Contacts of the strand formed by residues 215 - 220 (chain L) in PDB entry 6R90
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 MET 215 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209L VAL* 3.3 6.5 - - - +
210L SER* 2.9 34.2 + - - +
213L SER* 3.3 37.5 - - - +
214L ARG* 1.3 82.7 - - - +
216L VAL* 1.3 65.9 + - - +
217L VAL* 6.3 0.7 - - + -
227L LEU* 4.0 25.8 - - + -
228L LEU 3.6 7.2 - - - +
229L ASN* 4.4 11.4 - - - +
250L LEU* 5.3 10.8 - - + -
255L ASP 5.7 0.2 - - - +
272L LEU* 4.8 19.7 - - + -
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Residues in contact with VAL 216 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173L TYR* 3.4 35.9 - - + +
194L PHE* 3.7 15.7 - - + -
207L LEU* 5.5 3.4 - - + -
208L ASP 3.7 4.3 - - - -
209L VAL* 3.5 19.3 - - + -
215L MET* 1.3 77.0 - - - +
217L VAL* 1.3 62.2 + - - +
227L LEU* 3.3 6.9 - - - +
228L LEU* 2.9 62.9 + - + +
229L ASN 3.7 11.2 - - - +
230L MET* 5.2 2.5 - - + -
250L LEU* 5.9 0.2 - - - -
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Residues in contact with VAL 217 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207L LEU* 3.3 4.9 - - - +
208L ASP* 2.9 56.6 + - + +
215L MET* 6.3 0.4 - - + -
216L VAL* 1.3 76.0 - - - +
218L THR* 1.3 68.9 + - - +
225L VAL* 3.6 19.5 - - + -
226L ILE 3.2 14.4 - - - +
227L LEU* 4.7 10.1 - - + -
248L VAL* 4.2 14.4 - - + -
250L LEU* 4.5 20.2 - - + -
258L LEU* 4.4 21.1 - - + -
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Residues in contact with THR 218 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175L SER* 4.5 0.2 - - - -
181L THR* 3.6 32.6 - - + +
194L PHE* 6.5 0.4 - - + -
195L ALA* 5.3 1.8 - - + -
204L PHE* 4.4 5.0 - - + +
206L SER 2.4 27.4 + - - -
207L LEU* 4.0 11.8 - - - +
217L VAL* 1.3 79.8 - - - +
219L GLY* 1.3 62.3 + - - +
225L VAL* 3.4 7.1 - - - +
226L ILE* 2.9 60.1 + - + +
228L LEU* 6.0 1.3 - - + -
248L VAL* 4.9 2.2 - - - -
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Residues in contact with GLY 219 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204L PHE* 3.5 5.0 - - - +
205L CYS 2.6 30.4 + - - -
206L SER* 2.9 22.4 + - - +
218L THR* 1.3 73.5 - - - +
220L ASP* 1.3 57.7 + - - -
224L ASN 4.1 4.7 - - - -
225L VAL* 4.4 6.1 - - - -
245L VAL* 3.6 17.7 - - - -
248L VAL* 4.9 2.0 - - - +
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Residues in contact with ASP 220 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202L ILE* 5.1 5.6 - - - +
203L TRP 3.2 13.8 + - - +
204L PHE* 2.9 37.5 - - - -
205L CYS* 3.3 12.4 - - - -
219L GLY* 1.3 72.3 - - - -
221L ASN* 1.3 61.9 + - - +
222L VAL* 3.4 9.9 - - + +
223L GLY 4.7 0.2 - - - -
224L ASN* 2.9 43.2 + - - +
226L ILE* 4.3 12.6 - - - +
245L VAL* 2.9 33.3 + - - +
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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