Contacts of the strand formed by residues 278 - 284 (chain B) in PDB entry 5E9W
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 PHE 278 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200B THR* 3.7 14.1 - - + +
201B VAL 3.8 5.2 - - - -
202B LEU* 3.6 44.9 - - + -
224B VAL* 4.0 9.0 - - + -
271B PHE* 3.2 45.1 - + - -
276B MET* 3.5 27.6 - - + -
277B CYS* 1.3 72.8 - - - +
279B ASP* 1.3 63.7 + - - +
280B ILE 3.8 11.4 - - - +
281B CYS* 5.5 0.4 - - + -
303B ASN 5.2 2.5 - - - -
304B ALA 5.7 2.9 - - - -
307B ARG* 2.9 29.9 + - + -
308B LEU* 3.3 14.4 - - + +
309B SER* 2.9 27.6 + - - +
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Residues in contact with ASP 279 (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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191B VAL* 3.9 26.4 - - + +
196B LYS* 4.5 11.7 - - - +
198B ASP 3.5 6.9 - - - +
199B ILE* 3.3 16.0 - - + +
200B THR* 2.8 36.4 + - - +
278B PHE* 1.3 76.4 - - - +
280B ILE* 1.3 65.0 + - - +
308B LEU* 4.0 2.5 - - - -
309B SER* 4.3 14.0 + - - +
312B GLY* 3.2 10.2 - - - -
313B TYR 3.0 21.8 + - - -
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Residues in contact with ILE 280 (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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184B ILE 5.2 0.9 - - - +
187B PHE* 3.8 30.3 - - + +
188B LEU* 3.9 27.6 - - + +
191B VAL* 3.8 11.9 - - + -
199B ILE* 5.1 1.3 - - + -
200B THR 3.4 2.6 + - - -
201B VAL* 3.3 14.2 - - + +
202B LEU 2.8 24.3 + - - -
215B TRP* 4.3 14.4 - - + -
278B PHE* 3.8 3.6 - - - +
279B ASP* 1.3 88.1 - - + +
281B CYS* 1.3 75.2 + - - +
282B SER 4.0 2.7 - - - +
308B LEU* 4.0 3.6 - - - -
313B TYR* 3.3 15.9 - - + +
315B ILE* 4.0 20.0 - - + -
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Residues in contact with CYS 281 (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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202B LEU* 3.2 29.6 - - + -
204B LEU* 4.1 13.9 - - - -
278B PHE* 5.6 0.9 - - + -
280B ILE* 1.3 75.0 - - - +
282B SER* 1.3 63.2 + - - +
283B CYS* 3.9 0.8 + - - -
304B ALA* 3.3 50.0 - - + +
308B LEU* 3.7 4.1 - - + +
313B TYR 2.8 11.7 + - - +
314B PHE* 3.5 7.4 - - + -
315B ILE* 3.0 27.9 + - - +
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Residues in contact with SER 282 (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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184B ILE* 4.1 4.3 - - - +
202B LEU 2.8 11.4 + - - -
203B ASP* 3.4 11.9 + - - +
204B LEU 2.9 25.1 + - - -
211B ASP* 4.8 0.7 + - - -
215B TRP* 3.5 35.3 - - - -
280B ILE* 4.0 1.0 - - - -
281B CYS* 1.3 72.5 - - - +
283B CYS* 1.3 59.3 + - - +
284B GLN* 2.8 32.8 + - - +
315B ILE* 3.6 11.6 - - - +
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Residues in contact with CYS 283 (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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204B LEU* 3.7 25.8 - - + +
281B CYS* 3.9 2.0 + - - -
282B SER* 1.3 73.5 + - - +
284B GLN* 1.3 62.5 + - - +
285B PHE 3.7 0.9 + - - -
286B VAL* 3.4 33.6 + - - -
287B CYS* 3.4 26.3 - - - -
300B MET* 4.4 2.7 - - - -
304B ALA* 6.1 0.2 - - - -
314B PHE* 3.9 22.0 - - + -
315B ILE 2.9 9.2 + - - +
316B GLY* 3.1 19.4 - - - -
317B THR 3.4 5.4 + - - +
470B PHE* 4.6 1.4 - - - -
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Residues in contact with GLN 284 (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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180B LYS* 3.6 37.5 - - + +
183B LEU* 4.0 9.2 - - - +
184B ILE* 4.6 4.9 - - + +
203B ASP* 5.2 1.3 + - - +
204B LEU 4.3 0.8 + - - -
211B ASP* 3.6 9.9 - - - +
282B SER* 2.8 29.2 + - - +
283B CYS* 1.3 71.4 - - - +
285B PHE* 1.3 73.1 + - + +
286B VAL* 3.3 4.1 - - - +
315B ILE* 3.8 15.0 + - - +
316B GLY* 3.8 15.8 - - - -
317B THR* 3.0 31.3 + - - +
501B SAH 2.8 39.5 + - - +
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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