Contacts of the strand formed by residues 253 - 260 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A PHE 3.3 0.8 - - - -
252A LYS* 1.4 82.3 - - - +
254A VAL* 1.3 65.2 + - - +
255A GLU* 4.0 27.0 + - - +
273A CYS 3.4 3.8 - - - +
274A CYS* 3.6 1.0 - - - -
275A SER* 2.9 39.8 + - - +
277A THR 3.6 18.4 - - - +
278A ASP* 3.6 33.2 + - - +
279A THR 5.4 1.4 - - - -
280A GLY* 3.8 14.8 - - - -
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Residues in contact with VAL 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A ILE* 4.1 22.5 - - + +
247A ALA* 3.6 30.3 - - + +
248A LYS* 3.6 36.7 + - + +
251A PHE* 3.9 11.7 - - + +
253A LYS* 1.3 81.8 - - - +
255A GLU* 1.3 65.5 + - - +
272A LEU* 3.6 28.7 - - + -
273A CYS 3.1 6.3 - - - +
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Residues in contact with GLU 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A ILE* 5.7 1.1 - - - -
253A LYS* 4.0 29.8 + - - +
254A VAL* 1.3 79.3 - - - +
256A TYR* 1.3 58.8 + - - +
271A ILE 3.7 0.2 - - - +
272A LEU* 3.7 6.1 - - - +
273A CYS* 2.8 37.6 + - + +
275A SER* 4.5 1.9 + - - -
279A THR 4.6 1.6 - - - +
280A GLY* 3.4 16.7 - - - -
281A LEU* 2.8 27.2 + - - +
282A THR* 3.3 27.3 + - + +
308A PHE* 3.5 18.8 - - + -
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Residues in contact with TYR 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A CYS* 3.9 17.5 - - + -
231A GLU 2.3 32.6 + - - -
233A LEU* 3.6 18.7 + - + -
240A ILE* 3.7 31.6 - - + -
244A ILE* 4.3 17.3 - - + -
255A GLU* 1.3 75.6 - - - +
257A ALA* 1.3 72.4 + - - +
258A ASN* 4.8 1.5 + - + -
269A ILE 4.4 0.2 - - - -
270A GLY* 3.2 24.5 + - - -
271A ILE 3.4 10.8 - - - -
272A LEU* 4.7 3.6 - - + -
308A PHE* 3.6 13.7 - - - +
310A LEU* 3.6 28.9 - - + +
314A LEU* 3.9 28.0 - - + -
318A ILE* 5.0 2.9 - - + +
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Residues in contact with ALA 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A VAL* 6.2 0.2 - - + -
256A TYR* 1.3 80.5 - - - +
258A ASN* 1.3 60.2 + - - +
270A GLY* 3.1 5.7 - - - -
271A ILE* 2.9 47.3 + - + -
307A ALA* 3.2 24.9 - - + +
308A PHE* 3.8 27.1 - - + -
310A LEU* 4.6 0.4 - - - -
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Residues in contact with ASN 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A MET* 5.3 0.5 - - - +
233A LEU* 3.7 28.6 - - + +
256A TYR* 4.8 2.3 + - + -
257A ALA* 1.3 74.8 - - - +
259A ILE* 1.3 68.7 + - - +
260A SER* 4.9 2.2 - - - +
268A CYS* 3.5 35.9 - - - +
269A ILE 3.6 11.1 + - - +
270A GLY* 4.4 1.3 + - - -
298A TYR* 4.9 1.7 + - - -
307A ALA* 2.9 31.8 + - - +
310A LEU* 4.4 7.2 - - + -
311A PRO* 6.1 0.4 - - + +
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Residues in contact with ILE 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ALA 3.8 21.8 - - - +
102A TYR* 4.1 29.4 - - + -
105A MET* 3.6 28.5 - - + -
106A MET* 4.2 4.9 - - + -
258A ASN* 1.3 80.1 - - - +
260A SER* 1.3 71.6 + - - +
261A ILE* 3.5 5.7 + - + +
268A CYS* 3.1 8.8 - - - +
269A ILE* 2.9 42.1 + - + +
270A GLY 5.5 0.2 - - - +
271A ILE* 3.7 29.4 - - + -
298A TYR* 4.0 10.1 - - + +
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Residues in contact with SER 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ALA* 3.7 18.5 - - - +
258A ASN* 4.9 2.6 - - - +
259A ILE* 1.3 73.1 - - - +
261A ILE* 1.3 62.9 + - - +
262A PRO* 4.5 4.7 - - - +
267A GLY 3.7 9.2 + - - -
268A CYS* 4.4 2.9 - - - -
298A TYR* 3.2 23.9 + - - -
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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