Contacts of the helix formed by residues 348 - 361 (chain A) in PDB entry 2OR0
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 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A CYS* 4.0 20.6 - - + -
255A VAL* 6.2 3.8 - - + -
346A LYS 4.2 4.3 - - - +
347A THR* 1.4 85.3 - - - +
349A MSE 1.3 66.8 + - - +
351A ARG* 3.0 41.2 + - - +
352A PHE* 3.3 19.8 + - + -
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Residues in contact with MSE 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A ALA* 3.7 20.9 - - + +
251A CYS* 3.7 20.2 - - + -
252A HIS* 3.7 36.3 - - + +
255A VAL* 6.0 4.5 - - + -
331A ALA 4.6 1.1 - - - +
334A ILE* 3.7 33.2 - - + -
335A PHE* 3.7 33.7 - - + +
338A ALA* 4.0 14.6 - - - -
342A ALA* 4.9 7.2 - - + -
347A THR* 3.4 4.8 + - - +
348A PRO* 1.3 79.6 - - - +
350A GLN* 1.3 58.9 + - - +
352A PHE* 3.0 7.2 + - - +
353A TRP* 2.9 26.4 + - + +
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Residues in contact with GLN 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLU* 5.8 0.2 + - - -
335A PHE* 3.9 20.5 - - + -
342A ALA 3.5 19.4 + - - +
344A HIS 3.4 16.2 - - - +
345A TYR* 3.2 28.1 + - - +
347A THR* 2.8 26.1 + - - +
349A MSE 1.3 77.5 - - - +
351A ARG* 1.3 79.4 + - - +
353A TRP* 3.4 3.2 + - + +
354A ARG* 2.9 69.4 + - - +
181B ILE* 3.3 17.0 - - + +
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Residues in contact with ARG 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ALA* 4.1 23.4 + - - +
20A VAL* 3.4 29.5 - - - +
23A GLU* 3.7 37.0 + - + +
71A ASP* 4.7 13.7 - - - -
72A GLY 6.0 0.7 - - - +
345A TYR 4.1 17.0 + - - -
346A LYS 5.7 0.8 - - - -
348A PRO* 3.0 40.2 + - - +
350A GLN* 1.3 81.6 - - - +
352A PHE* 1.3 71.4 + - + +
354A ARG* 3.5 14.7 + - - +
355A ASP* 2.8 49.5 + - - +
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Residues in contact with PHE 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ALA 3.4 18.6 - - - -
69A ALA 3.4 28.3 - - - -
70A LEU 3.6 16.2 - - - -
71A ASP* 4.2 2.7 - - - -
72A GLY* 3.9 12.3 - - - -
244A ILE* 3.0 39.7 - - + +
247A GLY* 4.0 4.3 - - - -
248A ALA* 3.8 15.3 - - + +
251A CYS* 3.8 26.0 - - - -
348A PRO* 3.3 29.2 - - + -
349A MSE 3.0 6.5 + - - +
351A ARG* 1.3 89.6 - - + +
353A TRP* 1.3 61.5 + - - +
355A ASP* 4.1 2.9 - - - -
356A ALA* 3.0 21.0 + - - +
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Residues in contact with TRP 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A ALA* 4.5 6.7 - - + +
331A ALA* 4.1 15.9 - - + -
332A ASP* 2.9 25.9 + - - +
335A PHE* 3.6 55.4 - + + +
349A MSE 2.9 16.8 + - + +
350A GLN* 3.7 5.4 - - + +
352A PHE* 1.3 77.7 - - - +
354A ARG* 1.3 92.2 + - + +
356A ALA* 3.4 4.7 + - - +
357A HIS* 3.2 35.0 + + - -
181B ILE* 4.1 14.4 - - + -
353B TRP* 3.5 33.4 - + - -
354B ARG* 5.3 2.9 - - + -
357B HIS* 3.5 43.9 + + + -
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Residues in contact with ARG 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLU* 2.6 31.1 + - - -
181A ILE* 2.7 54.1 + - + +
182A GLY* 3.8 8.6 - - - -
184A ARG* 4.1 7.9 - - - +
345A TYR* 3.4 21.6 + - - -
350A GLN* 2.9 42.1 + - - +
351A ARG* 3.6 15.6 - - - +
353A TRP* 1.3 94.4 - - + +
355A ASP* 1.3 64.2 + - - +
357A HIS* 3.2 7.5 + - - +
358A ALA* 2.9 28.2 + - - +
181B ILE* 3.6 19.5 - - + +
345B TYR* 5.6 1.1 + - - -
353B TRP* 5.1 2.5 - - + -
354B ARG* 5.1 9.4 - - - +
