Contacts of the strand formed by residues 245 - 259 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59F ALA* 4.9 1.5 - - + -
60F ASP* 4.4 14.6 + - - -
61F ASN* 4.8 7.4 + - - -
206F LYS* 4.1 28.7 + - + +
207F PRO 2.8 14.1 + - - +
208F LYS* 3.3 23.3 - - + +
209F LEU* 2.8 23.1 + - - -
244F THR* 1.3 74.6 - - - +
246F PRO* 1.3 94.6 - - - +
247F HIS 3.2 0.2 + - - -
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Residues in contact with PRO 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F LEU* 3.5 35.9 - - + +
59F ALA* 3.9 5.4 - - - +
61F ASN* 5.6 2.9 - - - +
208F LYS* 5.9 0.3 + - - -
209F LEU* 3.7 7.6 - - + +
235F THR* 4.6 5.2 - - + -
236F HIS* 3.5 32.1 - - + +
239F ALA* 3.7 24.0 - - + -
244F THR 3.8 1.3 - - - +
245F GLU* 1.3 104.2 - - - +
247F HIS* 1.3 58.8 + - - +
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Residues in contact with HIS 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F SER* 3.7 5.9 + - - -
58F LEU* 2.8 25.3 + - - +
59F ALA* 3.7 10.2 + - - +
196F SER* 5.6 4.0 - - - -
208F LYS* 3.8 46.4 + - + +
209F LEU 2.7 17.2 + - - +
210F SER* 3.5 17.7 - - - +
246F PRO* 1.3 76.3 - - - +
248F GLU* 1.3 73.5 + - + +
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Residues in contact with GLU 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E PHE* 5.5 0.9 - - - +
55F ARG* 2.6 53.2 + - + +
56F PHE 3.5 15.5 - - - +
57F SER* 5.1 1.8 - - - +
58F LEU* 4.1 8.1 - - - +
209F LEU 3.6 0.6 + - - +
210F SER* 3.2 16.9 + - - +
211F CYS 2.9 24.3 + - - +
247F HIS* 1.3 96.3 + - + +
249F PHE* 1.3 65.6 + - - +
250F ILE* 3.8 13.0 - - + +
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Residues in contact with PHE 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F PHE 3.9 0.5 - - - +
55F ARG* 3.5 2.3 - - - -
56F PHE* 2.9 53.4 + + + +
58F LEU* 4.1 19.7 - - + -
211F CYS* 3.3 20.6 - - + +
213F MET* 3.8 17.0 - - + -
227F ASN 4.5 2.9 - - - -
228F ILE* 3.9 33.7 - - + -
231F TYR* 3.5 28.7 - + + -
232F ALA* 4.7 7.6 - - + -
235F THR* 5.3 0.2 - - - +
248F GLU* 1.3 74.8 - - - +
250F ILE* 1.3 77.4 + - - +
251F LEU* 3.8 31.6 - - + -
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Residues in contact with ILE 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E PHE* 4.3 9.6 - - + -
50E ALA* 4.0 15.7 - - + -
252E GLN* 5.6 1.8 - - - +
53F SER* 3.8 22.0 - - - +
54F PHE 3.3 10.3 - - - +
55F ARG* 3.8 30.3 - - + +
210F SER* 4.8 0.2 - - - -
211F CYS 2.7 22.4 + - - +
212F LEU* 3.2 22.3 - - + -
213F MET 2.9 26.3 + - - -
248F GLU* 3.8 26.7 - - + +
249F PHE* 1.3 87.2 - - - +
251F LEU* 1.3 63.4 + - - +
252F GLN* 4.2 0.9 - - + -
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Residues in contact with LEU 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F SER* 3.3 6.0 - - - -
54F PHE* 2.9 45.5 + - + +
