Contacts of the helix formed by residues 296 - 306 (chain C) in PDB entry 5DO7
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 ASN 296 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252C PRO 2.8 8.7 + - - +
253C ARG 3.7 0.8 + - - -
254C SER* 2.9 30.6 - - - +
257C PHE* 5.2 0.2 - - - +
295C SER* 1.3 68.8 - - - +
297C PRO* 1.3 60.6 - - - +
298C PHE* 2.5 10.3 + - - +
299C ASP* 2.2 58.0 + - + +
274D SER* 3.3 10.5 - - - +
312D PRO* 2.4 24.4 + - - -
313D ARG* 2.6 43.2 + - + -
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Residues in contact with PRO 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C PHE* 4.0 25.1 - - + -
281C LEU* 4.2 4.9 - - + -
291C CYS* 3.5 32.5 - - - -
292C PRO 5.4 1.1 - - - +
293C GLU* 5.5 0.9 - - - +
295C SER* 3.2 4.0 - - - +
296C ASN* 1.3 87.1 - - - +
298C PHE* 1.3 57.0 + - - +
300C PHE* 2.8 11.5 + - + +
301C TYR* 2.8 48.3 + - + +
311D CYS* 4.5 16.8 - - - +
312D PRO* 4.1 11.4 - - + +
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Residues in contact with PHE 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C CYS* 4.0 20.2 - - - -
85C LEU* 3.5 24.4 - - + +
249C ILE* 4.6 4.3 - - + -
251C GLN 3.2 26.5 - - - -
252C PRO* 3.3 12.8 - - + -
253C ARG 2.9 28.0 - - - -
256C LEU* 4.3 9.6 - - + -
257C PHE* 3.6 35.0 - + + -
260C PHE* 4.5 5.8 - + - -
263C ILE* 3.7 27.8 - - + -
280C MET* 5.3 3.1 - - - -
296C ASN* 2.5 10.6 + - - +
297C PRO* 1.3 78.4 - - - +
299C ASP* 1.3 58.6 + - - +
301C TYR* 5.1 1.4 - - - +
302C MET* 3.4 22.2 + - - +
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Residues in contact with ASP 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C PRO* 3.8 18.1 - - - +
295C SER 4.0 0.4 - - - +
296C ASN* 2.2 51.9 + - + +
298C PHE* 1.3 69.0 - - - +
300C PHE* 1.3 64.1 + - - +
302C MET* 3.7 12.3 - - - +
303C ASP* 3.8 14.3 + - - +
245D SER* 4.9 1.8 + - - -
273D ARG* 3.3 28.7 - - - +
274D SER* 2.6 35.8 + - - -
275D ASP* 3.9 3.6 + - - +
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Residues in contact with PHE 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C TYR* 5.6 2.0 - - + -
290C PRO 4.6 8.5 - - - -
291C CYS* 3.5 32.5 - - + -
292C PRO* 5.5 5.2 - - + -
295C SER* 3.7 24.2 - - - +
296C ASN 3.1 1.0 + - - -
297C PRO* 2.8 11.5 + - + +
299C ASP* 1.3 75.7 - - - +
301C TYR* 1.3 70.9 - + - +
302C MET* 2.1 24.9 + - - -
303C ASP* 2.3 46.1 + - + -
304C LEU* 4.4 32.1 - - + -
274D SER* 5.8 1.6 - - - -
278D ARG* 5.8 7.4 - - - -
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Residues in contact with TYR 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C LEU* 6.5 0.2 - - + -
257C PHE* 4.9 0.2 - + - -
265C ILE* 5.8 3.1 - - + -
280C MET* 3.6 31.6 - - + -
281C LEU* 3.4 26.4 - - + +
284C PHE* 3.4 49.5 - + + -
285C ASN* 3.8 12.0 + - - -
289C TYR 3.9 9.2 - - - -
290C PRO* 4.4 0.2 - - - +
291C CYS* 3.3 30.8 + - + -
297C PRO* 2.8 45.6 + - + +
298C PHE 5.3 0.7 - - - +
300C PHE* 1.3 84.0 - + - +
302C MET* 1.3 54.5 + - - +
303C ASP 3.4 0.2 - - - -
304C LEU* 3.2 6.9 + - + +
305C THR* 2.8 35.3 + - + +
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Residues in contact with MET 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C LEU* 2.9 59.7 - - + -
86C GLY 4.1 22.4 - - - +
87C SER* 4.6 5.6 - - - +
249C ILE 5.2 0.2 - - - +
250C HIS* 5.1 7.6 - - + +
252C PRO* 5.0 9.9 - - - -
265C ILE* 4.8 4.7 - - + +
298C PHE 3.4 12.7 + - - +
299C ASP* 3.7 10.1 - - - +
300C PHE 2.1 12.6 + - - +
301C TYR* 1.3 67.9 - - - +
303C ASP* 1.3 67.1 + - - +
305C THR* 2.6 23.7 + - - +
306C SER* 3.2 13.5 + - - -
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Residues in contact with ASP 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C ASP* 4.0 13.3 - - - +
300C PHE* 2.3 49.2 + - + +
302C MET* 1.3 70.7 - - - +
304C LEU* 1.3 61.1 + - - +
306C SER 3.4 16.8 - - - +
321C ARG* 4.2 6.3 + - - -
245D SER* 3.9 23.4 + - - -
246D PHE* 5.4 7.2 + - - -
275D ASP* 3.9 28.5 + - - +
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Residues in contact with LEU 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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284C PHE* 3.8 25.8 - - + -
289C TYR* 3.4 48.0 - - + -
300C PHE* 3.6 24.5 + - + -
301C TYR* 3.2 13.8 + - + +
302C MET 3.2 0.4 - - - -
303C ASP* 1.3 81.9 - - - +
305C THR* 1.3 60.9 + - - +
306C SER 3.5 1.7 + - - +
307C VAL* 6.1 0.2 - - - +
321C ARG* 3.4 53.6 + - + +
322C VAL* 4.9 5.0 - - - +
325C ILE* 5.0 5.8 - - + +
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Residues in contact with THR 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C SER* 4.6 1.5 + - - -
265C ILE* 3.6 36.8 - - + +
267C SER* 3.9 3.2 + - - -
272C ILE* 3.9 14.4 - - + +
284C PHE* 3.7 26.9 - - + -
301C TYR 2.8 26.1 + - - +
302C MET* 2.6 29.6 + - - +
304C LEU* 1.3 73.8 - - - +
306C SER* 1.3 59.1 + - - +
322C VAL* 2.9 31.3 - - - +
325C ILE* 5.6 3.6 - - + -
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Residues in contact with SER 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C SER* 2.7 43.9 - - - -
267C SER* 4.3 3.6 - - - -
268C PHE* 4.5 4.3 - - - -
302C MET 3.2 12.0 + - - -
303C ASP 3.4 13.4 - - - +
304C LEU 3.4 2.3 - - - +
305C THR* 1.3 78.9 + - - +
307C VAL* 1.3 71.8 + - - +
308C ASP* 3.7 4.9 + - - +
318C THR* 5.3 1.1 - - - +
321C ARG* 5.5 1.4 + - - -
246D PHE* 4.7 9.4 - - - -
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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