Contacts of the strand formed by residues 206 - 211 (chain B) in PDB entry 5KYT
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 LYS 206 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120B ILE* 4.1 5.6 - - - -
197B ASN* 3.3 12.3 + - - -
198B SER* 2.8 32.1 + - - +
199B SER 3.0 28.3 + - - -
204B LEU 4.1 7.8 + - - +
205B PRO* 1.3 78.2 - - - +
207B GLY* 1.3 61.1 + - - +
401B TYR* 3.6 50.8 + - + -
404B ASN* 4.4 12.1 - - + +
407B ALA* 4.0 18.4 - - + -
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Residues in contact with GLY 207 (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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120B ILE* 3.9 27.4 - - - +
195B ILE* 3.9 9.9 - - - -
196B MET 3.5 4.0 - - - -
197B ASN* 4.4 4.7 - - - -
206B LYS* 1.3 73.5 - - - +
208B VAL* 1.3 61.0 + - - -
209B ALA 3.8 0.4 - - - -
401B TYR* 3.1 6.9 - - - -
402B VAL* 2.7 35.0 + - - +
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Residues in contact with VAL 208 (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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194B LEU 3.4 1.9 - - - +
195B ILE* 3.2 6.0 - - - +
196B MET 2.6 40.7 + - - +
198B SER* 3.6 31.9 - - - +
207B GLY* 1.3 71.8 - - - -
209B ALA* 1.3 59.6 + - - +
210B LEU* 3.5 9.8 + - + +
343B THR* 3.7 30.7 - - + +
344B GLU* 3.9 5.2 - - + -
398B MET* 3.6 29.4 - - + -
400B GLY 4.3 2.5 - - - -
401B TYR* 3.6 18.6 - - + -
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Residues in contact with ALA 209 (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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192B ILE* 4.1 11.4 - - + -
194B LEU 3.7 4.0 - - - -
195B ILE* 4.6 3.1 - - + +
207B GLY 3.7 2.0 + - - -
208B VAL* 1.3 71.1 - - - +
210B LEU* 1.3 59.9 + - - +
211B PRO* 3.9 1.3 - - - -
398B MET* 3.4 5.9 - - - +
399B SER* 3.0 38.4 + - - +
400B GLY 3.2 19.4 + - - +
402B VAL* 4.1 8.3 - - + -
604B EDO 4.0 25.6 - - - +
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Residues in contact with LEU 210 (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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192B ILE* 3.9 2.8 - - - +
193B ALA* 2.9 25.1 + - + +
194B LEU* 2.8 20.6 + - + +
196B MET* 3.5 29.2 - - + -
208B VAL* 3.7 21.5 - - + +
209B ALA* 1.3 78.9 - - - +
211B PRO* 1.3 67.1 - - - +
214B THR* 3.7 11.9 - - + +
250B PHE* 3.6 28.0 - - + -
343B THR 4.1 8.7 - - - +
346B THR* 3.4 26.5 - - - +
396B MET 4.4 0.2 - - - +
398B MET* 3.8 16.2 - - + +
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Residues in contact with PRO 211 (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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188B ARG 3.6 6.7 - - - +
189B ASP 3.3 27.8 - - - +
191B THR 3.4 8.5 - - - +
192B ILE* 4.0 8.5 - - + -
193B ALA* 4.3 1.6 - - - +
209B ALA 3.5 9.6 - - - +
210B LEU* 1.3 88.8 - - - +
212B HIS* 1.3 67.1 + - - +
213B ARG* 4.1 19.7 - - - +
214B THR* 3.1 30.7 + - + -
215B ALA* 3.9 1.0 + - - +
398B MET 4.7 0.2 - - - -
399B SER* 3.8 28.0 - - - +
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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