Contacts of the strand formed by residues 288 - 292 (chain A) in PDB entry 3EDY
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 SER 288 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A ASN 4.0 13.5 + - - -
224A SER* 3.2 12.0 - - - -
225A GLN* 2.9 25.3 + - - +
254A GLN* 3.8 16.3 + - - +
258A ALA* 4.1 17.5 - - - +
287A ILE* 1.3 73.4 - - - +
289A THR* 1.3 58.5 + - - +
290A TRP* 5.0 1.6 - - - -
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Residues in contact with THR 289 (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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225A GLN* 2.9 19.6 + - - +
227A CYS* 4.9 0.7 - - - -
254A GLN* 4.8 1.6 + - - -
256A SER 5.7 0.2 + - - -
257A VAL* 3.5 6.0 - - + +
258A ALA* 2.7 36.3 + - - +
277A VAL* 4.6 8.7 - - + -
280A LEU* 3.9 24.5 - - + -
281A MET* 3.4 34.2 - - + +
287A ILE 2.8 19.8 + - - -
288A SER* 1.3 69.7 - - - +
290A TRP* 1.3 80.2 + - - +
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Residues in contact with TRP 290 (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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224A SER* 4.9 8.5 - - - -
225A GLN 2.8 12.4 + - - +
226A ALA* 4.1 9.6 - - + -
227A CYS* 3.3 22.3 + - - -
258A ALA* 4.1 10.6 - - + +
259A ARG* 3.3 59.2 - - + +
261A VAL* 4.1 17.7 - - + -
288A SER* 5.0 3.0 - - - -
289A THR* 1.3 90.2 - - - +
291A VAL* 1.3 67.1 + - - +
314A GLU* 4.5 3.1 - - - -
316A ALA 3.8 16.2 - - - -
317A LEU* 4.0 14.6 - - + -
318A PRO* 3.4 37.8 - - + +
321A HIS* 6.0 0.7 - + - -
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Residues in contact with VAL 291 (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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227A CYS* 3.8 11.9 - - - +
235A PHE* 4.1 24.5 - - + -
257A VAL* 3.2 33.0 - - + -
259A ARG 2.9 10.1 + - - +
260A VAL* 3.4 8.1 - - + +
261A VAL* 2.7 35.5 + - - +
273A ALA 5.6 1.6 - - - +
276A ASP* 5.3 5.6 - - - +
277A VAL* 3.9 18.2 - - + -
290A TRP* 1.3 76.7 - - - +
292A TYR* 1.3 60.0 + - - +
293A SER* 4.0 19.5 - - - -
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Residues in contact with TYR 292 (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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227A CYS 3.0 10.2 + - - +
228A ALA* 3.7 17.4 - - + -
229A GLN* 3.6 22.6 + - - +
230A PHE* 3.9 27.8 - + - -
261A VAL* 3.4 37.5 - - + -
262A GLY* 4.6 3.5 - - - -
276A ASP* 5.4 0.2 - - - +
291A VAL* 1.3 74.6 - - - +
293A SER* 1.3 67.2 + - - +
294A SER* 3.8 26.2 + - - -
303A PRO* 4.2 2.5 + - + +
306A GLN* 3.3 29.5 - - - +
307A TRP* 3.6 34.6 + + + +
310A LEU* 4.7 11.1 - - + +
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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