Contacts of the strand formed by residues 248 - 255 (chain B) in PDB entry 1SHY
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 248 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180B LEU 4.9 6.7 - - - +
181B GLY* 5.7 2.5 - - - -
200B THR* 4.0 19.9 - - + +
246B PRO* 4.1 22.0 - - - +
247B ILE* 1.3 71.6 - - - +
249B TYR* 1.3 61.9 + - - +
250B VAL* 3.9 4.9 + - + -
263B THR* 3.1 9.0 + - - -
264B VAL* 3.0 49.7 + - + +
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Residues in contact with TYR 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B GLY 5.0 0.8 - - - -
182B ALA* 4.9 3.1 + - - +
183B LYS* 3.4 35.8 + - + +
198B GLY* 3.6 14.4 - - - +
199B ASN 3.3 39.0 - - - -
200B THR* 3.7 6.5 + - - +
213B SER* 3.4 31.6 + - - -
214B ILE* 4.1 15.3 - - + +
247B ILE* 3.2 51.2 - - + +
248B LYS* 1.3 74.0 - - - +
250B VAL* 1.3 61.9 + - - +
251B HIS 3.6 0.7 - - - -
261B PHE* 4.2 15.0 - + + -
262B LEU 3.7 5.4 - - - +
263B THR* 3.9 11.2 - - - -
279B ILE* 4.4 13.8 - - + +
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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
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183B LYS* 3.3 19.5 + - - +
248B LYS* 4.6 6.5 - - + +
249B TYR* 1.3 73.7 - - - +
251B HIS* 1.3 65.8 + - + +
262B LEU 2.9 10.6 + - - +
263B THR* 4.5 1.8 - - - +
264B VAL* 4.1 16.8 - - + -
317B LEU* 3.8 40.6 - - + +
318B GLN 3.9 29.2 - - - +
319B ALA* 4.2 7.2 - - - +
488B PRO* 6.0 2.7 - - + +
489B GLU* 5.0 1.0 - - - +
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Residues in contact with HIS 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LYS* 4.3 11.4 - - + +
249B TYR 3.6 1.4 - - - -
250B VAL* 1.3 85.7 - - + +
252B ALA* 1.3 76.0 + - - +
253B PHE* 3.7 27.5 - + + +
261B PHE* 3.4 5.7 - - - -
262B LEU* 2.6 50.0 + - + +
320B ALA* 3.7 38.4 + - + +
321B TYR* 4.7 4.3 - + - -
322B VAL* 4.1 14.3 - - + +
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Residues in contact with ALA 252 (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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183B LYS* 4.7 10.0 - - + +
184B VAL 5.8 0.2 - - - -
185B LEU* 3.8 18.0 - - + +
251B HIS* 1.3 84.6 + - - +
253B PHE* 1.3 69.9 + - - +
260B TYR 3.1 11.7 - - - +
261B PHE* 3.3 40.4 - - + -
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Residues in contact with PHE 253 (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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185B LEU* 3.5 12.5 - - - +
251B HIS* 3.7 15.9 - - + -
252B ALA* 1.3 80.4 - - - +
254B GLU* 1.3 69.6 + - - +
255B SER* 4.2 7.9 - - - -
260B TYR* 2.8 66.5 + + + +
262B LEU* 4.5 10.8 - - + -
278B ILE* 5.4 2.7 - - + -
322B VAL* 3.7 34.8 - - + -
342B LEU* 4.2 19.1 - - + -
367B ILE* 4.0 26.5 - - + -
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Residues in contact with GLU 254 (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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185B LEU* 3.7 11.7 - - + +
187B SER* 2.9 38.9 + - - -
188B VAL 5.4 0.5 - - - +
189B LYS* 4.4 7.4 + - - +
253B PHE* 1.3 76.6 - - - +
255B SER* 1.3 66.8 + - - +
257B ASN* 5.4 4.8 - - - +
258B PHE 3.4 11.4 - - - +
259B ILE* 3.6 22.6 - - + +
283B SER* 3.5 16.9 + - - +
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Residues in contact with SER 255 (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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253B PHE* 4.0 18.9 + - - -
254B GLU* 1.3 77.9 - - - +
256B ASN* 1.3 71.5 + - - +
257B ASN 3.2 3.6 + - - +
258B PHE 3.1 10.2 + - - -
260B TYR* 3.2 20.0 + - - -
322B VAL* 5.6 1.1 - - - -
340B ASP* 3.3 25.3 + - - -
367B ILE* 3.0 27.6 - - - +
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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