Contacts of the strand formed by residues 251 - 264 (chain C) in PDB entry 2RJF
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 HIS 251 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248C ASP* 3.0 36.9 + - + +
250C GLN* 1.3 91.4 - - + +
252C PRO* 1.3 60.2 - - - +
253C SER* 3.0 13.8 + - - +
254C MET* 3.0 43.4 + - + +
384C ASP* 5.4 4.9 - - + -
385C THR* 3.6 26.6 - - + +
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Residues in contact with PRO 252 (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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247C ILE* 3.7 16.5 - - + +
248C ASP 3.6 8.1 - - - +
249C PRO* 4.0 13.0 - - + +
250C GLN 3.7 5.6 - - - +
251C HIS* 1.3 84.9 - - - +
253C SER* 1.3 59.7 + - - +
254C MET 3.4 0.7 - - - -
376C LEU* 4.5 4.9 - - + -
384C ASP 4.2 15.7 - - - +
385C THR* 4.7 5.8 - - - +
387C ASP* 3.5 24.0 - - + +
388C TYR* 4.9 1.1 - - - -
389C TRP* 2.9 43.4 + - + -
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Residues in contact with SER 253 (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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251C HIS 4.6 1.4 + - - -
252C PRO* 1.3 80.2 - - - +
254C MET* 1.3 71.6 + - - +
255C TYR* 3.8 17.9 - - - -
368C THR* 5.5 0.4 - - - -
369C ASP* 4.9 2.3 - - - +
376C LEU* 3.6 17.0 - - - +
384C ASP* 3.7 25.1 - - - +
387C ASP* 3.4 20.8 + - - -
389C TRP* 5.5 0.7 - - - -
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Residues in contact with MET 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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247C ILE* 3.3 7.1 - - - +
248C ASP 3.1 25.8 + - - -
251C HIS* 3.0 37.0 + - + +
253C SER* 1.3 91.0 - - - +
255C TYR* 1.3 62.6 + - - +
256C PHE* 3.9 22.2 - - + -
302C LYS 5.6 0.2 - - - -
304C GLN* 3.5 41.3 - - + +
384C ASP* 6.3 2.0 - - - -
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Residues in contact with TYR 255 (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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245C GLU* 5.4 1.6 - - + -
246C GLY* 3.3 16.4 - - - +
247C ILE* 3.3 31.0 - - + +
253C SER 3.8 15.3 - - - -
254C MET* 1.3 75.9 - - - +
256C PHE* 1.3 57.5 - - - +
291C HIS* 4.0 9.3 + + - -
295C TRP* 3.6 37.4 - + + -
296C PHE* 5.8 0.9 - - + -
301C HIS* 3.6 23.7 + + + -
302C LYS 3.6 24.5 + - - +
303C LEU* 3.9 11.7 - - + -
304C GLN* 2.8 37.0 + - - +
369C ASP* 2.8 22.7 + - - -
371C VAL* 4.0 1.6 - - - +
389C TRP* 3.5 17.0 - + - -
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Residues in contact with PHE 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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245C GLU* 3.2 4.2 - - - -
246C GLY 2.8 32.6 + - - +
248C ASP* 3.6 35.2 - - + -
254C MET* 3.9 29.2 - - + -
255C TYR* 1.3 76.7 - - - +
257C ILE* 1.3 63.8 + - - +
258C LEU* 3.6 3.0 + - + +
272C PHE* 3.6 39.9 - + + -
275C TYR* 4.4 28.9 - + - -
303C LEU* 3.8 8.1 - - - -
304C GLN* 3.5 35.0 - - + -
305C PRO 4.9 1.8 - - - -
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Residues in contact with ILE 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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243C LYS* 4.8 1.3 - - + -
244C LEU 3.4 4.3 - - - +
256C PHE* 1.3 73.9 - - - +
258C LEU* 1.3 68.5 - - - +
272C PHE* 3.8 1.9 - - - +
273C ASP* 3.2 44.8 + - + +
303C LEU* 3.9 20.9 - - + -
304C GLN 4.0 7.3 + - - +
305C PRO* 4.4 0.4 - - + -
306C PRO* 3.2 34.5 - - + -
314C PHE* 3.2 31.2 - - + -
316C TRP* 3.7 27.6 - - + -
319C TYR* 4.1 7.9 - - + -
