Contacts of the strand formed by residues 245 - 259 (chain N) in PDB entry 2AAZ
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 GLU 245 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59N ALA* 4.9 1.5 - - + -
60N ASP* 4.5 14.0 + - - -
61N ASN* 4.8 7.3 + - - -
206N LYS* 4.2 28.2 + - + +
207N PRO 2.8 14.1 + - - +
208N LYS* 3.3 22.8 - - + +
209N LEU* 2.8 24.9 + - - -
244N THR* 1.3 74.1 - - - +
246N PRO* 1.3 93.3 - - - +
247N HIS 3.2 0.2 + - - -
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Residues in contact with PRO 246 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58N LEU* 3.5 39.8 - - + +
59N ALA* 3.9 4.5 + - - +
61N ASN* 5.6 2.9 - - - +
208N LYS* 5.9 0.5 + - - -
209N LEU* 3.7 7.6 - - + +
235N THR* 4.5 5.4 - - + -
236N HIS* 3.6 27.6 - - + +
239N ALA* 3.7 24.4 - - + -
244N THR 3.9 1.3 - - - +
245N GLU* 1.3 106.6 - - - +
247N HIS* 1.3 59.1 + - - +
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Residues in contact with HIS 247 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57N SER* 3.7 6.3 + - - -
58N LEU* 2.8 25.3 + - - +
59N ALA* 3.7 10.5 + - - +
196N SER* 5.6 3.8 - - - -
208N LYS* 3.8 45.3 + - + +
209N LEU 2.7 16.7 + - - +
210N SER* 3.5 17.5 - - - +
246N PRO* 1.3 74.8 - - - +
248N GLU* 1.3 73.5 + - + +
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Residues in contact with GLU 248 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49M PHE* 5.5 0.9 - - - +
55N ARG* 2.5 54.2 + - + +
56N PHE 3.5 15.5 - - - +
57N SER* 5.1 1.3 - - - -
58N LEU* 4.1 7.9 - - - +
209N LEU 3.7 0.6 + - - +
210N SER* 3.2 16.3 + - - +
211N CYS 2.9 24.8 + - - +
247N HIS* 1.3 96.4 + - + +
249N PHE* 1.3 65.8 + - - +
250N ILE* 3.8 13.2 - - + +
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Residues in contact with PHE 249 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54N PHE 3.8 0.7 - - - +
55N ARG* 3.5 2.8 - - - -
56N PHE* 2.9 52.4 + + + +
58N LEU* 4.0 20.2 - - + -
211N CYS* 3.3 24.7 - - + -
213N MET* 3.8 16.6 - - + -
227N ASN 4.5 3.4 - - - -
228N ILE* 3.8 33.9 - - + -
231N TYR* 3.5 29.8 - + + -
232N ALA* 4.8 7.4 - - + -
235N THR* 5.3 0.2 - - - +
248N GLU* 1.3 74.7 - - - +
250N ILE* 1.3 72.3 + - - +
251N LEU* 3.8 31.2 - - + -
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Residues in contact with ILE 250 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49M PHE* 4.2 9.9 - - + -
50M ALA* 3.9 17.0 - - + +
252M GLN* 5.4 2.2 - - - +
53N SER* 3.8 22.2 - - - +
54N PHE 3.2 10.8 - - - +
55N ARG* 3.8 28.9 - - - +
210N SER* 4.8 0.2 - - - -
211N CYS 2.7 20.6 + - - +
212N LEU* 3.2 23.0 - - + -
213N MET 2.8 26.5 + - - -
248N GLU* 3.8 26.2 - - + +
249N PHE* 1.3 88.3 - - - +
251N LEU* 1.3 64.3 + - - +
252N GLN* 4.2 0.9 - - + -
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Residues in contact with LEU 251 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53N SER* 3.4 6.0 - - - -
54N PHE* 2.9 42.4 + - + +
213N MET* 3.4 42.6 - - + +
215N GLN* 4.1 16.6 - - + +
224N VAL* 4.5 4.0 - - + -
227N ASN* 5.0 0.2 - - + -
228N ILE* 3.7 32.1 - - + +
249N PHE* 3.8 16.1 + - + -
250N ILE* 1.3 75.0 - - - +
252N GLN* 1.3 67.1 + - - +
253N MET* 4.0 27.7 + - + +
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Residues in contact with GLN 252 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53M SER* 4.8 6.9 + - - -
212M LEU* 3.6 14.3 - - + +
250M ILE* 5.4 1.1 - - - +
252M GLN* 3.6 34.7 - - + +
50N ALA* 3.9 4.0 - - - +
51N PRO 3.4 13.7 + - - +
53N SER* 3.2 32.5 - - - +
212N LEU* 4.7 7.8 - - + +
213N MET 2.9 9.6 + - - +
214N TYR* 3.4 30.7 - - + -
215N GLN 2.9 25.6 + - - -
250N ILE* 4.2 1.4 - - + +
251N LEU* 1.3 74.0 - - - +
