Contacts of the strand formed by residues 268 - 275 (chain C) 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 CYS 268 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260B SER* 4.1 8.1 - - - +
232C SER* 3.5 38.1 - - - -
233C LEU* 4.4 8.3 - - - -
234C TRP* 3.7 25.1 - - - -
258C ASN* 3.4 27.8 - - - +
259C ILE 3.0 15.5 - - - +
260C SER* 4.6 1.1 - - - -
261C ILE* 3.7 5.0 + - - -
264C TYR* 4.1 4.4 + - - +
265C PRO 3.6 5.4 + - - +
266C CYS 3.3 4.1 - - - +
267C GLY* 1.3 81.1 - - - +
269C ILE* 1.3 63.3 + - - +
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Residues in contact with ILE 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C TYR* 3.8 24.5 - - + -
229C GLN* 3.5 12.8 - - + +
231C GLU* 3.5 22.0 - - - +
232C SER* 5.8 0.2 - - - -
258C ASN* 3.6 4.7 - - - -
259C ILE* 2.9 37.5 + - + +
261C ILE* 3.8 9.0 - - + -
264C TYR* 3.7 26.7 - - + -
268C CYS* 1.3 74.8 - - - +
270C GLY* 1.3 68.7 + - - +
501C JFQ 3.3 43.5 - - + -
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Residues in contact with GLY 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C TYR* 5.7 0.2 - - - -
106C MET* 5.1 0.9 - - - +
229C GLN* 3.6 5.9 - - - +
230C CYS 2.8 28.4 + - - -
231C GLU 2.6 14.8 + - - -
256C TYR* 3.2 22.6 + - - -
257C ALA 3.0 11.2 - - - -
258C ASN* 4.3 1.3 - - - -
269C ILE* 1.3 79.5 - - - +
271C ILE* 1.3 60.0 - - - +
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Residues in contact with ILE 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C MET* 3.8 28.7 - - + +
106C MET* 4.0 17.7 - - - +
109C VAL* 4.4 10.8 - - + -
227C VAL* 3.5 31.4 - - + -
228C ALA 3.6 3.8 - - - +
229C GLN* 4.9 0.2 - - - +
256C TYR* 3.3 8.9 - - - -
257C ALA* 2.7 45.0 + - + +
259C ILE* 3.6 36.1 - - + -
270C GLY* 1.3 71.9 - - - +
272C LEU* 1.3 61.7 + - - +
273C CYS* 3.5 13.7 + - - -
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Residues in contact with LEU 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C TYR* 3.6 38.4 - - + +
226C CYS 3.8 0.5 - - - +
227C VAL* 3.1 7.6 - - - +
228C ALA* 2.9 39.2 + - + +
230C CYS* 3.8 19.6 - - + +
243C MET* 4.1 24.5 - - + +
244C ILE* 3.6 37.7 - - + +
247C ALA* 4.4 0.7 - - + -
254C VAL* 3.8 18.8 - - + -
255C GLU 3.8 3.4 - - - +
256C TYR* 4.5 3.1 - - + -
271C ILE* 1.3 70.7 - - - +
273C CYS* 1.3 58.2 + - - +
274C CYS* 3.9 10.7 - - - -
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Residues in contact with CYS 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C VAL* 4.5 6.3 - - - -
226C CYS 3.8 3.1 - - - -
227C VAL* 3.9 9.2 - - - -
253C LYS 3.7 1.2 - - - +
254C VAL* 3.2 7.8 - - - +
255C GLU* 2.7 49.9 + - + +
257C ALA* 4.5 0.4 - - - -
271C ILE* 3.5 33.0 - - - -
272C LEU* 1.3 73.7 - - - +
274C CYS* 1.3 60.1 + - - +
275C SER* 5.1 0.2 - - - -
281C LEU* 3.6 18.2 - - + -
308C PHE* 3.6 33.0 - - + -
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Residues in contact with CYS 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C TYR* 4.3 7.6 - - - -
225C TYR* 3.4 8.0 - - - +
226C CYS* 2.7 41.3 + - + +
228C ALA* 6.2 0.2 - - - -
247C ALA* 3.7 28.0 - - - -
251C PHE* 3.5 34.9 - - + -
253C LYS 3.7 3.8 - - - -
254C VAL* 4.8 0.4 - - - +
272C LEU* 3.9 20.0 - - - -
273C CYS* 1.3 77.2 - - - +
275C SER* 1.3 63.3 + - - +
281C LEU* 3.8 2.2 - - - +
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Residues in contact with SER 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C GLY 4.4 0.4 - - - -
225C TYR* 3.3 27.4 - - - -
251C PHE* 3.5 7.0 - - - +
252C LYS 3.4 6.1 + - - -
253C LYS* 2.9 33.5 + - - +
255C GLU* 4.5 0.9 + - - -
273C CYS 5.1 0.2 - - - -
274C CYS* 1.3 73.6 - - - +
276C LYS* 1.3 61.2 + - - +
277C THR* 3.7 15.3 - - - -
280C GLY* 3.2 30.3 - - - -
281C LEU* 3.4 8.1 + - - +
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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