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Residues in contact with LEU 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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243C LYS* 3.3 4.9 - - - +
244C LEU* 2.8 44.9 + - + +
245C GLU 4.5 1.1 - - - -
246C GLY* 3.7 29.2 - - - +
247C ILE 4.8 0.2 - - - +
256C PHE* 3.7 9.6 - - + +
257C ILE* 1.3 79.4 - - - +
259C THR* 1.3 63.1 + - - +
270C LEU* 3.9 21.5 - - + -
271C HIS 3.1 15.9 - - - +
272C PHE* 3.5 39.9 - - + -
273C ASP* 3.6 1.1 - - - -
281C PHE* 3.9 27.6 - - + -
290C ILE* 4.8 0.7 - - + -
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Residues in contact with THR 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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241C GLY* 3.6 34.1 - - - +
242C MET 3.3 3.8 - - - -
243C LYS* 2.9 22.0 + - - +
258C LEU* 1.3 72.6 + - - +
260C VAL* 1.3 69.9 + - - +
261C ALA* 3.2 1.8 + - - -
270C LEU* 3.4 6.1 - - - -
271C HIS* 2.9 42.1 + - - +
273C ASP* 2.5 24.5 + - - -
347E VAL* 5.8 4.3 - - + +
348E GLY* 6.4 2.2 - - - -
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Residues in contact with VAL 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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238C PHE* 4.0 18.8 - - + -
239C LYS 3.4 25.1 - - - +
240C LEU* 3.7 2.9 - - - +
241C GLY* 2.8 27.9 + - - +
242C MET* 2.9 22.3 + - + +
244C LEU* 3.8 19.7 - - + -
259C THR* 1.3 72.8 - - - +
261C ALA* 1.3 60.0 + - - +
262C GLU 3.7 9.6 - - - +
263C VAL* 3.6 31.4 - - + -
268C LEU* 4.1 13.5 - - + -
269C ARG 3.7 4.9 - - - +
270C LEU* 4.1 1.6 - - + -
347E VAL* 4.5 3.5 - - - +
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Residues in contact with ALA 261 (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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240C LEU* 3.7 10.3 - - - +
259C THR* 3.2 2.7 + - - -
260C VAL* 1.3 72.8 - - - +
262C GLU* 1.3 63.4 + - - +
269C ARG* 2.8 42.2 + - - +
271C HIS* 4.2 14.8 - - + -
280C ASP* 4.0 8.1 - - - +
346E GLN* 4.8 5.1 - - + +
347E VAL* 4.1 26.1 + - + +
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Residues in contact with GLU 262 (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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240C LEU* 3.6 7.2 - - + +
260C VAL* 3.5 1.7 - - - +
261C ALA* 1.3 84.0 - - - +
263C VAL* 1.3 73.5 + - - +
264C CYS* 4.7 6.1 - - - +
268C LEU* 3.4 5.0 - - - +
269C ARG* 2.8 71.4 + - + +
282C TRP* 3.7 23.2 - - + -
464C ALA* 5.9 0.3 - - - +
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Residues in contact with VAL 263 (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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236C ASN* 3.3 29.8 - - - +
238C PHE* 3.6 19.3 - - + +
240C LEU* 4.0 6.4 - - + +
260C VAL* 3.6 21.1 - - + -
262C GLU* 1.3 88.3 - - - +
264C CYS* 1.3 65.5 + - - +
265C GLY 3.9 3.4 - - - +
267C ARG 3.5 3.1 - - - +
268C LEU* 4.4 6.7 - - + +
282C TRP* 4.8 0.2 - - - -
297E GLU 4.5 1.8 - - - +
298E LYS 3.4 16.0 - - - +
299E THR* 3.5 12.7 + - - +
300E GLY* 3.5 30.1 - - - +
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Residues in contact with CYS 264 (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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262C GLU* 4.7 5.2 - - - +
263C VAL* 1.3 76.1 - - - +
265C GLY* 1.3 66.1 + - - +
267C ARG* 2.9 23.7 + - - +
282C TRP* 4.0 21.9 - - + -
464C ALA 5.6 0.7 - - - -
511C GLY 4.7 1.3 - - - -
512C HIS* 3.2 36.2 - - + +
513C PRO* 3.6 25.6 - - - -
298E LYS 3.4 2.9 - - - -
299E THR* 6.0 0.2 - - - -
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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