253N MET* 1.3 78.8 + - - +
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Residues in contact with MET 253 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212M LEU* 3.9 2.6 - - - +
26N LEU* 3.9 12.1 - - + -
50N ALA* 3.4 13.7 - - - -
51N PRO* 4.3 14.2 + - + -
52N PRO 6.1 0.4 - - - +
53N SER* 5.4 0.6 - - - +
54N PHE* 3.4 44.4 - - + -
214N TYR* 4.3 3.1 - - - -
215N GLN 3.5 3.8 - - - -
218N CYS* 3.4 29.2 - - - -
220N LEU* 4.4 4.3 - - + -
224N VAL* 4.2 19.7 - - + -
251N LEU* 4.0 18.1 + - + +
252N GLN* 1.3 95.7 + - - +
254N GLY* 1.3 59.2 + - - +
256N ALA* 3.9 20.2 - - + -
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Residues in contact with GLY 254 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192M GLN* 3.4 22.0 - - - -
48N LEU 3.6 0.2 - - - +
49N PHE* 3.3 16.2 - - - -
50N ALA* 2.9 23.3 + - - -
51N PRO* 4.1 0.9 - - - +
214N TYR* 3.4 7.5 + - - -
215N GLN 2.8 15.0 + - - -
218N CYS* 4.3 0.2 - - - -
253N MET* 1.3 72.9 - - - +
255N ASP* 1.3 59.6 + - - -
256N ALA 3.1 7.3 + - - -
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Residues in contact with ASP 255 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165M THR 4.8 0.3 - - - +
166M ASP 5.2 0.5 - - - +
167M ARG* 3.1 39.1 - - + +
192M GLN* 4.2 5.7 - - - +
194M PHE* 3.7 25.7 - - + -
37N ARG* 4.6 8.1 + - - -
45N THR* 5.4 0.2 + - - -
47N ALA* 3.7 14.2 - - - +
48N LEU 4.2 2.2 - - - -
49N PHE* 4.0 4.8 - - - -
216N ARG 2.8 17.9 + - - +
217N SER* 4.3 0.2 - - - -
218N CYS 2.8 26.3 + - - -
254N GLY* 1.3 71.4 - - - +
256N ALA* 1.3 56.9 + - - +
257N HIS* 3.0 18.7 + - - -
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Residues in contact with ALA 256 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26N LEU* 4.7 0.7 - - + -
30N ILE* 3.9 10.9 - - + +
47N ALA* 3.1 2.8 - - - +
48N LEU* 2.9 40.3 + - + +
51N PRO* 4.1 18.4 - - + -
218N CYS* 4.0 6.7 - - - -
220N LEU* 4.0 9.2 - - + -
253N MET* 3.9 26.5 - - + -
254N GLY 3.1 1.8 + - - -
255N ASP* 1.3 69.9 + - - +
257N HIS* 1.3 59.7 + - - +
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Residues in contact with HIS 257 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167M ARG* 3.4 18.8 + - - -
30N ILE* 4.6 0.7 - - - -
45N THR* 3.7 15.3 - - + +
46N VAL 3.3 11.2 - - - +
47N ALA* 3.5 11.7 - - + -
217N SER* 3.1 27.6 - - - -
218N CYS 3.0 37.4 + - - +
219N ASP* 3.9 1.1 - - - -
220N LEU* 3.2 20.3 + - - +
255N ASP* 3.0 25.8 + - - +
256N ALA* 1.3 74.1 - - - +
258N VAL* 1.3 63.6 + - - +
259N TYR* 3.6 21.3 - + - -
600N UMP 2.9 23.2 + - - -
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Residues in contact with VAL 258 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27N ILE* 4.5 11.0 - - + +
30N ILE* 3.8 28.0 - - + -
31N ILE* 4.7 5.4 - - + -
45N THR* 3.4 2.6 - - - -
46N VAL* 2.9 40.0 + - + +
220N LEU* 4.4 10.3 - - + +
221N GLY 5.5 2.0 - - - +
257N HIS* 1.3 76.5 - - - +
259N TYR* 1.3 76.4 + - - +
260N ARG* 4.5 0.2 - - - -
262N HIS* 4.1 3.4 - - + -
263N VAL* 4.2 15.7 - - + -
266N LEU* 3.5 33.9 - - + -
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Residues in contact with TYR 259 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167M ARG* 3.2 20.8 + - - -
39N ASP* 3.5 7.6 - - - -
41N THR* 3.5 27.1 - - + +
43N THR* 3.0 19.3 - - - -
44N GLY 3.6 2.9 - - - -
45N THR* 3.6 11.0 - - + -
219N ASP* 3.4 28.7 + - - -
257N HIS* 3.6 15.9 - + - -
258N VAL* 1.3 76.1 - - - +
260N ARG* 1.3 60.4 + - - +
261N ASP* 3.4 15.3 - - - +
262N HIS* 2.8 39.5 + + + +
263N VAL* 3.5 5.6 + - - +
316N SER* 3.7 18.6 + - - -
600N UMP 3.1 32.8 + - - -
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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