Contacts of the strand formed by residues 245 - 259 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59M ALA* 4.9 1.5 - - + -
60M ASP* 4.5 13.5 + - - -
61M ASN* 4.9 7.1 + - - -
206M LYS* 4.2 28.5 + - + +
207M PRO 2.8 14.7 + - - +
208M LYS* 3.3 24.1 - - + +
209M LEU* 2.8 24.5 + - - -
244M THR* 1.3 73.7 - - - +
246M PRO* 1.3 94.1 - - - +
247M HIS 3.2 0.2 + - - -
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Residues in contact with PRO 246 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58M LEU* 3.6 34.1 - - + +
59M ALA* 3.8 5.9 - - - +
61M ASN* 5.6 3.1 - - - +
208M LYS* 5.9 0.2 + - - -
209M LEU* 3.7 7.6 - - + +
235M THR* 4.5 6.1 - - + -
236M HIS* 3.6 33.9 - - + +
239M ALA* 3.6 24.3 - - + -
244M THR 3.8 1.6 - - - +
245M GLU* 1.3 104.7 - - - +
247M HIS* 1.3 59.7 + - - +
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Residues in contact with HIS 247 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57M SER* 3.7 6.1 + - - -
58M LEU* 2.9 24.0 + - - +
59M ALA* 3.7 11.8 + - + +
196M SER* 5.5 4.9 - - - -
208M LYS* 3.8 45.7 + - + +
209M LEU 2.7 16.1 + - - +
210M SER* 3.5 17.0 - - - +
246M PRO* 1.3 75.0 - - - +
248M GLU* 1.3 75.1 + - + +
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Residues in contact with GLU 248 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55M ARG* 2.6 52.2 + - - +
56M PHE 3.5 15.9 - - - +
57M SER* 5.0 1.8 - - - +
58M LEU* 4.1 8.2 - - - +
209M LEU 3.7 0.9 + - - +
210M SER* 3.1 16.8 + - - +
211M CYS 2.9 24.6 + - - +
247M HIS* 1.3 97.6 + - + +
249M PHE* 1.3 66.7 + - - +
250M ILE* 3.8 12.6 - - + +
49N PHE* 5.5 0.9 - - - +
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Residues in contact with PHE 249 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54M PHE 3.8 0.7 - - - +
55M ARG* 3.5 1.9 - - - -
56M PHE* 2.9 53.9 + + + +
58M LEU* 4.0 20.9 - - + -
211M CYS* 3.2 24.2 - - + +
213M MET* 3.8 16.2 - - + -
227M ASN 4.5 3.1 - - - -
228M ILE* 3.8 33.9 - - + -
231M TYR* 3.5 30.7 - - + -
232M ALA* 4.8 7.0 - - + -
248M GLU* 1.3 73.8 - - - +
250M ILE* 1.3 72.1 + - - +
251M LEU* 3.9 31.2 - - + -
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Residues in contact with ILE 250 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53M SER* 3.8 21.8 - - - +
54M PHE 3.2 11.0 - - - +
55M ARG* 3.8 30.3 - - + +
210M SER* 4.9 0.4 - - - -
211M CYS 2.7 21.2 + - - +
212M LEU* 3.2 23.0 - - + -
213M MET 2.8 26.2 + - - -
248M GLU* 3.8 26.5 - - + +
249M PHE* 1.3 85.3 - - - +
251M LEU* 1.3 64.3 + - - +
252M GLN* 4.1 1.1 - - + +
49N PHE* 4.3 10.3 - - + -
50N ALA* 3.9 15.5 - - + -
252N GLN* 5.4 2.5 - - - +
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Residues in contact with LEU 251 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53M SER* 3.3 5.2 - - - -
54M PHE* 2.9 45.7 + - + +
56M PHE* 5.3 0.2 - - + -
213M MET* 3.4 42.6 - - + +
215M GLN* 4.1 16.8 - - + +
224M VAL* 4.5 3.6 - - + -
228M ILE* 3.7 33.4 - - + +
249M PHE* 3.9 16.1 + - + -
250M ILE* 1.3 72.7 - - - +
252M GLN* 1.3 66.3 + - - +
253M MET* 4.0 27.1 + - + +
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Residues in contact with GLN 252 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50M ALA* 4.0 4.2 - - - +
51M PRO 3.3 14.4 + - - +
52M PRO* 5.1 0.2 - - - +
53M SER* 3.2 32.1 - - - +
212M LEU* 4.7 7.2 - - + +
213M MET 2.9 10.0 + - - +
214M TYR* 3.4 31.9 - - + -
215M GLN* 2.9 25.3 + - - -
250M ILE* 4.1 1.0 - - - +
251M LEU* 1.3 72.8 - - - +
253M MET* 1.3 78.6 + - - +
53N SER* 4.7 8.0 + - - -
212N LEU* 3.7 14.0 - - + +
250N ILE* 5.4 1.1 - - - +
252N GLN* 3.6 35.5 - - + +
