Contacts of the strand formed by residues 298 - 307 (chain C) in PDB entry 5Y7K
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 HIS 298 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C TYR* 4.1 2.6 + - - -
263C ASN* 6.0 0.7 - - - +
264C PRO 4.8 6.6 - - - +
265C THR* 5.9 0.5 - - - -
266C VAL* 4.5 18.2 + - + +
289C ALA* 4.3 1.4 - - + +
293C MET* 3.0 38.2 + - + +
294C LEU* 3.9 24.7 - - + +
296C GLY 3.1 13.4 + - - -
297C ASP* 1.3 76.7 - - - +
299C TYR* 1.3 73.4 + - - +
315C TRP* 3.7 34.8 - + - -
316C LEU 3.1 17.3 - - - +
317C ARG* 4.2 2.5 - - - -
318C ARG* 3.9 2.7 - - - +
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Residues in contact with TYR 299 (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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202C VAL* 6.1 0.2 - - + -
203C TYR* 3.2 31.2 - + + +
207C VAL* 5.3 4.3 - - + -
263C ASN* 2.8 36.5 + - + -
264C PRO* 5.4 2.7 - - + -
266C VAL* 4.6 0.7 - - - -
297C ASP* 6.4 0.7 - - + -
298C HIS* 1.3 81.9 - - - +
300C LEU* 1.3 64.0 + - - +
301C CYS* 3.9 3.1 - - + +
315C TRP* 3.4 15.8 - - - +
316C LEU* 2.6 52.3 + - + +
317C ARG 4.1 4.0 - - - -
318C ARG* 3.7 31.4 - - + +
320C GLN* 3.9 21.6 + - + -
664C SER* 4.1 0.5 + - - -
665C VAL* 3.6 37.0 - - + +
668C GLU* 3.8 6.4 + - - -
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Residues in contact with LEU 300 (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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203C TYR* 3.2 15.8 + - + +
207C VAL* 3.3 1.1 - - - +
208C PHE* 3.0 34.2 - - + -
215C TRP* 4.6 0.2 - - + -
226C ALA* 3.9 18.8 - - + -
266C VAL* 4.1 16.8 - - + +
268C PHE* 3.7 26.5 - - + -
299C TYR* 1.3 71.8 - - - +
301C CYS* 1.3 58.4 + - - +
302C ASP 3.9 11.9 - - - +
303C VAL* 3.9 12.3 - - + -
313C LEU* 4.1 12.3 - - + -
314C GLN 3.6 15.3 - - - +
315C TRP* 3.8 35.0 - - + -
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Residues in contact with CYS 301 (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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207C VAL* 3.6 13.0 - - + -
208C PHE* 4.1 2.9 - - - -
299C TYR* 3.9 2.9 - - + -
300C LEU* 1.3 72.9 - - - +
302C ASP* 1.3 57.4 + - - +
314C GLN* 3.2 35.0 + - - -
315C TRP 4.2 1.8 - - - -
316C LEU* 4.1 23.6 - - + -
358C ARG* 2.7 41.1 + - + -
359C PRO* 3.8 34.9 - - + +
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Residues in contact with ASP 302 (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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208C PHE* 4.2 2.8 - - - -
300C LEU* 3.7 3.6 - - - +
301C CYS* 1.3 82.3 - - - +
303C VAL* 1.3 80.3 + - - +
304C THR* 3.0 22.5 + - - -
312C SER* 4.5 2.4 + - - +
313C LEU* 3.7 1.6 - - - -
314C GLN* 3.2 58.9 + - + +
358C ARG* 4.3 13.3 + - - +
359C PRO 4.8 4.9 - - - +
360C SER 4.6 0.2 - - - -
361C GLU* 3.4 25.6 + - - +
362C PRO* 3.5 9.0 - - - +
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Residues in contact with VAL 303 (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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208C PHE* 4.7 3.0 - - + -
215C TRP* 3.5 59.8 + - + +
268C PHE* 3.7 23.3 - - + -
300C LEU* 3.9 18.4 - - + -
302C ASP* 1.3 83.4 + - - +
304C THR* 1.3 68.2 + - - +
305C TRP* 5.1 0.4 - - - +
311C ILE* 3.8 26.9 - - + -
312C SER 3.6 4.0 - - - +
313C LEU* 4.5 2.9 - - + -
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Residues in contact with THR 304 (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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302C ASP* 3.0 21.9 + - - -
303C VAL* 1.3 75.7 + - - +
305C TRP* 1.3 69.2 + - - +
311C ILE* 4.2 3.4 - - - -
312C SER* 2.6 57.1 + - - +
361C GLU* 4.3 4.5 - - + +
362C PRO* 3.5 33.3 - - + +
364C PHE* 4.6 4.9 - - + +
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Residues in contact with TRP 305 (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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215C TRP* 3.1 25.2 + + + +
216C TRP 2.9 25.0 + - - +
217C SER* 3.7 23.8 - - - -
218C PRO* 3.9 15.7 - - + +
222C PHE* 3.5 26.0 - - + -
224C ALA* 3.9 13.2 - - + -
270C VAL* 4.3 3.6 - - + -
303C VAL* 5.2 0.4 - - + -
304C THR* 1.3 86.7 - - - +
306C ALA* 1.3 61.8 + - - +
307C THR 3.5 9.0 - - - -
308C GLN 4.0 7.9 - - - -
310C ARG 3.5 18.8 - - - -
311C ILE* 3.6 35.2 - - + +
337C TRP* 3.6 29.4 - + - -
364C PHE* 4.3 3.6 - - - +
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Residues in contact with ALA 306 (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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218C PRO* 5.0 3.8 - - - +
304C THR 3.7 2.0 + - - -
305C TRP* 1.3 75.1 - - - +
307C THR* 1.3 67.3 + - + +
310C ARG* 2.8 36.8 + - + +
311C ILE* 5.1 1.1 - - - -
312C SER 5.2 0.4 - - - +
364C PHE* 3.5 48.7 - - + +
365C THR 4.7 4.9 - - - +
366C LEU 5.2 1.2 - - - +
368C GLY* 4.5 0.4 - - - -
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Residues in contact with THR 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C PRO* 3.5 21.5 - - - +
305C TRP* 3.5 2.9 - - - -
306C ALA* 1.3 84.7 - - + +
308C GLN* 1.3 66.9 + - - +
309C GLU* 3.5 3.6 + - - +
310C ARG* 3.1 38.9 + - + +
366C LEU 4.4 5.8 - - - +
367C ASP 3.4 28.9 - - - +
368C GLY* 3.5 12.3 - - - +
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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