Contacts of the helix formed by residues 333 - 348 (chain B) in PDB entry 2ONL
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 333 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62B ILE* 3.5 7.6 - - - -
332B LEU* 1.3 82.6 - - - +
334B ILE* 1.3 65.8 + - + +
335B ASP* 3.4 9.9 - - + +
336B GLU* 3.0 34.3 + - + +
337B TRP* 3.1 22.5 + - - -
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Residues in contact with ILE 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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59B PHE* 3.2 27.6 - - + +
60B GLN 4.7 1.1 - - - +
61B SER* 3.4 11.9 - - - +
62B ILE* 3.2 44.0 - - + +
65B ALA* 4.1 16.3 - - + +
333B LEU* 1.3 75.5 - - + +
335B ASP* 1.3 64.2 + - - +
337B TRP* 3.4 2.9 + - - +
338B LYS* 3.0 26.3 + - + +
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Residues in contact with ASP 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 5.9 0.2 - - - +
333B LEU* 3.4 7.6 - - + +
334B ILE* 1.3 80.6 - - - +
336B GLU* 1.3 62.5 + - + +
338B LYS* 3.5 18.3 + - + +
339B SER* 2.8 28.1 + - - -
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Residues in contact with GLU 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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332B LEU* 3.3 27.9 - - + +
333B LEU* 3.0 55.1 + - + +
334B ILE 3.2 0.2 - - - -
335B ASP* 1.3 76.3 - - + +
337B TRP* 1.3 61.9 + - - +
338B LYS 3.1 0.2 - - - -
339B SER* 3.7 5.4 - - - -
340B LEU* 3.0 33.1 + - + +
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Residues in contact with TRP 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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59B PHE* 4.4 0.4 - - - -
62B ILE* 3.7 34.9 - - + +
65B ALA* 3.4 27.4 - - + +
66B LYS* 3.7 31.2 - - + +
69B TYR* 3.8 42.6 - + + +
327B PHE* 3.5 25.6 - + + -
330B ARG* 3.1 26.4 + - + -
332B LEU* 3.8 34.8 + - + +
333B LEU 3.1 23.3 + - - +
334B ILE 3.8 0.7 - - - +
336B GLU* 1.3 76.2 - - - +
338B LYS* 1.3 60.1 + - - +
340B LEU* 4.0 11.7 - - + +
341B THR* 3.1 26.9 + - - -
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Residues in contact with LYS 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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59B PHE* 3.5 40.3 - - + -
96B LEU* 4.0 17.8 + - + -
97B GLU 4.4 8.7 + - - -
99B PHE* 2.8 40.8 + - + -
100B ASN* 4.2 15.4 + - - +
334B ILE* 3.0 17.8 + - + +
335B ASP* 3.5 19.0 + - + +
336B GLU 3.1 0.2 - - - -
337B TRP* 1.3 77.2 - - - +
339B SER* 1.3 66.1 + - - +
341B THR* 3.1 4.7 + - - -
342B TYR* 2.9 22.3 + - - +
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Residues in contact with SER 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 3.3 33.1 - - - +
335B ASP 2.8 18.1 + - - -
336B GLU* 3.4 7.8 + - - -
338B LYS* 1.3 76.7 - - - +
340B LEU* 1.3 64.0 + - - +
342B TYR* 2.9 4.0 + - - +
343B ASP* 2.9 36.1 + - - +
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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
----------------------------------------------------------
69B TYR* 3.5 33.3 - - + +
327B PHE* 6.3 0.7 - - + -
330B ARG* 4.0 30.3 - - - +
332B LEU* 4.4 11.7 - - + -
336B GLU 3.0 19.0 + - - +
337B TRP* 4.0 12.3 - - + +
338B LYS 3.3 0.2 - - - -
339B SER* 1.3 76.1 - - - +
341B THR* 1.3 60.6 + - - +
343B ASP* 3.6 15.8 + - + +
344B GLU* 3.2 32.6 + - - +
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Residues in contact with THR 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B PHE* 3.8 25.1 - - + -
