.9 + - - +
327B LEU* 3.2 7.1 + - + +
328B LEU* 2.8 35.4 + - - +
345B PHE* 3.4 40.6 - - + -
346B TRP* 4.0 15.4 - - + -
349B LEU* 4.5 3.1 - - + -
365B PHE* 3.8 32.5 - - + -
368B TYR* 3.8 29.8 - - + -
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Residues in contact with GLU 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B LEU 3.1 8.4 + - - +
322B ARG* 3.1 24.7 - - + +
323B THR 3.1 0.4 - - - -
324B LEU* 1.3 77.1 - - - +
326B LEU* 1.3 54.1 + - + +
328B LEU* 3.2 5.8 + - - +
329B ILE* 2.8 44.1 + - + +
368B TYR* 3.3 16.5 + - - -
371B ARG* 2.9 43.6 + - - -
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Residues in contact with LEU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B VAL* 4.6 6.7 - - + -
274B LEU* 3.9 31.2 - - + +
277B GLU* 4.0 38.6 - - + +
280B TYR* 6.5 0.4 - - + -
299B PHE* 3.8 45.8 - - + -
302B LEU* 4.7 3.6 - - + -
322B ARG* 2.8 18.6 + - + +
323B THR* 3.0 11.9 + - - +
325B GLU* 1.3 73.3 - - + +
327B LEU* 1.3 57.3 + - - +
329B ILE* 3.1 13.6 + - + +
330B CYS* 2.8 33.0 + - - -
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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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296B CYS* 4.8 6.1 - - - +
299B PHE* 4.3 5.8 - - + +
300B THR* 3.7 34.3 - - - +
303B CYS* 3.3 32.5 - - + -
323B THR 2.9 7.0 + - - +
324B LEU* 3.2 8.9 + - + +
326B LEU* 1.3 75.6 - - - +
328B LEU* 1.3 58.3 + - - +
330B CYS* 3.2 7.6 + - + +
331B ALA* 2.8 26.9 + - - +
342B SER* 3.7 16.6 + - - -
345B PHE* 3.4 37.7 - - + -
346B TRP* 4.3 17.9 + - + +
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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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324B LEU 2.8 21.6 + - - +
325B GLU* 3.6 4.3 - - - +
327B LEU* 1.3 70.3 - - - +
329B ILE* 1.3 65.4 + - - +
331B ALA* 3.2 11.0 + - + +
332B GLY* 3.1 18.9 + - - -
346B TRP* 3.9 20.9 - - + -
368B TYR* 3.5 26.0 - - + +
371B ARG* 3.3 55.2 - - + +
372B LEU* 3.9 28.5 - - + +
375B ALA* 6.0 0.2 - - + -
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Residues in contact with ILE 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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277B GLU* 3.5 29.6 - - + +
280B TYR* 3.5 34.8 + - + -
281B HIS* 3.9 17.0 - - + +
299B PHE* 6.5 0.4 - - + -
325B GLU* 2.8 32.3 + - + +
326B LEU* 3.4 16.2 - - + +
328B LEU* 1.3 76.6 - - - +
330B CYS* 1.3 61.8 + - - +
332B GLY* 3.2 13.3 + - - -
333B HIS 3.9 1.6 + - - -
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Residues in contact with CYS 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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280B TYR* 3.6 19.3 - - - -
296B CYS* 3.8 36.3 - - + -
299B PHE* 3.5 35.9 - - - -
326B LEU 2.8 12.0 + - - -
327B LEU* 3.3 13.5 - - + +
329B ILE* 1.3 78.8 - - - +
331B ALA* 1.3 60.7 + - - +
332B GLY 3.1 1.2 + - - -
333B HIS* 3.1 17.3 + - - +
338B VAL* 4.0 4.5 - - + +
339B VAL* 3.3 13.1 - - - +
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Residues in contact with ALA 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 LEU 2.8 16.6 + - - +
328B LEU* 3.2 23.7 + - + +
330B CYS* 1.3 72.8 - - - +
332B GLY* 1.3 55.5 + - - +
333B HIS 3.2 0.7 - - - -
339B VAL* 3.5 24.5 - - + -
346B TRP* 5.9 1.1 - - - +
372B LEU* 4.6 9.4 - - + -
375B ALA* 3.6 26.0 - - + +
378B ARG* 4.2 0.9 + - - -
379B HIS* 3.2 23.2 + - - -
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Residues in contact with GLY 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 LEU 3.1 10.5 + - - -
329B ILE 3.2 6.9 + - - -
330B CYS 3.0 2.0 - - - -
331B ALA* 1.3 78.6 - - - +
333B HIS* 1.3 58.1 + - - +
334B PRO* 3.7 2.9 - - - +
375B ALA* 5.1 3.8 - - - -
378B ARG* 3.0 23.2 + - - -
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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