Contacts of the strand formed by residues 253 - 260 (chain B) in PDB entry 3RIE
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 253 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251B PHE 3.4 0.2 - - - -
252B LYS* 1.3 81.8 - - - +
254B VAL* 1.3 66.4 + - - +
255B GLU* 3.8 32.8 + - + +
273B CYS 3.8 1.1 - - - +
274B CYS* 3.7 0.3 - - - -
275B SER* 2.8 40.5 + - - +
277B THR 3.6 16.2 - - - +
278B ASP* 3.5 23.8 + - - +
279B THR 5.2 2.0 + - - -
280B GLY* 4.1 3.4 - - - -
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Residues in contact with VAL 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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244B ILE* 4.1 17.3 - - + +
247B ALA* 3.8 32.1 - - + +
248B LYS* 3.7 44.1 + - + +
251B PHE* 3.8 15.0 - - + +
253B LYS* 1.3 81.3 - - - +
255B GLU* 1.4 66.8 + - - +
272B LEU* 3.8 27.4 - - + -
273B CYS 3.3 7.6 - - - +
274B CYS* 4.6 1.8 - - - -
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Residues in contact with GLU 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ILE* 5.7 1.6 - - - -
253B LYS* 3.8 30.3 + - + +
254B VAL* 1.4 80.2 - - - +
256B TYR* 1.3 63.0 + - - +
272B LEU* 3.8 7.3 - - - +
273B CYS* 2.9 34.2 + - + +
275B SER* 4.4 2.3 + - - -
279B THR 4.5 1.9 - - - +
280B GLY* 3.5 5.0 - - - -
281B LEU* 2.8 35.0 + - - +
282B THR* 3.4 24.1 + - + +
308B PHE* 3.9 15.7 - - + -
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Residues in contact with TYR 256 (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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230B CYS* 3.0 24.8 + - + -
231B GLU 3.0 23.0 + - - -
233B LEU* 3.7 12.1 + - + -
240B ILE* 3.4 38.2 - - + +
244B ILE* 4.4 14.1 - - + -
255B GLU* 1.3 78.1 - - - +
257B ALA* 1.3 69.7 + - - +
258B ASN* 4.9 1.3 + - - -
270B GLY* 3.2 14.7 + - - -
271B ILE 3.4 13.5 - - - -
272B LEU* 4.6 8.7 - - + -
308B PHE* 3.4 15.8 - - - +
310B LEU* 3.6 41.0 - - + +
314B LEU* 4.0 18.4 - - + -
318B ILE* 4.5 4.0 - - + -
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Residues in contact with ALA 257 (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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109B VAL* 6.0 0.4 - - + -
256B TYR* 1.3 79.4 - - - +
258B ASN* 1.3 61.3 + - - +
270B GLY* 3.1 5.5 - - - -
271B ILE* 2.8 53.3 + - + -
307B ALA* 3.3 25.6 - - + +
308B PHE* 3.8 25.7 - - + -
310B LEU* 4.3 0.7 - - - -
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Residues in contact with ASN 258 (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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105B MET* 5.3 0.3 - - - +
233B LEU* 3.7 29.8 + - + +
256B TYR* 4.9 1.7 + - + -
257B ALA* 1.3 74.3 - - - +
259B ILE* 1.4 69.0 + - - +
260B SER* 4.5 0.6 + - - +
268B CYS* 3.5 31.1 - - - +
269B ILE 3.3 13.3 - - - +
270B GLY* 4.3 1.6 + - - -
298B TYR* 4.8 2.4 + - - -
307B ALA* 2.9 33.3 + - - +
309B LYS 6.1 0.4 - - - +
310B LEU* 4.2 6.7 - - + -
311B PRO* 5.9 1.0 - - + +
260C SER* 4.3 14.5 + - - -
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Residues in contact with ILE 259 (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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101B ALA* 3.6 25.4 - - + +
102B TYR* 4.2 19.3 - - + +
105B MET* 3.7 25.4 - - + -
106B MET* 4.3 5.2 - - + -
258B ASN* 1.4 79.8 + - - +
260B SER* 1.3 73.1 + - - +
261B ILE* 3.5 5.6 + - + +
268B CYS* 3.0 28.3 - - - +
269B ILE* 2.9 30.1 + - + +
270B GLY 5.2 0.4 - - - +
271B ILE* 3.6 33.0 - - + -
298B TYR* 3.9 9.9 - - - +
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Residues in contact with SER 260 (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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101B ALA* 3.5 9.5 - - - +
258B ASN* 4.5 1.7 + - - +
259B ILE* 1.3 70.9 - - - +
261B ILE* 1.3 64.6 + - - +
267B GLY 3.7 7.0 + - - -
268B CYS* 4.5 2.5 - - - -
298B TYR* 3.1 20.7 + - - -
233C LEU* 5.2 1.0 - - - +
234C TRP* 3.0 38.3 + - - -
258C ASN* 4.5 13.0 + - - -
266C CYS 4.8 0.9 + - - -
268C CYS* 4.1 13.9 - - - +
311C PRO* 5.9 2.2 - - - -
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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