Contacts of the strand formed by residues 251 - 264 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248E ASP* 3.0 38.6 + - + +
250E GLN* 1.3 95.1 - - + +
252E PRO* 1.3 60.5 - - - +
253E SER 2.9 12.3 + - - -
254E MET* 2.9 34.4 + - + +
383E ASP* 5.5 0.4 - - - -
384E ASP* 3.1 27.4 - - - +
385E THR* 4.0 16.9 - - + +
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Residues in contact with PRO 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247E ILE* 3.5 19.0 - - + +
248E ASP 3.5 8.3 - - - +
249E PRO* 4.2 11.9 - - + +
250E GLN 3.8 5.4 - - - +
251E HIS* 1.3 85.3 - - - +
253E SER* 1.3 55.8 + - - -
254E MET 3.4 0.4 - - - -
376E LEU* 4.5 5.4 - - + -
384E ASP* 3.5 20.4 - - - +
385E THR* 4.8 4.0 - - - +
387E ASP* 3.6 23.3 - - + +
388E TYR* 5.0 1.3 - - - -
389E TRP* 3.0 40.8 + - + +
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Residues in contact with SER 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251E HIS 2.9 0.8 + - - -
252E PRO* 1.3 79.5 - - - +
254E MET* 1.3 65.9 + - - +
255E TYR* 3.9 17.0 - - - -
369E ASP* 5.0 1.4 - - - +
376E LEU* 3.6 26.8 - - - +
384E ASP* 2.6 28.3 + - - +
387E ASP* 3.6 12.5 + - - -
389E TRP* 5.5 0.4 - - - -
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Residues in contact with MET 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247E ILE* 3.3 6.1 - - - +
248E ASP* 3.0 26.6 + - - +
251E HIS* 2.9 34.1 + - + +
252E PRO 3.4 0.2 - - - -
253E SER* 1.3 87.8 - - - +
255E TYR* 1.3 62.2 + - - +
256E PHE* 3.9 23.6 - - + -
302E LYS 5.3 0.2 - - - -
304E GLN* 3.6 42.8 - - + +
384E ASP* 4.5 7.9 - - - +
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Residues in contact with TYR 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245E GLU* 5.4 2.7 - - + -
246E GLY* 3.3 19.7 - - - +
247E ILE* 3.4 33.7 - - + +
253E SER 3.9 15.3 - - - -
254E MET* 1.3 72.3 - - - +
256E PHE* 1.3 59.4 + - - +
291E HIS* 4.1 5.8 + + - -
295E TRP* 3.6 35.1 - + + -
296E PHE* 5.4 2.0 - - + -
301E HIS* 3.6 23.6 - - + -
302E LYS 3.6 23.2 + - - +
303E LEU* 3.7 10.5 - - + -
304E GLN* 2.8 36.9 + - - +
369E ASP* 2.9 22.5 + - - -
371E VAL* 3.9 2.3 - - - +
389E TRP* 3.3 19.8 - + - -
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Residues in contact with PHE 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245E GLU* 3.2 5.5 - - - +
246E GLY 2.9 31.5 + - - +
248E ASP* 3.6 34.1 - - + -
254E MET* 3.9 20.0 - - + -
255E TYR* 1.3 77.4 - - - +
257E ILE* 1.3 64.6 + - - +
258E LEU* 3.7 2.5 + - + +
272E PHE* 3.6 40.2 - + + -
275E TYR* 4.2 30.3 - + - -
303E LEU* 3.9 7.0 - - - -
304E GLN* 3.5 44.6 - - + -
305E PRO 5.6 0.2 - - - -
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Residues in contact with ILE 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243E LYS* 4.6 1.6 - - + -
244E LEU 3.5 4.0 - - - +
245E GLU* 4.6 0.2 - - - +
256E PHE* 1.3 75.0 - - - +
258E LEU* 1.3 69.2 + - - +
272E PHE* 3.8 1.6 - - - -
273E ASP* 3.2 44.4 + - + +
303E LEU* 3.6 22.6 - - + +
304E GLN 4.2 2.8 + - - -
306E PRO* 3.5 24.9 - - + -
314E PHE* 3.1 41.7 - - + -
