Contacts of the helix formed by residues 295 - 308 (chain E) in PDB entry 2ONK
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 ASN 295 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33E VAL* 3.5 24.0 - - - +
34E LYS 3.4 21.7 - - - +
35E LEU* 4.8 1.4 - - + +
85E ASP* 3.2 19.5 + - - +
293E ALA* 3.5 0.4 - - - -
294E GLU* 1.3 94.3 + - - +
296E ARG* 1.3 54.0 + - - +
297E GLU 3.2 2.7 - - - -
298E LEU* 3.0 23.0 + - + +
299E ALA* 2.8 34.2 + - - +
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Residues in contact with ARG 296 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E TRP* 5.4 4.8 - - - +
289E ILE* 3.3 29.8 + - - +
290E PRO 2.9 27.8 + - - -
291E LYS* 4.1 13.7 + - - +
293E ALA* 4.0 16.2 + - - +
294E GLU 3.7 2.0 + - - +
295E ASN* 1.3 71.6 - - - +
297E GLU* 1.3 58.0 + - + +
299E ALA* 2.9 7.8 - - - +
300E VAL* 2.8 42.7 + - + +
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Residues in contact with GLU 297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295E ASN 3.1 1.0 + - - -
296E ARG* 1.3 77.5 - - + +
298E LEU* 1.3 69.9 - - + +
300E VAL* 3.6 8.9 + - - +
301E GLU* 3.2 27.8 + - - +
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Residues in contact with LEU 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E VAL* 4.1 26.7 - - + -
34E LYS 5.7 0.2 - - - +
35E LEU* 4.1 13.4 - - + +
54E PHE* 3.8 11.1 - - + -
58E HIS* 4.5 22.4 - - + +
61E VAL* 4.7 21.8 - - + -
295E ASN* 3.0 27.8 + - + +
297E GLU* 1.3 77.3 - - + +
299E ALA* 1.3 69.3 + - - +
301E GLU* 3.2 10.0 + - + +
302E PHE* 3.1 18.5 + - - +
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Residues in contact with ALA 299 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E LEU* 4.2 9.6 - - - +
85E ASP* 3.8 11.7 - - + +
86E VAL* 4.5 3.1 - - - -
289E ILE* 3.2 34.8 - - + -
293E ALA* 5.5 0.2 - - + -
295E ASN 2.8 13.8 + - - +
296E ARG* 2.9 13.7 - - - +
298E LEU* 1.3 75.2 - - - +
300E VAL* 1.3 66.8 + - - +
302E PHE* 2.7 19.4 + - - +
303E VAL* 2.9 11.7 + - - +
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Residues in contact with VAL 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289E ILE* 3.3 16.4 - - + +
296E ARG* 2.8 27.4 + - + +
297E GLU* 3.6 11.0 - - - +
299E ALA* 1.3 73.0 - - - +
301E GLU* 1.3 68.1 + - - +
303E VAL* 3.0 3.9 + - - +
304E LYS* 2.7 54.1 + - - +
334E SER* 3.8 34.3 - - - +
335E LEU* 3.8 8.7 - - + -
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Residues in contact with GLU 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E PHE* 3.7 16.6 - - + -
57E LYS* 5.9 2.1 - - - -
58E HIS* 4.1 19.8 + - + +
297E GLU 3.2 16.4 - - - +
298E LEU* 3.2 12.1 + - + +
299E ALA 3.1 0.6 + - - -
300E VAL* 1.3 79.0 - - - +
302E PHE* 1.3 62.5 + - - +
304E LYS* 3.4 28.3 + - - +
305E LEU* 3.1 22.2 + - - +
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Residues in contact with PHE 302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E LEU* 3.7 27.4 - - + -
37E VAL* 4.2 7.9 - - + -
47E MET* 3.7 33.7 - - + -
50E PHE* 3.9 32.1 - - + -
51E LYS* 5.1 0.2 - - - -
54E PHE* 3.3 28.4 - + + -
63E VAL* 4.3 14.8 - - + -
86E VAL* 3.8 31.6 - - + -
287E ILE* 4.7 0.2 - - + -
298E LEU 3.1 4.9 + - - +
299E ALA 2.7 15.0 + - - +
301E GLU* 1.3 69.0 - - - +
303E VAL* 1.3 67.0 + - - +
305E LEU* 3.0 8.8 + - + +
306E VAL* 2.9 39.5 + - + +
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Residues in contact with VAL 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E VAL* 4.9 6.7 - - + -
106E TRP* 4.5 4.3 - - + -
108E ILE* 4.2 13.9 - - + -
287E ILE* 4.3 26.7 - - + -
289E ILE* 3.4 38.8 - - + -
299E ALA 2.9 6.2 + - - +
300E VAL 3.4 5.8 - - - +
302E PHE* 1.3 75.5 - - - +
304E LYS* 1.3 63.9 + - - +
306E VAL* 2.9 21.7 + - - +
307E ILE* 3.1 16.2 + - + +
335E LEU* 3.7 25.8 - - + -
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Residues in contact with LYS 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300E VAL* 2.7 36.7 + - + +
301E GLU* 3.4 30.1 - - - +
303E VAL* 1.3 72.3 - - - +
305E LEU* 1.3 59.1 + - - +
307E ILE* 3.1 15.4 - - - +
308E SER* 2.8 30.2 + - - -
334E SER* 2.8 24.8 + - - -
335E LEU* 3.6 12.6 - - + +
337E ALA* 5.9 1.4 - - - +
338E MET* 4.1 29.6 - - + +
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Residues in contact with LEU 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E PHE* 3.6 16.6 - - + +
53E ALA* 4.2 5.2 - - + -
54E PHE* 3.5 48.7 - - + +
301E GLU 3.1 9.0 + - - +
302E PHE* 3.0 13.4 + - + +
304E LYS* 1.3 79.8 - - - +
306E VAL* 1.3 65.6 + - - +
308E SER* 3.1 22.6 + - - +
310E GLU* 3.0 40.4 - - + +
311E GLY* 3.3 10.2 - - - +
314E ILE* 5.1 1.3 - - + -
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Residues in contact with VAL 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E MET* 5.0 2.9 - - + -
50E PHE* 4.0 25.6 - - + -
110E PHE* 3.7 41.0 - - + +
287E ILE* 3.8 20.4 - - + -
302E PHE* 2.9 46.4 + - + +
303E VAL* 2.9 9.4 + - - +
305E LEU* 1.3 79.5 - - - +
307E ILE* 1.3 61.2 + - + +
311E GLY* 3.5 16.8 - - - -
312E GLN* 4.0 1.7 + - - +
315E LEU* 4.8 4.3 - - - +
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Residues in contact with ILE 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E ILE* 4.2 14.1 - - + -
110E PHE* 4.2 15.3 - - + -
287E ILE* 5.6 0.9 - - + -
303E VAL* 3.1 22.6 + - + +
304E LYS* 3.1 21.5 - - - +
306E VAL* 1.3 79.3 - - + +
308E SER* 1.3 67.1 + - - +
312E GLN* 3.2 22.0 + - - +
326E PRO* 3.9 28.9 - - + +
335E LEU* 4.7 4.5 - - + -
338E MET* 3.7 22.4 - - + +
339E VAL* 3.6 25.8 - - + -
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Residues in contact with SER 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304E LYS 2.8 19.4 + - - -
305E LEU* 3.1 18.9 + - - +
307E ILE* 1.3 78.2 - - - +
309E GLU* 1.3 63.8 + - - +
310E GLU* 3.2 21.2 + - - +
311E GLY 3.0 2.8 + - - -
312E GLN* 2.9 16.3 + - - +
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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