Contacts of the strand formed by residues 263 - 271 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27K ASP* 2.6 39.2 + - + +
206K SER* 2.8 24.6 + - - -
207K PHE* 2.8 34.1 + - + -
208K TYR* 3.8 9.0 - + - -
210K PRO* 3.8 28.5 - - + -
254K ILE* 3.9 16.4 - - + -
255K LYS 3.7 4.0 - - - -
256K LYS* 3.7 43.8 + - + +
257K ASP* 3.4 5.2 - - - -
261K ASN 3.3 15.9 - - - -
262K THR* 1.3 82.2 + - - +
264K SER* 1.3 58.1 + - - +
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Residues in contact with SER 264 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204K VAL 3.4 8.5 - - - -
205K ASN* 3.8 10.8 + - - +
206K SER* 3.0 13.3 + - - -
207K PHE* 3.7 3.1 - - - -
253K ASN 3.7 0.5 - - - +
254K ILE* 3.2 5.0 - - - +
255K LYS* 3.0 37.8 + - - +
257K ASP* 2.7 27.5 + - - +
258K LYS* 5.3 1.0 + - - -
263K TYR* 1.3 71.1 - - - +
265K LEU* 1.3 61.7 + - - +
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Residues in contact with LEU 265 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202K CYS 5.1 0.7 - - - +
203K THR* 3.3 4.3 - - - -
204K VAL* 2.8 50.3 + - + +
205K ASN* 5.2 0.9 - - - +
207K PHE* 3.7 14.8 - - + -
212K VAL* 3.5 32.3 - - + +
214K THR* 5.1 7.4 - - - +
252K TRP* 4.3 20.9 - - + -
253K ASN 3.3 27.4 - - - +
254K ILE* 4.0 11.0 - - + -
264K SER* 1.3 76.5 - - - +
266K THR* 1.3 88.2 + - - +
267K ASP* 4.2 8.1 - - + +
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Residues in contact with THR 266 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201K GLU* 3.9 31.2 + - + +
202K CYS 3.6 3.4 - - - -
203K THR* 4.2 8.7 - - + +
253K ASN* 3.1 38.6 + - + +
265K LEU* 1.3 83.4 + - - +
267K ASP* 1.3 64.0 + - - +
268K LEU* 4.1 4.3 + - + +
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Residues in contact with ASP 267 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201K GLU* 3.4 2.3 - - - -
202K CYS* 2.7 49.0 + - + +
214K THR* 2.8 26.8 - - + +
216K TRP* 2.7 33.0 + - - -
239K ARG* 3.4 31.5 + - - -
252K TRP* 3.8 7.9 - - + -
253K ASN 5.9 0.2 + - - -
265K LEU* 4.2 11.3 - - + +
266K THR* 1.3 76.4 - - - +
268K LEU* 1.3 63.6 + - - +
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Residues in contact with LEU 268 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191K ASN* 5.2 0.4 - - - +
193K LEU* 4.1 22.2 - - + -
199K THR* 3.8 24.9 - - + +
200K LEU 3.3 14.8 - - - +
201K GLU* 3.4 31.9 - - + +
239K ARG* 4.8 7.4 + - - -
266K THR* 4.1 5.1 + - + -
267K ASP* 1.3 78.9 + - - +
269K VAL* 1.3 73.3 + - - +
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Residues in contact with VAL 269 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199K THR* 3.2 8.8 + - - -
200K LEU* 2.7 39.7 + - + +
216K TRP* 3.0 56.1 - - + +
237K TRP* 5.3 8.3 - - + -
239K ARG* 5.3 5.4 - - - -
267K ASP* 4.4 0.4 - - - +
268K LEU* 1.3 82.3 - - - +
270K ARG* 1.3 70.2 + - - +
271K THR* 3.2 6.5 + - - +
275K MET* 5.3 1.1 - - + -
279K PRO* 4.7 13.5 - - + -
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Residues in contact with ARG 270 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193K LEU* 6.1 6.9 - - + +
195K ASP* 3.2 22.4 + - - -
196K GLY* 2.9 37.8 - - - +
197K ASN* 3.6 17.8 + - - +
198K MET 4.3 5.4 - - - -
199K THR* 4.6 4.3 - - - +
269K VAL* 1.3 77.4 - - - +
271K THR* 1.3 53.5 + - - +
272K THR* 2.7 42.4 + - - +
275K MET* 4.5 3.5 - - - +
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Residues in contact with THR 271 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197K ASN* 2.5 32.2 + - - +
198K MET* 2.9 46.0 + - + +
200K LEU* 3.5 33.1 + - + +
269K VAL* 3.2 4.3 + - - +
270K ARG* 1.3 65.9 - - - +
272K THR* 1.3 55.4 + - - +
275K MET* 3.8 28.0 - - - -
278K GLN* 5.3 4.0 - - + -
279K PRO* 4.8 4.6 - - + +
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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