Contacts of the strand formed by residues 237 - 241 (chain K) 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 ILE 237 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230K ILE* 3.9 11.4 - - + -
231K ILE 3.5 4.9 - - - +
232K ILE* 3.5 37.7 - - + -
236K SER* 1.3 79.4 - - - +
238K THR* 1.3 63.9 + - - +
246K LEU 4.1 0.5 - - - +
247K ALA* 3.4 1.7 - - - -
248K ILE* 2.9 59.6 + - + +
250K PRO* 4.6 5.6 - - + -
253K ILE* 4.1 23.6 - - + -
258K ILE* 4.7 11.2 - - + -
273K LEU* 4.9 4.3 - - + -
283K LEU* 5.3 4.9 - - + -
300K LEU* 4.4 12.8 - - + +
302K VAL* 4.7 11.7 - - + -
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Residues in contact with THR 238 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212K VAL* 5.2 5.6 - - + +
213K GLU* 6.2 3.6 - - + +
230K ILE* 3.3 8.3 - - - +
231K ILE* 2.8 47.4 + - - +
236K SER* 4.8 9.4 - - - -
237K ILE* 1.3 83.5 - - - +
239K TYR* 1.3 59.4 - - - +
240K HIS* 3.2 29.5 + - + +
245K TYR* 6.0 1.8 - - + +
246K LEU 3.4 6.3 - - - -
247K ALA* 3.7 18.4 - - + -
300K LEU* 5.4 1.6 - - - -
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Residues in contact with TYR 239 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222K VAL* 3.8 11.7 - - + -
226K PHE* 3.1 13.5 + - + +
227K GLY 2.1 38.2 + - - -
229K ALA 3.0 27.8 - - - -
230K ILE* 3.6 18.4 - - + -
238K THR* 1.3 74.9 - - - +
240K HIS* 1.3 64.2 + - - +
241K ASN* 3.2 24.3 + - + -
244K LYS* 3.8 23.1 - - + -
245K TYR* 3.5 5.2 - - - -
246K LEU* 2.8 43.4 + - + +
296K THR* 5.3 3.8 - - + +
297K LEU* 3.9 37.2 - - + -
300K LEU* 4.7 4.5 - - + -
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Residues in contact with HIS 240 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190K VAL* 5.0 8.5 - - + -
207K TRP* 3.9 28.9 - + + -
210K GLU* 4.3 24.2 - - + +
211K ASN 5.5 3.1 - - - -
212K VAL* 4.9 7.9 - - - +
228K GLY* 3.6 0.7 - - - -
229K ALA* 2.9 33.4 + - + +
231K ILE* 4.6 13.5 - - + -
238K THR* 3.2 35.4 + - + +
239K TYR* 1.3 79.5 + - - +
241K ASN* 1.3 62.3 + - - +
242K GLY 5.9 0.7 - - - +
244K LYS 3.4 6.2 + - - +
245K TYR* 3.5 38.8 - + - -
246K LEU 6.4 0.2 - - - -
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Residues in contact with ASN 241 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207K TRP* 3.6 16.1 + - - -
226K PHE 3.1 20.4 + - - -
227K GLY* 3.1 2.0 - - - -
228K GLY* 3.0 30.3 + - - +
239K TYR* 3.2 16.6 + - + +
240K HIS* 1.3 76.3 - - - +
242K GLY* 1.3 63.9 + - - +
243K ASP 3.1 1.0 + - - -
244K LYS* 2.9 34.1 + - + +
296K THR* 6.2 0.8 - - + +
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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