316E TRP* 3.8 31.0 - - + -
319E TYR* 4.0 7.0 - - + -
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Residues in contact with LEU 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243E LYS* 3.4 4.7 - - - +
244E LEU* 2.9 43.7 + - + +
245E GLU 4.1 2.5 - - - +
246E GLY* 3.6 32.1 - - - +
247E ILE 4.8 0.2 - - - +
256E PHE* 3.9 7.6 - - + +
257E ILE* 1.3 82.4 - - - +
259E THR* 1.3 62.9 + - - +
270E LEU* 3.9 21.8 - - + -
271E HIS 3.2 13.5 - - - +
272E PHE* 3.8 29.2 - - + -
273E ASP* 3.6 1.5 - - - +
281E PHE* 3.9 32.8 - - + -
290E ILE* 4.6 2.2 - - + -
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Residues in contact with THR 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241E GLY* 3.7 32.8 - - - +
242E MET 3.3 3.4 - - - -
243E LYS* 2.8 22.8 + - - +
258E LEU* 1.3 74.2 + - - +
260E VAL* 1.3 70.3 + - - +
261E ALA* 3.3 1.1 + - - -
270E LEU* 3.4 6.4 - - - -
271E HIS* 2.9 41.5 + - + +
273E ASP* 2.5 23.3 + - - -
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Residues in contact with VAL 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238E PHE* 4.1 9.9 - - + -
239E LYS 3.4 23.6 - - - +
240E LEU* 3.7 3.3 - - - +
241E GLY* 2.9 26.5 + - - -
242E MET* 2.9 25.0 + - + +
244E LEU* 3.7 17.7 - - + -
259E THR* 1.3 74.0 - - - +
261E ALA* 1.3 60.8 + - - +
262E GLU 3.7 9.2 - - - +
263E VAL* 3.5 31.0 - - + -
268E LEU* 4.0 15.0 - - + -
269E ARG 3.7 5.4 - - - +
270E LEU* 3.9 8.1 - - + -
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Residues in contact with ALA 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240E LEU* 3.7 9.2 - - - +
259E THR* 3.3 1.9 + - - -
260E VAL* 1.3 72.6 - - - +
262E GLU* 1.3 63.6 + - - +
269E ARG* 2.8 46.6 + - - +
271E HIS* 4.1 15.5 - - + -
280E ASP* 3.8 9.4 - - - +
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Residues in contact with GLU 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240E LEU* 3.5 9.1 - - - +
260E VAL* 3.5 1.5 - - - +
261E ALA* 1.3 82.2 - - - +
263E VAL* 1.3 74.2 + - - +
264E CYS* 5.1 3.8 - - - +
268E LEU* 3.4 4.2 - - - +
269E ARG* 2.8 66.5 + - + +
282E TRP* 3.5 25.2 - - + -
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Residues in contact with VAL 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E ASN* 3.4 29.2 - - + +
238E PHE* 3.5 24.2 - - + +
239E LYS* 4.6 2.2 - - - +
240E LEU* 4.0 11.8 - - + +
260E VAL* 3.5 21.3 - - + -
262E GLU* 1.3 84.9 - - - +
264E CYS* 1.3 66.2 + - - +
265E GLY 3.9 7.6 - - - +
267E ARG 3.6 3.6 - - - -
268E LEU* 4.3 7.2 - - + +
282E TRP* 4.8 0.2 - - - -
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Residues in contact with CYS 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E GLU* 5.1 4.0 - - - +
263E VAL* 1.3 75.9 - - - +
265E GLY* 1.3 61.5 + - - +
266E TYR 3.2 0.5 + - - -
267E ARG* 2.9 28.9 + - - +
282E TRP* 4.0 23.9 - - + -
464E ALA 5.6 0.9 - - - -
511E GLY 4.7 1.3 - - - -
512E HIS* 3.4 27.2 - - + +
513E PRO* 3.6 31.4 - - - -
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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