Contacts of the strand formed by residues 266 - 277 (chain C) in PDB entry 5O67
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 266 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229C ARG 3.8 1.1 - - - +
230C VAL* 3.4 6.5 - - - +
231C LYS* 2.8 60.2 + - - +
264C VAL* 5.1 0.4 - - - -
265C TRP* 1.3 79.6 - - - +
267C ILE* 1.3 60.7 + - - +
268C THR* 4.7 2.1 + - - -
289C THR* 3.9 14.0 - - - +
290C HIS 3.4 9.6 - - - -
291C ASN* 3.4 21.1 - - - -
292C LEU* 4.8 3.4 - - - -
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Residues in contact with ILE 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C VAL* 3.5 26.9 - - + -
229C ARG 3.4 4.7 - - - +
230C VAL* 4.4 13.9 - - + +
266C SER* 1.3 74.9 - - - +
268C THR* 1.3 65.7 + - - +
269C PRO* 4.0 9.2 - - + +
288C TYR* 6.3 0.2 - - + -
289C THR* 3.6 0.2 - - - -
290C HIS* 3.0 49.8 + - + +
292C LEU* 5.4 6.9 - - + +
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Residues in contact with THR 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C SER 4.4 0.3 - - - -
228C VAL* 3.4 3.6 - - - -
229C ARG* 2.9 45.5 + - + +
266C SER* 4.7 2.6 + - - -
267C ILE* 1.3 81.3 + - - +
269C PRO* 1.3 68.8 - - - +
270C GLY 3.8 0.5 + - - -
287C SER* 4.3 13.2 - - - +
288C TYR 3.4 13.9 - - - +
289C THR* 2.9 29.6 + - - +
318C GLN* 4.5 2.2 - - - +
501C LDA 6.2 1.3 - - + -
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Residues in contact with PRO 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C VAL* 6.3 1.1 - - + -
227C SER 3.2 10.8 - - - +
228C VAL* 4.2 9.6 - - + -
267C ILE* 4.0 11.7 - - + +
268C THR* 1.3 87.1 - - - +
270C GLY* 1.3 57.5 + - - +
287C SER* 3.1 22.5 - - - -
288C TYR* 3.3 53.0 + - + +
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Residues in contact with GLY 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C VAL* 3.4 9.4 - - - +
227C SER* 2.8 44.4 + - - +
268C THR* 3.8 1.0 + - - -
269C PRO* 1.3 74.1 - - - +
271C LEU* 1.3 60.2 + - - +
286C VAL 3.5 9.9 - - - -
287C SER* 3.7 6.7 - - - -
501C LDA 5.3 5.4 - - - -
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Residues in contact with LEU 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C PHE* 3.8 30.3 - - + -
224C ALA* 5.2 1.3 - - + -
225C VAL 3.4 13.2 - - - +
226C VAL* 4.7 4.9 - - + -
227C SER* 4.4 0.4 + - - -
270C GLY* 1.3 74.7 - - - +
272C SER* 1.3 71.8 + - - +
273C MET* 4.4 20.0 - - + -
285C SER* 3.2 5.7 - - - -
286C VAL* 2.9 51.0 + - + +
501C LDA 4.9 4.1 - - - +
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Residues in contact with SER 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C ALA 5.0 1.8 - - - -
100C SER* 3.7 35.0 + - - -
223C ASP 3.5 1.2 + - - +
224C ALA* 3.5 6.1 - - - +
225C VAL* 3.1 39.9 + - - +
271C LEU* 1.3 78.5 - - - +
273C MET* 1.3 66.5 + - - +
274C VAL* 4.9 1.2 - - - +
284C GLY 3.3 10.5 - - - -
285C SER* 4.1 8.3 - - - +
501C LDA 4.9 5.6 - - - -
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Residues in contact with MET 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C PRO* 4.2 23.8 - - + -
223C ASP 3.4 4.9 - - - +
224C ALA* 4.6 8.1 - - + -
271C LEU* 4.4 24.2 - - + -
272C SER* 1.3 82.2 - - - +
274C VAL* 1.3 66.5 + - - +
283C PHE* 3.2 4.0 - - - -
284C GLY 2.8 47.1 + - - +
285C SER* 5.1 1.8 - - - +
286C VAL* 5.7 3.6 - - + -
505C C8E 4.2 29.4 - - + +
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Residues in contact with VAL 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C LEU* 5.4 0.4 - - + -
96C TYR* 3.2 35.4 - - + -
99C ALA* 4.0 17.9 - - + -
100C SER* 4.1 23.3 - - - +
217C GLU* 3.9 1.7 - - - +
222C PRO* 3.8 0.5 - - - +
223C ASP* 3.0 38.0 + - + +
272C SER* 4.9 0.7 - - - +
273C MET* 1.3 85.9 - - - +
275C LYS* 1.3 66.6 + - - +
281C VAL* 3.4 20.6 - - + -
282C LEU 3.3 7.2 - - - +
283C PHE* 3.9 11.0 - - + -
505C C8E 4.6 1.1 - - - -
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Residues in contact with LYS 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C TYR* 4.1 0.2 - - - -
217C GLU* 3.6 15.2 + - - +
218C SER 3.2 25.5 + - - -
219C ALA* 3.5 15.5 + - - +
220C THR* 4.3 10.3 - - - +
221C MET 3.5 13.9 + - - +
222C PRO* 4.0 8.3 - - + -
274C VAL* 1.3 79.6 - - - +
276C THR* 1.3 70.2 + - - +
277C PHE* 3.5 44.6 - - + -
281C VAL* 4.0 4.3 - - - -
282C LEU 2.9 30.4 + - - +
505C C8E 3.8 22.0 - - - +
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Residues in contact with THR 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C VAL* 5.8 0.7 - - - +
96C TYR* 2.8 21.8 + - - -
217C GLU* 3.2 15.0 + - - +
275C LYS* 1.3 81.6 + - - +
277C PHE* 1.3 71.4 + - - +
278C ASP* 3.6 28.0 - - + +
279C PRO 5.1 1.6 - - - -
280C ALA 3.5 10.1 - - - +
281C VAL* 3.8 15.2 - - + +
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Residues in contact with PHE 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A ASN* 3.0 14.7 + - - +
330A ARG* 5.4 12.1 - - - -
331A MET* 3.3 26.7 - - + -
275C LYS* 3.5 55.2 - - + -
276C THR* 1.3 72.9 - - - +
278C ASP* 1.3 65.9 + - - +
280C ALA* 2.8 22.7 + - - +
282C LEU* 3.6 32.3 - - + -
505C C8E 4.5 8.5 - - - -
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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