Contacts of the strand formed by residues 268 - 275 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232B SER* 3.3 34.6 - - - -
233B LEU* 4.5 5.2 - - - -
234B TRP* 3.7 23.6 - - - -
258B ASN* 3.5 27.6 - - - +
259B ILE 3.0 19.3 - - - +
260B SER* 4.5 1.3 - - - -
261B ILE* 3.7 6.5 + - - +
264B TYR* 4.1 5.2 + - - +
265B PRO 3.7 6.1 + - - +
266B CYS 3.2 5.8 + - - -
267B GLY* 1.3 79.6 - - - +
269B ILE* 1.3 63.4 + - - +
260C SER* 4.2 6.1 - - - +
267C GLY 6.1 0.4 - - - +
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Residues in contact with ILE 269 (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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102B TYR* 3.8 19.3 - - + -
229B GLN* 3.5 23.3 - - + +
230B CYS 4.4 1.1 - - - +
231B GLU* 3.8 14.1 - - - +
232B SER* 4.6 0.4 - - - +
258B ASN* 3.3 4.0 - - - +
259B ILE* 2.9 37.7 + - + +
261B ILE* 4.0 8.1 - - + -
264B TYR* 3.8 23.6 - - + -
268B CYS* 1.3 77.6 - - - +
270B GLY* 1.3 70.7 + - - +
501B JFQ 3.2 39.7 - - + -
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Residues in contact with GLY 270 (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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106B MET* 5.1 0.7 - - - +
229B GLN* 3.6 5.9 - - - +
230B CYS 2.8 33.6 + - - -
231B GLU 2.8 12.9 + - - -
256B TYR* 3.2 12.7 + - - -
257B ALA 3.1 11.4 - - - -
258B ASN* 4.4 1.1 - - - -
269B ILE* 1.3 81.7 - - - +
271B ILE* 1.3 64.4 + - - +
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Residues in contact with ILE 271 (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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105B MET* 4.0 25.6 - - + +
106B MET* 4.2 13.0 - - - +
109B VAL* 4.5 10.3 - - + -
227B VAL* 3.5 25.4 - - + -
228B ALA 3.5 6.5 - - - +
256B TYR* 3.4 9.3 - - - -
257B ALA* 2.8 45.4 + - + +
259B ILE* 3.6 39.7 - - + -
270B GLY* 1.3 75.1 - - - +
272B LEU* 1.3 61.4 + - - +
273B CYS* 3.5 22.7 + - - -
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Residues in contact with LEU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B TYR* 3.7 34.5 - - + +
226B CYS 3.7 1.2 - - - +
227B VAL* 3.1 5.7 - - - -
228B ALA* 2.8 42.5 + - + +
230B CYS* 3.8 17.0 - - + +
243B MET* 3.9 29.2 - - + +
244B ILE* 3.7 32.8 - - + +
247B ALA* 4.5 0.9 - - + -
254B VAL* 3.8 16.6 - - + -
255B GLU 3.8 5.8 - - - +
256B TYR* 4.6 6.7 - - + -
271B ILE* 1.3 69.6 - - - +
273B CYS* 1.3 59.0 + - - +
274B CYS* 4.1 12.6 - - - -
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Residues in contact with CYS 273 (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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109B VAL* 4.6 3.4 - - - -
226B CYS 3.7 3.6 - - - -
227B VAL* 4.1 9.2 - - - -
253B LYS 3.8 1.4 - - - +
254B VAL* 3.3 6.6 - - - +
255B GLU* 2.9 52.8 + - + +
271B ILE* 3.5 35.2 - - - -
272B LEU* 1.3 71.8 - - - +
274B CYS* 1.3 59.7 + - - +
275B SER* 5.0 0.4 - - - -
281B LEU* 3.6 18.2 - - + -
308B PHE* 3.7 27.4 - - + -
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Residues in contact with CYS 274 (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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213B TYR* 4.2 14.8 - - - -
225B TYR* 3.4 7.3 - - - +
226B CYS* 2.8 40.7 + - + +
247B ALA* 3.8 28.3 - - - -
251B PHE* 3.7 30.6 - - + -
253B LYS 3.7 3.6 - - - -
254B VAL* 4.6 1.3 - - - +
272B LEU* 4.1 17.9 - - - -
273B CYS* 1.3 76.9 - - - +
275B SER* 1.3 61.6 + - - +
281B LEU* 3.8 1.6 - - - +
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Residues in contact with SER 275 (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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224B GLY 4.3 0.4 - - - -
225B TYR* 3.3 28.6 - - - -
251B PHE* 3.5 6.3 - - - +
252B LYS 3.2 7.3 + - - -
253B LYS* 2.8 34.1 + - - +
255B GLU* 4.4 1.0 + - - -
273B CYS 5.0 0.2 - - - -
274B CYS* 1.3 73.5 - - - +
276B LYS* 1.3 60.8 + - - +
277B THR* 3.8 10.5 - - - -
280B GLY* 3.2 30.9 - - - -
281B LEU* 3.4 11.8 + - - +
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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