Contacts of the strand formed by residues 263 - 271 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27L ASP* 2.6 36.5 + - + +
206L SER* 2.8 24.9 + - - -
207L PHE* 2.8 34.2 + - + -
208L TYR* 3.8 15.3 - + - -
210L PRO* 3.8 21.1 - - + -
254L ILE* 3.9 15.9 - - + -
255L LYS 3.7 4.0 - - - -
256L LYS* 3.7 43.4 + - + +
257L ASP* 3.4 6.7 - - - -
261L ASN 3.3 17.9 - - - -
262L THR* 1.3 82.6 + - - +
264L SER* 1.3 56.2 + - - +
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Residues in contact with SER 264 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204L VAL 3.4 9.0 - - - -
205L ASN* 3.8 11.7 + - - +
206L SER* 3.0 13.2 + - - -
207L PHE* 3.7 3.4 - - - -
253L ASN 3.7 0.5 - - - +
254L ILE* 3.2 5.5 - - - +
255L LYS* 3.0 36.8 + - - +
257L ASP* 2.8 27.9 + - - +
258L LYS* 5.3 1.2 + - - -
263L TYR* 1.3 70.6 - - - +
265L LEU* 1.3 62.5 + - - +
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Residues in contact with LEU 265 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202L CYS 5.5 0.2 - - - +
203L THR* 3.3 4.2 - - - -
204L VAL* 2.8 47.1 + - + +
205L ASN* 5.2 0.7 - - - +
207L PHE* 3.7 14.1 - - + -
212L VAL* 3.5 32.8 - - + +
214L THR* 5.1 7.2 - - - +
252L TRP* 4.3 20.4 - - + -
253L ASN 3.2 29.6 - - - +
254L ILE* 4.0 10.3 - - + -
264L SER* 1.3 78.2 - - - +
266L THR* 1.3 89.3 + - - +
267L ASP* 4.2 8.7 - - + +
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Residues in contact with THR 266 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201L GLU* 3.9 31.9 + - + +
202L CYS 3.6 3.1 - - - -
203L THR* 4.2 9.2 - - + +
253L ASN* 3.1 37.9 + - + +
265L LEU* 1.3 82.6 + - - +
267L ASP* 1.3 63.4 + - - +
268L LEU* 4.1 4.7 + - + +
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Residues in contact with ASP 267 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201L GLU* 3.4 2.2 - - - -
202L CYS* 2.7 49.9 + - + +
214L THR* 2.9 26.4 - - + +
216L TRP* 2.7 32.4 + - - -
239L ARG* 3.4 31.9 + - - -
252L TRP* 3.7 8.6 - - + -
253L ASN 5.9 0.5 + - - -
265L LEU* 4.2 10.9 - - + +
266L THR* 1.3 76.0 - - - +
268L LEU* 1.3 64.3 + - - +
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Residues in contact with LEU 268 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191L ASN* 5.2 0.2 - - - +
193L LEU* 4.1 22.9 - - + -
199L THR* 3.8 24.0 - - + +
200L LEU 3.3 15.3 - - - +
201L GLU* 3.4 32.3 - - + +
239L ARG* 4.8 6.9 + - - -
266L THR* 4.1 4.8 + - + -
267L ASP* 1.3 79.9 + - - +
269L VAL* 1.3 74.2 + - - +
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Residues in contact with VAL 269 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199L THR* 3.2 8.8 + - - -
200L LEU* 2.7 39.9 + - + +
216L TRP* 3.0 56.8 - - + +
237L TRP* 5.3 8.3 - - + -
239L ARG* 5.3 5.6 - - - -
267L ASP* 4.3 0.4 - - - +
268L LEU* 1.3 81.2 - - - +
270L ARG* 1.3 71.0 + - - +
271L THR* 3.2 6.8 + - - +
275L MET* 5.3 0.9 - - + -
279L PRO* 4.7 13.7 - - + -
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Residues in contact with ARG 270 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193L LEU* 6.1 6.3 - - + +
195L ASP* 3.2 22.2 + - - -
196L GLY* 2.9 37.8 - - - +
197L ASN* 3.5 17.0 + - - +
198L MET 4.3 6.1 - - - -
199L THR* 4.6 4.7 - - - +
269L VAL* 1.3 77.5 - - - +
271L THR* 1.3 53.6 + - - +
272L THR* 2.7 43.2 + - - +
275L MET* 4.5 4.2 - - - +
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Residues in contact with THR 271 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197L ASN* 2.5 32.2 + - - +
198L MET* 2.9 46.5 + - + +
200L LEU* 3.6 33.5 + - + +
269L VAL* 3.2 4.1 + - - +
270L ARG* 1.3 65.9 - - - +
272L THR* 1.3 56.4 + - - +
275L MET* 3.8 28.5 - - + -
278L GLN* 5.2 4.3 - - + -
279L PRO* 4.8 4.9 - - + +
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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