Contacts of the strand formed by residues 243 - 253 (chain B) in PDB entry 2RIB
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 243 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239B SER* 3.6 1.7 + - - -
240B VAL* 2.9 38.3 + - + +
242B GLU* 1.3 79.9 - - - +
244B ILE* 1.3 72.2 + - - +
245B PHE* 3.6 21.8 - - + -
270B SER* 3.0 12.3 + - - -
272B ARG* 4.3 10.1 - - - +
276B GLU* 2.8 38.0 + - - +
354B GLU* 2.8 45.1 + - + +
355B PHE 3.7 10.8 - - - +
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Residues in contact with ILE 244 (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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227A GLN* 3.5 26.7 - - + +
228A TYR* 3.4 41.5 - - + +
231A VAL* 3.7 27.8 - - + -
233B LEU* 3.8 19.7 - - + -
238B GLN 3.4 5.8 - - - +
239B SER* 4.4 11.9 - - - +
242B GLU 5.0 0.9 - - - +
243B LYS* 1.3 81.0 - - - +
245B PHE* 1.3 76.7 + - - +
246B LYS 4.1 0.2 + - - -
353B CYS 3.8 0.2 - - - +
354B GLU* 3.2 3.5 - - - -
355B PHE* 2.8 40.5 + - - +
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Residues in contact with PHE 245 (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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237B GLY* 3.2 4.2 - - - -
238B GLN* 2.9 35.1 + - + +
240B VAL* 4.0 20.4 - - + -
243B LYS* 3.6 14.8 - - + -
244B ILE* 1.3 76.8 - - - +
246B LYS* 1.3 59.7 + - - +
269B ALA* 3.8 24.9 - - + -
270B SER 4.0 0.7 - - - -
271B PRO* 4.4 9.9 - - + -
276B GLU* 3.3 33.0 - - + -
279B ALA* 4.1 8.7 - - + -
280B LEU* 4.0 24.9 - - + -
283B LEU* 3.8 17.9 - - + -
352B VAL* 4.2 3.1 - - + -
353B CYS 3.3 6.3 - - - +
354B GLU* 3.6 33.9 - - + -
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Residues in contact with LYS 246 (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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231A VAL* 3.0 37.9 + - + +
232A GLU* 4.2 7.5 + - - +
234A PHE* 2.6 47.5 + - + +
235A PRO* 4.5 3.7 - - - +
232B GLU* 5.3 10.7 + - - +
233B LEU* 5.7 0.2 - - + -
236B ASN* 3.4 36.3 - - - +
237B GLY* 4.4 2.7 - - - -
244B ILE* 4.1 0.4 + - + -
245B PHE* 1.3 76.0 - - - +
247B THR* 1.3 66.6 + - - +
352B VAL* 3.6 2.9 - - - -
353B CYS* 2.9 29.2 + - - -
355B PHE* 4.0 16.8 - - + -
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Residues in contact with THR 247 (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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234A PHE* 4.2 2.0 - - - -
235A PRO* 4.7 1.7 - - - +
236B ASN* 3.0 43.2 + - + +
246B LYS* 1.3 81.7 - - - +
248B ALA* 1.3 63.0 + - - +
249B GLY 3.1 9.4 + - - +
283B LEU* 4.1 11.5 - - + +
287B LYS* 3.9 28.3 - - + +
350B LEU* 3.5 19.5 - - - +
351B VAL 3.0 14.7 + - - -
352B VAL* 3.8 13.5 - - - +
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Residues in contact with ALA 248 (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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234A PHE* 3.7 25.6 - - + -
235A PRO* 4.0 19.0 - - + +
236B ASN* 6.1 0.7 - - - -
247B THR* 1.3 71.9 - - - +
249B GLY* 1.3 60.7 + - - +
250B PHE* 3.3 44.5 - - + -
351B VAL* 2.9 17.9 + - + +
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Residues in contact with GLY 249 (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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236B ASN* 5.5 1.3 - - - -
247B THR* 3.1 15.5 + - - -
248B ALA* 1.3 79.2 - - - +
250B PHE* 1.3 60.7 + - - +
287B LYS* 4.6 18.8 - - - +
350B LEU* 3.9 10.1 - - - +
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Residues in contact with PHE 250 (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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235A PRO* 4.4 15.5 - - + -
286A ALA* 5.9 6.5 - - + -
287A LYS* 6.3 1.3 - - - -
248B ALA* 3.4 39.5 - - + -
249B GLY* 1.3 79.3 - - - +
251B VAL* 1.3 67.3 + - - +
252B LYS* 3.7 27.8 - - + -
260B LEU* 3.7 31.6 - - + -
350B LEU* 3.6 3.2 - - - +
351B VAL* 3.0 27.3 + - + +
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Residues in contact with VAL 251 (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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250B PHE* 1.3 78.9 - - - +
252B LYS* 1.3 78.2 + - - +
289B GLU* 4.0 26.2 - - + +
348B LYS* 3.9 25.9 - - + +
349B ARG* 3.1 16.6 - - - +
350B LEU* 3.6 20.6 - - + +
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Residues in contact with LYS 252 (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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286A ALA 5.5 4.4 + - - -
250B PHE* 3.7 32.3 - - + -
251B VAL* 1.3 81.8 - - - +
253B PRO* 1.3 80.4 - - + +
256B GLU* 3.7 22.8 + - + +
257B ALA* 4.1 8.4 - - - +
260B LEU* 4.2 11.0 - - + -
292B PHE* 3.6 5.7 - - - -
348B LYS* 3.8 7.9 - - - -
349B ARG 3.0 24.4 + - - +
351B VAL* 3.7 14.5 - - + +
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Residues in contact with PRO 253 (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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252B LYS* 1.3 90.1 - - + +
254B PHE* 1.3 65.8 + - - +
255B THR* 3.5 3.6 - - - +
256B GLU* 3.2 33.8 + - + +
257B ALA* 2.9 19.1 + - - +
292B PHE* 4.3 0.2 - - - -
345B CYS 4.0 3.6 - - - +
346B GLY* 3.9 17.7 - - - +
347B GLU 3.2 12.1 - - - +
348B LYS* 3.9 26.2 - - + +
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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