Contacts of the strand formed by residues 248 - 251 (chain B) in PDB entry 1X7O
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 248 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B VAL* 4.6 10.5 - - + -
207B LEU 3.2 3.1 + - - +
208B VAL* 3.4 10.0 - - + -
209B GLY 3.0 21.2 + - - -
215B ASP* 5.1 3.4 - - + -
216B CYS* 6.6 0.2 - - - -
221B PHE* 3.4 43.3 - + + -
225B GLN* 5.3 5.6 - - - -
246B CYS* 3.8 5.4 - - - +
247B ASP* 1.3 94.5 - - + +
249B THR* 1.3 68.3 + - - +
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Residues in contact with THR 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B GLY* 3.4 12.7 + - - +
211B ASP* 3.4 39.5 - - + +
213B HIS 5.2 0.4 - - - -
214B GLY* 4.2 8.3 - - - -
215B ASP* 3.4 41.2 + - - +
216B CYS* 3.5 6.8 + - - +
243B ARG* 5.0 8.9 + - + +
246B CYS* 4.5 9.4 - - - +
248B TYR* 1.3 81.5 + - - +
250B VAL* 1.3 68.7 + - - +
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Residues in contact with VAL 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B VAL* 3.9 16.8 - - + -
209B GLY 2.9 17.7 + - - +
210B THR* 3.4 15.6 - - + +
211B ASP 3.3 22.5 + - - -
214B GLY* 4.3 3.4 - - - -
216B CYS* 3.4 10.5 - - + +
217B ASP 4.4 0.4 - - - +
218B VAL* 4.0 28.5 - - + -
221B PHE* 3.7 38.4 - - + -
223B PHE* 4.5 4.0 - - + -
229B LEU* 4.8 1.3 - - + -
248B TYR* 5.5 0.2 - - + -
249B THR* 1.3 79.2 - - - +
251B SER* 1.3 60.4 + - - +
270B ILE* 4.7 4.7 - - + -
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Residues in contact with SER 251 (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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210B THR* 6.0 0.2 - - - -
211B ASP 3.7 15.3 - - - +
212B GLU 5.4 1.3 - - - -
214B GLY* 3.4 28.7 + - - -
216B CYS 3.0 12.1 + - - -
217B ASP* 3.6 9.9 + - - +
218B VAL* 3.1 24.1 + - - -
250B VAL* 1.3 75.8 - - - +
252B ILE* 1.3 68.2 + - - +
253B PRO* 3.7 2.3 - - - +
270B ILE* 6.3 0.4 - - - -
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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