Contacts of the strand formed by residues 249 - 255 (chain B) in PDB entry 1RE3
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 TRP 249 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211B CYS* 3.4 2.7 - - - -
240B CYS* 3.3 7.1 - - - -
241B ASP* 2.9 50.3 + - + +
244B THR* 2.7 38.7 + - + -
245B GLU* 3.6 9.9 + - - -
247B GLY 3.8 6.7 - - - -
248B GLY* 1.3 76.9 - - - +
250B THR* 1.3 61.0 + - - +
251B VAL 3.7 0.5 + - - -
309B GLU* 3.9 10.1 - - + -
311B LEU* 3.7 26.8 - - + +
325B HIS* 3.7 23.3 - + - -
453B LYS* 3.7 39.0 - - + -
454B ILE* 3.4 22.2 - - - -
455B ARG* 3.5 51.2 - - + +
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Residues in contact with THR 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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210B GLU* 3.8 7.9 + - + +
211B CYS* 3.1 34.1 + - - +
212B GLU 4.7 0.2 + - - -
227B ILE* 4.6 5.6 - - + -
238B VAL* 3.3 29.6 - - + -
248B GLY 3.7 1.4 + - - -
249B TRP* 1.3 68.8 - - - +
251B VAL* 1.3 57.9 + - - +
252B ILE* 3.1 22.4 + - + +
294B LEU* 4.9 0.9 - - + -
302B LEU* 4.2 13.9 - - + -
453B LYS* 4.3 1.1 - - - -
454B ILE* 3.0 42.1 + - - -
455B ARG* 5.7 0.3 - - - -
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Residues in contact with VAL 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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238B VAL* 3.4 10.4 - - - +
239B TYR* 3.1 38.5 + - + +
241B ASP* 4.7 6.3 - - + +
250B THR* 1.3 68.9 - - - +
252B ILE* 1.3 63.1 + - - +
253B GLN 3.8 19.3 - - - +
254B ASN* 4.1 10.8 - - + -
289B PRO* 5.6 2.2 - - + -
292B TYR* 2.7 50.9 + - + +
294B LEU* 4.5 1.2 - - - +
451B SER* 5.6 0.2 - - - -
452B MET 3.7 5.4 - - - +
453B LYS* 4.1 26.5 - - + -
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Residues in contact with ILE 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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250B THR* 3.1 27.4 - - + +
251B VAL* 1.3 78.3 - - - +
253B GLN* 1.3 61.8 + - + +
292B TYR* 4.5 2.5 - - - -
293B TRP* 3.7 7.4 - - + -
294B LEU* 3.0 45.5 + - + -
299B ILE* 3.6 40.8 - - + -
302B LEU* 4.0 0.4 - - + -
329B PHE* 5.6 2.5 - - + -
452B MET* 2.7 34.8 + - + +
454B ILE* 3.5 39.9 - - + -
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Residues in contact with GLN 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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251B VAL* 3.7 4.8 - - - +
252B ILE* 1.3 79.2 - - - +
254B ASN* 1.3 66.9 + - - +
255B ARG* 3.4 11.9 - - - +
262B PHE* 4.4 2.0 - - + -
292B TYR 3.3 9.4 - - - +
293B TRP* 3.3 24.0 - - + -
412B PRO* 3.0 35.9 - - - +
413B ASN* 3.0 21.9 - - - +
450B MET* 3.8 3.4 + - - +
451B SER* 3.2 30.4 - - - +
452B MET* 2.8 42.6 + - + +
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Residues in contact with ASN 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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251B VAL* 4.1 14.5 - - + +
253B GLN* 1.3 78.2 - - - +
255B ARG* 1.3 72.5 + - - +
256B GLN* 3.3 30.7 + - - +
289B PRO* 4.1 15.0 - - + +
290B GLY 2.9 26.1 + - - +
291B GLU* 3.1 23.4 - - - +
292B TYR* 3.1 15.2 + - + +
450B MET 3.6 4.2 - - - +
451B SER* 3.3 19.2 - - - -
453B LYS* 5.8 0.3 - - - -
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Residues in contact with ARG 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 GLN* 3.4 18.6 - - - +
254B ASN* 1.3 78.8 - - - +
256B GLN* 1.3 66.7 + - - +
260B VAL 4.5 5.1 + - - -
262B PHE* 3.2 52.7 - - - +
291B GLU* 3.4 11.9 + - - +
412B PRO 2.8 32.8 + - - +
413B ASN* 3.4 11.3 - - - +
414B GLY 2.7 30.5 + - - +
415B ARG* 4.6 0.4 - - - +
416B TYR* 3.9 34.3 - - + +
435B VAL* 3.8 8.2 - - + +
449B LYS* 3.6 4.4 - - - +
450B MET* 2.7 42.5 + - + +
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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