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Residues in contact with MET 253 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26M LEU* 3.9 12.1 - - + -
50M ALA* 3.3 13.9 - - - -
51M PRO* 3.9 9.6 + - + +
52M PRO 6.2 0.2 - - - +
53M SER* 5.4 0.6 - - - +
54M PHE* 3.4 45.1 - - + -
214M TYR* 4.3 3.4 - - - -
215M GLN 3.5 3.6 - - - -
218M CYS* 3.4 32.1 - - - -
220M LEU* 4.4 4.5 - - + -
224M VAL* 4.2 20.2 - - + -
251M LEU* 4.0 16.8 + - + +
252M GLN* 1.3 95.8 + - - +
254M GLY* 1.3 61.1 + - - +
256M ALA* 3.9 23.8 - - + -
212N LEU* 3.9 2.3 - - - +
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Residues in contact with GLY 254 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48M LEU 3.6 0.3 - - - +
49M PHE* 3.3 16.0 - - - -
50M ALA* 2.9 24.4 + - - -
51M PRO* 4.0 0.7 - - - +
214M TYR* 3.4 20.8 + - - -
215M GLN 2.8 12.9 + - - -
216M ARG 3.7 1.3 - - - -
218M CYS* 4.3 0.2 - - - -
253M MET* 1.3 73.1 - - - +
255M ASP* 1.3 59.7 + - - +
256M ALA 3.1 7.1 + - - -
192N GLN* 3.5 8.1 - - - -
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Residues in contact with ASP 255 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37M ARG* 4.6 7.8 + - - -
45M THR* 5.5 0.3 + - - -
47M ALA* 3.6 14.1 - - - +
48M LEU 4.2 3.1 - - - -
49M PHE* 4.0 5.2 - - - +
216M ARG 2.7 18.3 + - - +
217M SER* 4.3 0.2 - - - -
218M CYS* 2.8 26.9 + - - -
254M GLY* 1.3 69.8 - - - +
256M ALA* 1.3 56.9 + - - +
257M HIS* 3.0 18.0 + - - -
166N ASP 5.2 0.5 - - - +
167N ARG* 3.2 37.3 - - + +
192N GLN* 4.2 6.7 - - - +
194N PHE* 3.7 27.7 - - + -
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Residues in contact with ALA 256 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26M LEU* 4.7 0.9 - - + -
30M ILE* 3.8 11.3 - - + +
47M ALA* 3.1 2.6 - - - +
48M LEU* 3.0 39.7 + - + +
51M PRO* 4.0 19.3 - - + -
218M CYS* 4.0 7.0 - - - -
220M LEU* 4.0 9.6 - - + -
253M MET* 3.9 25.6 - - + -
254M GLY 3.1 2.2 + - - -
255M ASP* 1.3 70.7 - - - +
257M HIS* 1.3 59.2 + - - +
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Residues in contact with HIS 257 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M ILE* 4.5 0.9 - - - -
45M THR* 3.8 14.6 - - + +
46M VAL 3.3 12.1 - - - +
47M ALA* 3.5 11.7 - - + -
217M SER* 3.1 27.8 - - - -
218M CYS 3.0 36.6 + - - +
219M ASP* 3.9 1.1 - - - -
220M LEU* 3.2 20.5 + - - +
255M ASP* 3.0 25.8 + - - +
256M ALA* 1.3 73.7 - - - +
258M VAL* 1.3 64.8 + - - +
259M TYR* 3.6 21.9 - + - -
550M UMP 2.9 22.2 + - - -
167N ARG* 3.6 20.0 + - - -
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Residues in contact with VAL 258 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27M ILE* 4.4 11.7 - - + +
30M ILE* 3.8 26.9 - - + -
31M ILE* 4.7 5.6 - - + -
45M THR* 4.2 2.0 - - - -
46M VAL* 3.0 40.4 + - + +
220M LEU* 4.4 10.1 - - + +
221M GLY 5.5 1.8 - - - +
257M HIS* 1.3 78.0 - - - +
259M TYR* 1.3 75.4 + - - +
260M ARG* 3.6 0.5 + - - -
262M HIS* 4.1 4.0 - - + -
263M VAL* 4.2 15.7 - - + +
266M LEU* 3.5 33.4 - - + -
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Residues in contact with TYR 259 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39M ASP* 3.5 19.1 - - - -
41M THR* 3.5 15.6 - - + +
43M THR* 3.1 19.3 - - - -
44M GLY 3.7 2.5 - - - -
45M THR* 3.6 10.8 - - + -
219M ASP* 3.4 34.1 - - - -
257M HIS* 3.6 17.5 - + - -
258M VAL* 1.3 78.8 - - - +
260M ARG* 1.3 60.3 + - - +
261M ASP* 3.2 15.7 - - - +
262M HIS* 2.9 37.8 + + + +
263M VAL* 3.4 5.4 + - - +
316M SER* 3.7 18.0 + - - -
550M UMP 3.0 27.7 + - - -
167N ARG* 3.3 19.6 + - - -
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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