Contacts of the strand formed by residues 274 - 281 (chain A) in PDB entry 5E8T
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 274 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A PHE 4.6 0.2 - - - +
235A SER* 4.7 1.4 - - - -
236A SER* 4.1 26.7 + - - -
267A ASN* 4.0 24.9 - - + +
268A LYS 3.5 9.6 - - - +
269A ASP* 3.8 19.4 + - + +
273A TRP* 1.3 85.6 - - - +
275A GLN* 1.3 74.1 + - - +
276A LEU* 4.3 8.2 + - + +
601A GOL 4.8 1.2 + - - -
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Residues in contact with GLN 275 (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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207A LEU* 5.0 3.8 - - - +
233A ILE* 3.7 31.2 - - + +
234A PHE 3.7 4.7 - - - +
235A SER* 5.4 0.7 - - - +
267A ASN* 3.4 4.5 - - - -
268A LYS* 2.8 42.7 + - - +
270A ASN* 5.5 5.7 - - + +
273A TRP* 3.8 31.3 + - + +
274A THR* 1.3 75.7 - - - +
276A LEU* 1.3 62.5 + - - +
277A TRP* 2.9 35.4 + - + +
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ILE* 3.6 3.5 - - - -
234A PHE* 2.8 43.6 + - + +
235A SER 3.6 22.0 - - - +
236A SER* 4.2 7.9 - - - -
239A GLU* 3.6 36.6 - - + -
242A TRP* 3.7 31.9 - - + -
266A ASP 3.7 2.5 - - - -
267A ASN* 3.5 32.8 - - - +
274A THR* 4.3 8.3 - - + +
275A GLN* 1.3 75.6 - - - +
277A TRP* 1.3 59.8 + - - +
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Residues in contact with TRP 277 (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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202A ALA* 3.6 22.7 - - + -
205A ILE* 3.7 34.1 - - + -
207A LEU* 3.8 30.7 - - + -
231A VAL* 3.5 22.2 - - + -
232A LYS 3.5 2.9 - - - +
233A ILE* 3.8 10.3 - - + +
242A TRP* 3.0 16.6 + - - +
264A ALA 4.5 0.2 - - - -
265A ALA* 3.4 2.3 - - - -
266A ASP* 2.8 41.4 + - + +
268A LYS* 3.5 41.0 - - + +
275A GLN* 2.9 42.1 + - + +
276A LEU* 1.3 80.2 - - - +
278A LEU* 1.3 58.9 + - - +
279A VAL* 4.0 13.9 - - + -
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Residues in contact with LEU 278 (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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230A ALA 3.8 0.7 - - - +
231A VAL* 3.5 2.1 - - - -
232A LYS* 2.8 47.4 + - + +
234A PHE* 3.6 20.9 - - + -
242A TRP* 3.6 29.6 - - + +
245A GLU* 3.6 40.8 - - + +
246A ALA* 3.8 26.9 - - + +
249A TYR* 5.3 3.6 - - + -
262A PHE* 4.6 7.9 - - + -
264A ALA 3.5 2.5 - - - +
265A ALA* 3.9 8.1 - - + -
277A TRP* 1.3 72.6 - - - +
279A VAL* 1.3 61.5 + - - +
280A SER* 4.2 1.7 + - - -
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Residues in contact with VAL 279 (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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200A THR* 4.7 0.4 - - + -
201A ILE 6.1 0.2 - - - -
202A ALA* 5.6 2.9 - - + +
205A ILE* 3.9 32.8 - - + -
229A VAL* 3.9 19.1 - - + -
230A ALA 3.3 9.4 - - - +
231A VAL* 4.3 3.8 - - + -
262A PHE* 4.1 5.4 - - - -
263A ILE* 2.8 38.1 + - + -
264A ALA* 2.8 32.0 + - + +
266A ASP* 5.8 2.0 - - + -
277A TRP* 4.0 22.9 - - + -
278A LEU* 1.3 75.3 - - - +
280A SER* 1.3 64.4 + - - +
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Residues in contact with SER 280 (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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229A VAL* 3.8 1.6 - - - -
230A ALA* 2.9 42.7 + - - +
249A TYR* 6.0 1.6 - - - -
260A LEU* 3.6 25.6 - - - +
261A GLY 3.3 15.9 - - - -
262A PHE* 4.5 3.4 - - - -
263A ILE* 3.6 14.9 - - - +
278A LEU 5.3 1.7 + - - -
279A VAL* 1.3 75.2 - - - +
281A ASP* 1.3 68.3 + - - +
602A GOL 4.5 0.2 + - - -
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Residues in contact with ASP 281 (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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228A GLU 5.6 0.4 - - - -
229A VAL* 5.3 0.7 - - - +
230A ALA* 3.7 0.9 - - - +
255A ARG* 4.9 8.0 + - - -
260A LEU* 3.6 7.8 - - + +
261A GLY* 2.9 37.4 + - - +
263A ILE* 3.7 19.0 - - - +
280A SER* 1.3 79.7 + - - +
282A TYR* 1.3 60.3 + - - +
283A HIS* 3.8 24.3 + - + +
342A LYS* 5.8 2.1 + - - -
602A GOL 3.0 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