68B THR* 4.6 10.1 - - + +
69B TYR* 3.2 32.9 + - - +
72B LEU* 3.9 13.5 - - + +
99B PHE* 4.0 10.1 - - + -
102B VAL* 4.9 4.7 - - + -
337B TRP 3.1 15.3 + - - -
338B LYS 3.1 8.6 + - - -
339B SER 3.1 0.8 - - - -
340B LEU* 1.3 76.5 - - - +
342B TYR* 1.3 65.7 + - - +
344B GLU* 3.6 4.9 + - - +
345B VAL* 3.2 22.4 + - + +
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Residues in contact with TYR 342 (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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91B THR* 4.4 13.9 - - + -
93B ALA* 4.7 5.5 + - + -
94B ARG 4.4 4.3 + - - -
95B SER* 4.0 32.5 + - - -
96B LEU* 3.7 28.9 - - + -
99B PHE* 3.4 40.8 - + + -
338B LYS 2.9 12.1 + - - +
339B SER 2.9 7.2 + - - +
341B THR* 1.3 74.9 - - - +
343B ASP* 1.3 75.3 + - - +
345B VAL* 2.9 17.2 + - + +
346B ILE* 3.0 48.3 + - + +
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Residues in contact with ASP 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 5.6 1.2 - - - +
339B SER* 2.9 31.2 + - - +
340B LEU* 3.7 21.6 - - + +
342B TYR* 1.3 84.2 - - - +
344B GLU* 1.3 57.6 + - + +
346B ILE* 3.1 8.1 + - - +
347B SER* 2.9 29.7 + - - -
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Residues in contact with GLU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B TYR* 3.3 21.2 + - + -
72B LEU* 4.0 18.2 - - + -
73B ARG* 3.2 29.7 + - + -
76B LYS* 2.3 51.4 + - - +
89B VAL* 5.2 0.2 - - - +
340B LEU* 3.2 22.2 + - + +
341B THR 3.9 5.2 - - - +
342B TYR 3.2 0.4 - - - -
343B ASP* 1.3 76.8 - - + +
345B VAL* 1.3 61.2 + - - +
347B SER* 2.9 7.8 + - - -
348B PHE* 3.1 5.9 + - - +
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Residues in contact with VAL 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LEU* 3.8 8.1 - - + -
89B VAL* 3.7 27.0 - - + +
90B PHE* 4.9 6.1 - - - -
91B THR* 3.7 26.5 - - + -
99B PHE* 4.7 1.6 - - + -
102B VAL* 3.6 30.7 - - + -
341B THR* 3.2 17.5 + - + +
342B TYR* 2.9 16.7 + - + +
344B GLU* 1.3 77.0 - - - +
346B ILE* 1.3 67.8 + - + +
348B PHE* 3.6 14.0 - - - +
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Residues in contact with ILE 346 (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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342B TYR* 3.0 55.6 + - + +
343B ASP* 3.7 9.0 - - - +
345B VAL* 1.3 80.8 - - + +
347B SER* 1.3 61.7 + - - +
348B PHE 3.3 4.5 + - - +
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Residues in contact with SER 347 (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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76B LYS* 2.5 30.5 + - - -
343B ASP 2.9 11.0 + - - -
344B GLU* 2.9 12.8 + - - -
346B ILE* 1.3 77.1 - - - +
348B PHE* 1.3 66.4 + - - +
349B VAL* 3.3 14.9 + - - +
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Residues in contact with PHE 348 (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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76B LYS* 3.9 22.0 - - + +
79B LYS* 5.2 6.3 - - - -
86B LEU* 3.0 54.5 - - + -
87B LEU 3.4 19.1 - - - -
88B ASP* 3.9 15.7 - - - -
89B VAL* 3.4 23.3 - - + -
344B GLU 3.1 10.7 + - - +
345B VAL 3.6 8.5 - - - +
346B ILE 3.3 6.1 - - - +
347B SER* 1.3 77.9 - - - +
349B VAL* 1.3 65.9 + - - +
350B PRO* 3.5 37.4 - - + +
351B PRO* 4.5 0.2 - - + -
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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