Contacts of the helix formed by residues 327 - 340 (chain B) in PDB entry 2ORY
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 PRO 327 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B TYR* 4.0 7.6 - - - +
44B TRP* 3.4 45.1 - - + +
325B ASP 3.3 11.0 - - - +
326B ILE* 1.3 78.6 - - - +
328B LEU* 1.3 65.1 + - - +
329B THR 3.3 3.1 - - - -
330B ASP* 3.0 24.7 + - + +
331B ILE* 3.0 15.8 + - - +
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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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14B TYR* 3.7 35.9 - - + -
313B VAL* 4.3 5.8 - - + -
314B VAL* 4.0 25.1 - - + -
317B PRO* 4.0 20.4 - - + -
323B MET* 4.4 9.2 - - - +
326B ILE* 2.9 22.4 + - + +
327B PRO* 1.3 69.8 - - - +
329B THR* 1.3 56.4 + - - +
331B ILE* 3.3 2.4 + - + +
332B PHE* 2.9 50.2 + - + +
342B HIS* 3.1 27.1 + - + +
345B HIS* 4.4 6.5 - - + +
346B HIS* 5.8 5.0 - - + -
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Residues in contact with THR 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B PRO 3.3 0.8 - - - -
328B LEU* 1.3 77.0 - - - +
330B ASP* 1.3 57.5 + - - +
333B GLU* 2.9 30.0 + - - +
334B ASP* 4.4 13.9 - - - +
337B ALA* 4.0 20.0 - - + -
342B HIS* 3.3 25.7 - - - +
343B HIS* 5.8 5.2 + - + -
346B HIS* 3.9 13.7 + - - -
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Residues in contact with ASP 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TYR* 2.7 38.5 + - - -
36B LYS* 3.3 18.9 + - - -
327B PRO* 3.0 24.0 + - + +
329B THR* 1.3 79.8 - - - +
331B ILE* 1.3 60.5 + - - +
333B GLU* 4.4 7.4 + - - +
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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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14B TYR* 3.6 11.9 - - + +
15B MET* 4.9 0.2 - - - -
17B TYR* 3.4 49.6 - - + +
18B TYR* 3.7 28.4 - - + +
19B GLY 4.7 5.2 + - - -
20B ILE* 4.1 5.2 - - - +
21B THR* 4.6 1.6 + - - +
44B TRP* 3.5 30.5 - - + -
326B ILE* 4.1 15.5 - - + -
327B PRO 3.0 16.7 + - - +
328B LEU* 3.9 3.8 - - - +
330B ASP* 1.3 80.7 - - - +
332B PHE* 1.3 72.8 + - + +
333B GLU* 3.4 5.8 + - - +
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Residues in contact with PHE 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B TYR* 4.4 6.3 - + - -
17B TYR* 3.5 40.2 - + + -
20B ILE* 3.9 18.4 - - + -
21B THR* 3.3 15.7 - - - +
93B ASN* 4.7 1.3 - - - -
94B PRO* 4.1 19.5 - - + -
95B VAL* 4.8 5.4 - - + -
313B VAL* 3.7 29.8 - - + -
328B LEU* 2.9 37.1 + - + +
331B ILE* 1.3 85.5 - - + +
333B GLU* 1.3 73.3 + - - +
336B ILE* 3.5 38.4 + - + +
337B ALA* 5.6 0.4 - - - +
340B LEU* 6.2 0.2 - - + -
342B HIS* 5.6 4.3 - + - +
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Residues in contact with GLU 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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21B THR* 2.7 28.6 + - + +
22B HIS* 5.1 8.2 + - - -
329B THR* 2.9 21.6 + - - +
330B ASP 4.6 7.2 - - - +
331B ILE 4.3 6.7 - - - +
332B PHE* 1.3 84.6 - - - +
334B ASP* 1.3 60.4 + - - +
335B ALA* 4.7 3.6 - - + +
337B ALA* 3.0 27.7 + - - +
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Residues in contact with ASP 334 (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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329B THR* 4.4 13.9 - - - +
333B GLU* 1.3 74.7 - - - +
335B ALA* 1.3 58.6 + - - +
337B ALA* 3.4 5.8 - - - +
338B GLY* 2.8 27.4 + - - -
343B HIS* 5.3 7.1 - - - -
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Residues in contact with ALA 335 (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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23A THR* 5.9 4.0 - - - +
333B GLU* 3.6 3.1 - - + +
334B ASP* 1.3 78.7 - - - +
336B ILE* 1.3 68.6 + - + +
338B GLY* 3.2 1.2 + - - -
339B LEU* 3.1 28.5 + - + +
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Residues in contact with ILE 336 (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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65A PHE* 4.5 11.0 - - + -
21B THR* 4.0 15.5 - - + -
93B ASN* 4.3 9.6 - - - +
95B VAL* 4.0 33.0 - - + -
332B PHE* 3.5 42.3 + - + +
333B GLU 3.7 1.2 + - - -
335B ALA* 1.3 79.2 - - + +
337B ALA* 1.3 58.5 + - - +
339B LEU* 3.3 8.4 + - + +
340B LEU* 2.9 51.8 + - + +
342B HIS* 5.3 0.7 - - + -
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Residues in contact with ALA 337 (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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329B THR* 4.0 19.7 - - + -
332B PHE* 5.6 0.2 - - - +
333B GLU 3.0 22.5 + - - +
334B ASP* 3.4 12.1 - - - +
335B ALA 3.2 0.2 - - - -
336B ILE* 1.3 74.8 - - - +
338B GLY* 1.3 65.7 + - - +
340B LEU 3.4 0.5 + - - -
341B HIS 3.2 3.1 + - - -
342B HIS* 3.0 51.3 + - + +
343B HIS* 4.8 9.4 + - + -
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Residues in contact with GLY 338 (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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334B ASP 2.8 14.8 + - - -
335B ALA* 3.7 3.1 - - - -
337B ALA* 1.3 77.3 - - - +
339B LEU* 1.3 61.9 + - - +
341B HIS* 3.1 26.0 + - - -
343B HIS* 5.5 7.4 - - - -
344B HIS* 5.3 0.9 - - - -
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Residues in contact with LEU 339 (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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28A LYS* 4.7 15.0 - - - +
64A PRO* 4.1 27.4 - - + -
65A PHE* 3.7 35.4 - - + +
301B LEU* 4.1 4.2 - - - +
306B VAL* 3.6 20.8 - - + +
335B ALA* 3.1 18.3 + - + +
336B ILE* 3.3 5.6 + - + +
338B GLY* 1.3 77.7 - - - +
340B LEU* 1.3 59.4 + - - +
341B HIS* 3.2 7.6 + - - -
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Residues in contact with LEU 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 3.8 22.2 - - + -
95B VAL* 5.0 2.5 - - + -
301B LEU* 4.3 6.7 - - - +
306B VAL* 4.1 5.2 - - + +
309B ALA* 3.8 11.2 - - + +
310B TYR* 3.7 49.6 - - + +
313B VAL* 4.7 10.8 - - + -
314B VAL* 3.9 11.7 - - + -
332B PHE* 6.1 0.2 - - + -
336B ILE* 2.9 33.3 + - + +
339B LEU* 1.3 73.3 - - - +
341B HIS* 1.3 71.4 + - - +
342B HIS* 3.1 35.0 + - + +
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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