Contacts of the strand formed by residues 253 - 260 (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 LYS 253 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251C PHE 3.3 0.4 - - - -
252C LYS* 1.3 79.2 - - - +
254C VAL* 1.3 67.9 + - - +
255C GLU* 3.3 27.5 - - + +
273C CYS 3.7 1.4 - - - +
275C SER* 2.9 35.1 + - - +
277C THR 3.5 18.6 - - - +
278C ASP* 3.7 32.3 + - - +
279C THR 4.9 1.8 - - - -
280C GLY* 3.7 21.1 - - - +
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Residues in contact with VAL 254 (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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244C ILE* 3.9 23.1 - - + +
247C ALA* 3.7 48.5 - - + +
248C LYS* 3.7 18.8 - - + +
251C PHE* 3.8 12.1 - - + +
252C LYS 5.2 0.2 - - - -
253C LYS* 1.3 83.0 - - - +
255C GLU* 1.3 64.8 + - - +
272C LEU* 3.8 19.7 - - + -
273C CYS 3.2 6.1 - - - +
274C CYS* 4.9 1.1 - - - -
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Residues in contact with GLU 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C ILE* 5.7 1.1 - - - -
253C LYS* 3.3 37.9 + - + +
254C VAL* 1.3 80.9 - - - +
256C TYR* 1.3 60.8 + - - +
272C LEU* 3.7 7.3 - - - +
273C CYS* 2.7 37.1 + - + +
275C SER* 4.5 1.4 + - - -
279C THR 4.5 1.7 - - - +
280C GLY* 3.5 3.6 - - - -
281C LEU* 2.7 37.5 + - - +
282C THR* 3.5 22.4 + - + +
308C PHE* 3.9 15.9 - - + -
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Residues in contact with TYR 256 (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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230C CYS* 3.0 29.1 + - + -
231C GLU 2.9 26.2 + - - -
233C LEU* 3.9 12.4 + - + -
240C ILE* 3.4 37.5 - - + +
244C ILE* 4.3 17.5 - - + -
255C GLU* 1.3 77.6 - - - +
257C ALA* 1.3 70.6 + - - +
258C ASN* 5.0 0.6 + - - -
270C GLY* 3.2 12.1 + - - -
271C ILE 3.3 12.1 - - - -
272C LEU* 4.5 5.6 - - - -
308C PHE* 3.5 17.6 - - - +
310C LEU* 3.7 41.6 - - + +
314C LEU* 4.0 16.4 - - + -
318C ILE* 4.5 4.3 - - + -
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Residues in contact with ALA 257 (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* 5.6 0.4 - - + -
256C TYR* 1.3 77.4 - - - +
258C ASN* 1.3 60.0 - - - +
270C GLY* 3.0 5.4 - - - -
271C ILE* 2.7 57.6 + - + -
307C ALA* 3.3 23.3 - - + +
308C PHE* 3.8 27.6 - - + -
310C LEU* 4.6 0.2 - - - -
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Residues in contact with ASN 258 (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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260B SER* 4.5 13.1 + - - -
105C MET* 5.3 0.3 - - - +
233C LEU* 3.6 23.5 + - + +
256C TYR* 5.0 0.9 - - + -
257C ALA* 1.3 74.8 - - - +
259C ILE* 1.3 66.8 + - - +
260C SER* 4.4 0.4 + - - +
268C CYS* 3.4 30.8 - - - +
269C ILE 3.3 17.8 - - - +
270C GLY* 4.1 2.0 + - - -
298C TYR* 4.5 3.8 + - - -
307C ALA* 2.9 33.1 + - - +
310C LEU* 4.2 14.8 - - + +
311C PRO* 5.7 2.0 - - + +
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Residues in contact with ILE 259 (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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101C ALA* 3.7 24.7 - - + +
102C TYR* 4.2 20.2 - - + +
105C MET* 3.7 23.3 - - + -
106C MET* 4.5 1.8 - - + -
257C ALA* 5.8 0.2 - - + -
258C ASN* 1.3 82.2 - - - +
260C SER* 1.3 73.0 + - - +
261C ILE* 3.7 5.2 + - + +
268C CYS* 3.0 28.7 - - - +
269C ILE* 2.9 33.5 + - + +
271C ILE* 3.6 34.5 - - + -
298C TYR* 3.7 13.2 - - + +
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Residues in contact with SER 260 (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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233B LEU* 5.1 1.2 - - - +
234B TRP* 2.9 27.6 + - - -
258B ASN* 4.3 13.2 + - - -
266B CYS 5.2 0.3 + - - -
268B CYS* 4.2 12.6 - - - +
311B PRO* 5.7 2.7 - - - -
101C ALA* 3.4 7.6 - - - +
258C ASN 4.4 0.2 + - - -
259C ILE* 1.3 68.0 - - - +
261C ILE* 1.3 65.2 + - - +
267C GLY 3.6 9.2 + - - -
268C CYS* 4.5 2.0 - - - +
298C TYR* 3.1 34.7 + - - -
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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