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Residues in contact with ASP 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLU* 5.3 1.2 - - - +
71A ASP* 5.4 0.3 - - - +
72A GLY* 3.8 19.9 + - - -
73A ALA* 4.3 2.8 + - - -
182A GLY* 3.8 2.1 - - - -
183A LEU* 2.7 54.0 + - + +
184A ARG 4.4 1.4 + - - -
244A ILE* 3.8 15.1 - - + +
351A ARG* 2.8 43.9 + - - +
352A PHE* 3.6 7.4 - - - +
354A ARG* 1.3 79.0 + - - +
356A ALA* 1.3 57.6 + - - +
358A ALA* 3.3 2.1 + - - +
359A GLY* 2.8 26.5 + - - -
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Residues in contact with ALA 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A VAL* 4.4 5.8 - - + +
244A ILE* 3.7 11.6 - - + +
245A THR* 3.8 29.4 - - + -
328A VAL* 3.8 19.5 - - + +
331A ALA* 5.2 3.6 - - + -
352A PHE 3.0 13.3 + - - +
353A TRP* 3.7 10.3 - - - +
354A ARG 3.2 0.4 - - - -
355A ASP* 1.3 77.7 - - - +
357A HIS* 1.3 59.3 + - + +
359A GLY* 3.3 1.8 + - - -
360A LEU* 3.0 27.4 + - - +
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Residues in contact with HIS 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ILE* 4.6 3.8 - - + -
328A VAL* 3.5 19.3 - - + +
332A ASP* 2.5 40.9 + - - -
353A TRP* 3.2 32.8 + + - -
354A ARG 3.2 7.9 + - - +
356A ALA* 1.3 75.5 - - + +
358A ALA* 1.3 66.1 + - - +
360A LEU* 3.3 17.2 + - - +
361A ALA* 3.5 10.9 + - - +
611A ACT 3.6 8.7 + - - -
332B ASP* 5.0 3.1 - - + -
335B PHE* 5.0 9.9 - - + -
336B ALA* 5.8 3.2 - - + +
343B LEU* 4.3 4.7 - - - +
353B TRP* 3.4 43.6 - + + -
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Residues in contact with ALA 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A PHE* 4.7 6.5 - - + -
178A TRP* 5.8 0.4 - - + -
181A ILE* 4.4 1.6 - - - +
182A GLY* 3.5 38.4 - - - +
183A LEU* 3.9 10.2 - - + +
354A ARG 2.9 12.6 + - - +
355A ASP 3.6 5.8 - - - +
357A HIS* 1.3 71.8 - - - +
359A GLY* 1.3 63.2 + - - +
361A ALA* 3.2 18.2 + - - +
362A HIS 4.1 1.9 + - - -
343B LEU* 3.8 27.8 - - + +
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Residues in contact with GLY 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A TRP* 3.5 28.2 - - - -
183A LEU* 3.6 3.2 - - - +
241A VAL* 3.9 9.6 - - - -
244A ILE* 6.0 0.2 - - - -
355A ASP 2.8 18.6 + - - -
356A ALA 3.7 3.1 - - - -
358A ALA* 1.3 72.0 - - - +
360A LEU* 1.3 58.5 + - - +
362A HIS* 3.2 13.3 + - - +
365A HIS* 2.9 22.1 + - - -
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Residues in contact with LEU 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A VAL* 4.4 1.5 - - - +
324A ALA* 4.0 26.5 - - + +
325A TRP* 3.8 37.3 + - + +
328A VAL* 4.1 20.4 - - + -
356A ALA 3.0 15.4 + - - +
357A HIS* 3.7 11.7 - - - +
358A ALA 3.3 1.0 - - - -
359A GLY* 1.3 76.2 - - - +
361A ALA* 1.3 57.7 + - - +
362A HIS 3.2 1.8 - - - +
365A HIS* 3.3 24.6 - - + +
611A ACT 3.5 32.1 - - + +
336B ALA* 3.8 23.1 - - + +
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Residues in contact with ALA 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A PHE* 5.4 1.8 - - + -
357A HIS 3.5 3.4 + - - +
358A ALA 3.2 13.2 + - - +
359A GLY 3.2 1.0 - - - -
360A LEU* 1.3 75.0 - - - +
362A HIS* 1.3 64.9 + - - +
363A ALA* 3.6 1.6 + - - -
366A VAL* 5.7 2.1 - - - +
335B PHE 6.0 1.6 - - - +
336B ALA 5.1 7.2 - - - +
339B GLY* 3.9 29.7 - - - +
340B GLY* 3.9 15.0 + - - +
343B LEU* 4.1 22.7 - - + -
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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