Contacts of the strand formed by residues 233 - 240 (chain C) in PDB entry 1DVM
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 LEU 233 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C TRP* 4.1 7.6 - - + -
87C ASN* 3.7 32.3 - - - +
90C GLU* 4.8 2.2 - - - +
91C ILE* 5.5 0.7 - - + -
171C PHE* 3.8 26.5 - - + -
227C PRO* 3.8 1.2 - - - +
228C TYR* 3.1 38.1 + - + +
229C HIS 5.7 0.7 - - - +
231C ASP* 3.1 4.4 - - - +
232C THR* 1.3 84.4 + - - +
234C SER* 1.3 66.0 + - - +
362C VAL* 3.6 21.3 - - + -
363C ARG 3.6 13.9 - - - +
364C HIS* 4.2 2.0 - - + +
365C ASN* 3.5 6.2 + - - -
371C LEU* 3.6 30.3 - - + -
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Residues in contact with SER 234 (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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225C GLU* 2.8 45.7 + - - +
226C LEU 3.6 12.3 + - - -
227C PRO* 3.7 3.0 - - - -
228C TYR* 3.5 7.7 - - - -
233C LEU* 1.3 81.6 - - - +
235C MET* 1.3 61.0 + - - +
236C PHE* 4.0 6.7 - - - -
361C VAL 3.3 1.7 - - - +
362C VAL* 3.3 3.8 - - - -
363C ARG* 3.0 30.4 + - - -
365C ASN* 3.6 15.5 - - - -
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Residues in contact with MET 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C TRP* 4.1 11.4 - - - -
224C LEU 3.6 0.5 - - - +
225C GLU* 3.4 2.8 - - - -
226C LEU* 2.6 50.4 + - + +
228C TYR* 3.4 23.6 - - + +
234C SER* 1.3 74.7 + - - +
236C PHE* 1.3 68.6 + - - +
237C ILE* 3.4 24.0 - - + -
275C LEU* 5.5 1.3 - - - -
278C PHE* 4.8 5.4 - - - -
326C ILE* 3.9 17.7 - - + -
328C VAL* 4.2 14.4 - - + -
360C PHE* 3.9 20.0 - - + -
361C VAL 3.4 5.6 - - - +
362C VAL* 3.4 26.0 - - + -
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Residues in contact with PHE 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C ILE* 4.1 21.1 - - + -
224C LEU 3.0 12.6 - - - +
225C GLU* 3.6 26.2 - - + -
234C SER* 4.0 12.3 - - - -
235C MET* 1.3 74.8 - - - +
237C ILE* 1.3 62.9 + - - +
238C ALA* 4.0 1.0 + - - +
259C ILE* 4.8 7.4 - - + -
262C TRP* 4.5 14.6 - + + -
263C LYS* 3.8 36.1 - - + -
266C MET* 4.3 5.8 - - + -
359C LEU 3.5 0.5 - - - +
360C PHE* 2.9 8.7 - - - +
361C VAL* 2.8 54.4 + - + +
363C ARG* 3.2 37.2 - - + -
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Residues in contact with ILE 237 (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 ASP 3.4 1.6 - - - +
223C ILE* 3.3 4.0 - - - +
224C LEU* 2.8 41.2 + - + +
226C LEU* 3.3 40.2 - - + -
235C MET* 3.4 25.8 - - + -
236C PHE* 1.3 72.6 - - - +
238C ALA* 1.3 64.2 + - - +
239C ALA* 5.6 0.9 - - + -
273C LEU* 6.4 1.8 - - + -
275C LEU* 4.4 9.0 - - + -
354C ILE* 4.4 25.8 - - + -
358C PHE* 3.8 38.6 - - + -
359C LEU 3.3 2.9 - - - -
360C PHE* 4.9 0.4 - - + -
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Residues in contact with ALA 238 (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 ASP 3.1 10.3 - - - +
223C ILE* 4.2 6.7 - - + -
236C PHE 4.0 0.6 - - - +
237C ILE* 1.3 75.8 - - - +
239C ALA* 1.3 62.4 + - - +
247C LEU* 4.3 0.2 - - - +
250C LEU* 3.9 13.6 - - + +
262C TRP* 3.8 33.7 - - + -
358C PHE* 3.5 1.9 - - - +
359C LEU* 2.8 42.8 + - + +
361C VAL* 6.5 0.2 - - + -
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Residues in contact with ALA 239 (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 ASP* 2.9 29.6 + - - +
237C ILE* 5.6 1.3 - - + -
238C ALA* 1.3 77.5 - - - +
240C PRO* 1.3 77.6 - - + +
247C LEU* 4.5 0.9 - - - -
250C LEU* 3.6 10.1 - - - +
354C ILE* 5.4 8.5 - - + -
356C ARG* 5.1 6.1 - - + +
357C PRO 3.8 18.4 - - - +
358C PHE* 3.8 9.2 - - + -
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Residues in contact with PRO 240 (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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220C TYR 3.9 2.2 - - - +
221C TYR* 3.7 11.2 - - + -
239C ALA* 1.3 91.5 - - + +
241C TYR* 1.3 65.8 + - - +
242C GLU 3.7 5.3 - - - +
243C LYS* 4.8 2.3 + - - -
245C VAL* 3.4 48.5 - - + +
246C PRO 4.1 5.2 - - - +
247C LEU* 4.2 13.2 - - + -
250C LEU* 3.2 28.2 - - + -
356C ARG* 5.9 3.1 - - - +
357C PRO 4.9 1.6 - - - +
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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