Contacts of the strand formed by residues 215 - 221 (chain B) in PDB entry 5IYB
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 TYR 215 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210B LYS* 3.0 33.6 - - + +
211B LYS* 4.6 0.9 - - - -
213B SER* 3.2 17.8 + - - +
214B LYS* 1.3 102.1 - - + +
216B ALA* 1.3 64.3 + - - +
217B TYR 3.8 2.9 - - - +
218B THR* 3.8 22.7 - - + +
236B TRP* 6.4 1.1 - - + -
238B SER* 3.8 26.9 - - - -
239B MET 3.3 7.9 - - - +
240B LEU* 3.5 22.4 - - + -
241B ALA* 4.7 0.2 - - - -
242B ARG* 5.3 0.6 + - - -
257B VAL* 4.8 5.6 - - + -
259B THR* 4.3 7.2 + - - -
266B GLU* 3.3 28.1 + - + +
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Residues in contact with ALA 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B ALA* 4.5 1.4 - - - +
210B LYS 4.1 11.4 + - - -
211B LYS* 4.7 4.8 + - - +
214B LYS 3.5 4.6 + - - -
215B TYR* 1.3 73.6 - - - +
217B TYR* 1.3 81.4 + - + +
239B MET* 2.6 25.1 + - + +
240B LEU 3.7 5.8 - - - +
241B ALA* 3.6 22.4 - - + -
242B ARG* 6.2 0.4 - - - +
253B GLY* 5.6 1.3 - - - -
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Residues in contact with TYR 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B VAL* 4.8 3.4 - - + -
208B PHE 3.9 7.0 - - - +
209B ALA* 4.5 19.1 - - + -
210B LYS 4.9 2.2 - - - +
215B TYR* 3.8 3.2 - - - +
216B ALA* 1.3 96.2 - - + +
218B THR* 1.3 67.4 + - - +
238B SER* 3.6 1.7 - - - -
239B MET* 3.0 41.6 + - + +
372B LEU* 3.8 18.2 - - + -
375B ALA* 4.4 7.7 + - + -
376B ALA* 3.5 46.4 + - + -
382B LEU* 4.9 17.3 - - + -
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Residues in contact with THR 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B TYR 3.6 1.2 - - - +
207B VAL* 3.5 4.3 - - - +
208B PHE* 3.2 60.0 + - + -
210B LYS* 4.5 8.0 - - + +
215B TYR* 3.8 22.2 - - + +
217B TYR* 1.3 80.2 + - - +
219B GLY* 1.3 73.2 + - - +
220B GLU 4.1 0.3 + - - -
236B TRP* 4.1 17.7 - - + -
237B VAL 3.5 4.0 - - - -
238B SER* 3.8 14.6 + - - +
372B LEU* 3.9 4.9 - - - -
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Residues in contact with GLY 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B VAL* 4.8 6.3 - - - -
206B TYR 3.5 8.3 - - - -
207B VAL* 4.6 4.5 - - - -
218B THR* 1.3 74.2 - - - +
220B GLU* 1.3 61.9 + - - -
235B ILE 3.8 0.3 - - - +
236B TRP* 3.2 4.9 - - - -
237B VAL* 2.5 48.1 + - - +
368B MET* 4.1 7.7 - - - +
372B LEU* 3.9 8.3 - - - +
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Residues in contact with GLU 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B MET* 3.1 28.6 - - - +
204B THR 3.8 1.4 - - - +
205B VAL* 3.6 2.4 - - - +
206B TYR* 3.3 35.9 + - + +
208B PHE* 3.5 19.1 - - + -
218B THR 4.0 0.8 - - - -
219B GLY* 1.3 73.1 - - - -
221B CYS* 1.3 68.6 + - - +
222B ARG* 3.5 17.5 - - + +
234B THR 4.9 0.9 - - - +
235B ILE 3.7 3.4 - - - +
236B TRP* 3.6 29.7 + - + +
385B ARG* 3.3 26.0 + - - -
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Residues in contact with CYS 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B ASN* 4.3 5.6 - - - -
204B THR 4.0 28.5 - - - +
205B VAL* 4.3 4.5 - - - -
220B GLU* 1.3 79.2 - - - +
222B ARG* 1.3 69.0 + - - +
223B SER* 3.6 4.4 + - - -
234B THR 4.4 0.9 - - - -
235B ILE* 2.8 37.2 + - + +
348B LEU* 4.4 8.5 - - - +
350B HIS* 4.7 1.8 - - - -
364B PHE* 4.2 24.9 - - - -
368B MET* 3.6 23.8 - - + -
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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