Contacts of the strand formed by residues 263 - 271 (chain J) in PDB entry 3IT8
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 TYR 263 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27J ASP* 2.5 37.8 + - + +
206J SER* 2.8 25.3 + - - -
207J PHE* 2.8 33.7 + - + -
208J TYR* 3.8 8.3 - + - -
210J PRO* 3.8 26.5 - - + -
254J ILE* 3.9 17.9 - - + -
255J LYS 3.7 3.4 - - - -
256J LYS* 3.7 45.3 + - + +
257J ASP* 3.4 4.5 - - - -
261J ASN 3.3 16.2 - - - -
262J THR* 1.3 82.6 + - - +
264J SER* 1.3 58.9 + - - +
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Residues in contact with SER 264 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204J VAL 3.4 8.1 - - - -
205J ASN* 3.8 11.0 + - - +
206J SER* 3.0 13.3 + - - -
207J PHE* 3.7 3.1 - - - -
253J ASN 3.7 0.7 - - - +
254J ILE* 3.2 5.5 - - - +
255J LYS* 3.0 36.9 + - - +
257J ASP* 2.7 28.7 + - - +
258J LYS* 5.3 0.9 + - - -
263J TYR* 1.3 70.4 - - - +
265J LEU* 1.3 62.0 + - - +
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Residues in contact with LEU 265 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203J THR* 3.3 4.3 - - - -
204J VAL* 2.8 48.4 + - + +
205J ASN* 5.3 0.5 - - - +
207J PHE* 3.9 14.8 - - + -
212J VAL* 3.5 31.9 - - + +
214J THR* 5.1 7.0 - - - -
252J TRP* 4.3 20.9 - - + -
253J ASN 3.3 28.0 - - - +
254J ILE* 4.0 10.8 - - + -
264J SER* 1.3 76.0 - - - +
266J THR* 1.3 89.2 + - - +
267J ASP* 4.2 8.7 - - + +
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Residues in contact with THR 266 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201J GLU* 3.9 32.3 + - + +
202J CYS 3.5 3.6 - - - +
203J THR* 4.2 8.4 - - + +
253J ASN* 3.1 38.0 + - + +
265J LEU* 1.3 82.4 + - - +
267J ASP* 1.3 63.9 + - - +
268J LEU* 4.1 4.4 + - + +
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Residues in contact with ASP 267 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201J GLU* 3.4 2.1 - - - -
202J CYS* 2.7 49.5 + - + +
214J THR* 2.8 27.7 - - + +
216J TRP* 2.8 32.3 + - - -
239J ARG* 3.5 30.4 + - - -
252J TRP* 3.8 7.7 - - - -
253J ASN 5.9 0.5 + - - -
265J LEU* 4.2 11.8 - - + +
266J THR* 1.3 76.1 - - - +
268J LEU* 1.3 64.0 + - - +
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Residues in contact with LEU 268 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191J ASN* 5.2 0.4 - - - +
193J LEU* 4.2 22.9 - - + -
199J THR* 3.8 24.5 - - + +
200J LEU 3.3 8.1 - - - +
201J GLU* 3.4 38.8 - - + +
239J ARG* 4.8 7.1 + - - -
266J THR* 4.1 4.7 + - + -
267J ASP* 1.3 79.6 + - - +
269J VAL* 1.3 72.8 + - - +
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Residues in contact with VAL 269 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199J THR* 3.2 8.6 + - - -
200J LEU* 2.7 40.4 + - + +
216J TRP* 3.0 56.1 - - + +
237J TRP* 5.3 8.3 - - + -
239J ARG* 5.3 6.1 - - - -
267J ASP* 4.4 0.4 - - - +
268J LEU* 1.3 81.4 - - - +
270J ARG* 1.3 71.0 + - - +
271J THR* 3.2 6.8 + - - +
275J MET* 5.3 0.9 - - + -
279J PRO* 4.7 13.9 - - + -
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Residues in contact with ARG 270 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193J LEU* 6.0 6.3 - - + +
195J ASP* 3.2 23.2 + - - -
196J GLY* 2.9 37.8 - - - +
197J ASN* 3.5 17.8 + - - +
198J MET 4.3 5.6 + - - -
199J THR* 4.6 4.5 - - - +
269J VAL* 1.3 77.0 - - - +
271J THR* 1.3 54.7 + - - +
272J THR* 2.7 42.4 + - - +
275J MET* 4.4 3.5 - - - +
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Residues in contact with THR 271 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197J ASN* 2.5 32.1 + - - +
198J MET* 2.9 45.6 + - + +
200J LEU* 3.6 32.9 + - + +
269J VAL* 3.2 3.3 + - - +
270J ARG* 1.3 67.9 - - - +
272J THR* 1.3 54.7 + - - +
275J MET* 3.8 28.5 - - + -
278J GLN* 5.2 4.0 - - + -
279J PRO* 4.8 5.3 - - + +
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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