Contacts of the helix formed by residues 280 - 288 (chain E) in PDB entry 2W3S
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 THR 280 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203E ALA* 3.4 15.5 - - + +
204E GLY 5.0 0.2 - - - +
245E ALA 3.3 12.6 + - - -
246E GLY* 3.4 33.9 - - - +
247E VAL 3.3 7.4 - - - +
248E THR* 4.1 3.1 - - + +
249E ILE* 4.0 5.6 - - - -
278E VAL 4.0 7.4 - - - +
279E ALA* 1.3 78.2 - - - +
281E ILE* 1.3 59.5 + - - +
283E GLY 3.3 12.5 + - - -
284E ASN* 3.0 24.8 + - - +
1465E FAD 2.6 29.6 + - - +
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Residues in contact with ILE 281 (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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243E ILE* 3.9 17.0 - - + +
244E GLY 3.2 28.3 - - - +
245E ALA* 3.3 14.6 - - - +
247E VAL* 3.3 13.8 + - + +
249E ILE* 3.7 19.5 - - + +
252E LEU* 3.7 28.5 - - + -
267E LEU* 6.0 0.4 - - + -
280E THR* 1.3 69.4 - - - +
282E GLY* 1.3 58.3 + - - +
284E ASN* 3.6 11.7 - - + +
285E ILE* 2.7 51.7 + - + +
294E GLY* 5.2 8.1 - - - -
298E LEU* 5.1 10.5 - - + -
339E VAL* 4.9 6.7 - - + -
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Residues in contact with GLY 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245E ALA* 2.9 40.9 + - - -
280E THR* 4.3 0.2 - - - -
281E ILE* 1.3 79.5 - - - +
283E GLY* 1.3 51.1 + - - +
285E ILE* 3.6 2.2 - - - +
286E ALA* 2.7 38.5 + - - +
336E VAL* 4.3 10.3 - - - +
1465E FAD 4.2 6.5 - - - -
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Residues in contact with GLY 283 (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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280E THR* 3.3 10.3 + - - -
282E GLY* 1.3 70.4 - - - +
284E ASN* 1.3 66.5 + - - +
287E ASN* 2.8 28.9 + - - +
1465E FAD 3.5 53.4 + - - +
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Residues in contact with ASN 284 (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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249E ILE* 5.2 0.2 - - - -
270E PHE* 3.7 9.6 - - + -
280E THR 3.0 15.2 + - - +
281E ILE* 3.6 13.7 - - + +
282E GLY 3.2 0.2 - - - -
283E GLY* 1.3 79.5 - - - +
285E ILE* 1.3 61.7 + - + +
287E ASN* 3.5 9.0 + - - +
288E GLY* 3.6 7.6 + - - -
289E SER* 4.8 2.1 + - - -
292E GLY* 4.2 7.3 - - - -
294E GLY* 3.1 35.2 + - - -
295E PRO* 3.5 9.7 - - - +
1465E FAD 3.0 54.8 + - - +
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Residues in contact with ILE 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281E ILE* 2.7 34.7 + - + +
282E GLY* 3.7 4.0 - - - +
284E ASN* 1.3 70.4 - - + +
286E ALA* 1.3 66.0 + - - +
288E GLY* 3.1 10.6 + - - -
294E GLY 5.8 0.2 - - - -
295E PRO* 4.6 15.5 - - + -
298E LEU* 4.2 12.6 - - + -
305E LEU* 4.3 12.3 - - + -
318E LEU* 3.9 24.5 - - + -
321E PHE* 3.5 27.9 - - + -
322E PHE* 3.4 18.7 - - + -
336E VAL* 4.8 4.9 - - + -
339E VAL* 3.6 31.4 - - + -
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Residues in contact with ALA 286 (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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282E GLY 2.7 20.6 + - - +
285E ILE* 1.3 73.8 - - - +
287E ASN* 1.3 64.5 + - - +
288E GLY* 3.0 1.2 + - - -
321E PHE* 4.1 11.5 - - - -
328E GLN* 3.8 17.7 - - - +
330E ARG* 5.1 8.3 + - - +
336E VAL* 3.8 11.0 - - + +
1465E FAD 3.3 43.5 - - + +
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Residues in contact with ASN 287 (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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207E ASP* 3.1 35.2 + - - +
211E TRP* 5.2 7.8 + - - -
283E GLY 2.8 20.4 + - - +
284E ASN* 3.6 6.6 + - - +
285E ILE 3.2 0.2 - - - -
286E ALA* 1.3 76.3 - - - +
288E GLY* 1.3 60.5 + - - +
289E SER* 3.3 25.9 + - - +
328E GLN* 4.7 4.2 + - - +
1465E FAD 3.5 18.3 + - - +
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Residues in contact with GLY 288 (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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284E ASN 3.6 3.6 + - - -
285E ILE 3.1 14.3 + - - -
286E ALA 3.0 5.2 + - - -
287E ASN* 1.3 79.9 - - - +
289E SER* 1.3 64.9 + - - +
290E PRO* 3.4 6.6 - - - +
295E PRO* 6.3 0.2 - - - -
322E PHE* 3.6 21.0 - - - -
325E TYR* 5.4 0.5 - - - -
326E ARG* 5.1 6.1 + - - -
328E GLN* 4.0 19.2 + - - -
389E GLY 5.1 2.1 - - - +
391E PRO* 4.9 1.7 - - - +
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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