56F PHE* 5.3 0.2 - - + -
213F MET* 3.4 42.2 - - + +
215F GLN* 4.0 16.4 - - + +
224F VAL* 4.5 3.8 - - + -
227F ASN* 4.9 0.2 - - + -
228F ILE* 3.6 34.5 - - + +
249F PHE* 3.8 15.2 - - + -
250F ILE* 1.3 75.1 - - - +
252F GLN* 1.3 67.2 + - - +
253F MET* 4.0 26.2 + - + +
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Residues in contact with GLN 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E SER* 4.6 7.9 + - - -
212E LEU* 3.6 14.1 - - + +
250E ILE* 5.5 1.4 - - - +
252E GLN* 3.5 35.5 - - + +
50F ALA* 4.0 3.5 - - - +
51F PRO 3.3 14.4 + - - +
52F PRO* 5.1 0.2 - - - +
53F SER* 3.3 30.4 - - - +
212F LEU* 4.8 7.2 - - + -
213F MET 2.9 10.6 + - - +
214F TYR* 3.4 30.7 - - + -
215F GLN 2.9 25.6 + - - -
250F ILE* 4.2 1.2 - - + +
251F LEU* 1.3 75.2 - - - +
253F MET* 1.3 79.0 + - - +
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Residues in contact with MET 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212E LEU* 3.9 2.6 - - - +
26F LEU* 3.9 11.7 - - + -
50F ALA* 3.3 13.7 - - - -
51F PRO* 4.3 9.2 + - + -
52F PRO 6.1 0.4 - - - +
53F SER* 5.4 0.6 - - - +
54F PHE* 3.4 44.6 - - + -
214F TYR* 4.3 3.1 - - - -
215F GLN 3.4 4.0 - - - -
218F CYS* 3.4 29.6 - - - -
220F LEU* 4.5 4.3 - - + -
224F VAL* 4.1 19.7 - - + -
251F LEU* 4.0 17.6 + - + +
252F GLN* 1.3 97.4 + - - +
254F GLY* 1.3 59.7 + - - +
256F ALA* 3.9 25.1 - - + -
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Residues in contact with GLY 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192E GLN* 3.4 9.2 - - - -
48F LEU 3.6 0.2 - - - +
49F PHE* 3.4 16.0 - - - -
50F ALA* 2.9 23.4 + - - -
51F PRO* 4.0 1.0 - - - +
214F TYR* 3.4 20.1 + - - -
215F GLN 2.8 13.5 + - - -
216F ARG 3.7 1.3 - - - -
218F CYS* 4.4 0.2 - - - -
253F MET* 1.3 73.1 - - - +
255F ASP* 1.3 59.6 + - - -
256F ALA 3.1 8.3 + - - -
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Residues in contact with ASP 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E THR 4.9 0.9 - - - +
166E ASP 5.2 1.0 - - - +
167E ARG* 3.6 26.5 + - + +
192E GLN* 4.0 6.9 - - - +
194E PHE* 3.5 27.6 - - + -
37F ARG* 4.3 8.8 + - - -
45F THR* 5.4 0.2 + - - -
47F ALA* 3.7 11.8 - - - +
48F LEU 4.2 2.5 - - - -
49F PHE* 3.9 6.1 - - - -
216F ARG 2.8 17.9 + - - +
217F SER* 4.3 3.4 - - - -
218F CYS* 2.8 27.1 + - - -
254F GLY* 1.3 70.3 - - - +
256F ALA* 1.3 56.2 + - - +
257F HIS* 2.9 30.9 + - - -
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Residues in contact with ALA 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F LEU* 4.7 0.7 - - + -
30F ILE* 3.8 10.4 - - + +
47F ALA* 3.2 2.4 - - - +
48F LEU* 2.9 44.6 + - + +
51F PRO* 4.0 18.6 - - + -
218F CYS* 4.1 6.5 - - - -
220F LEU* 4.0 9.4 - - + -
253F MET* 3.9 26.7 - - + -
254F GLY 3.1 1.6 + - - -
255F ASP* 1.3 70.1 + - - +
257F HIS* 1.3 59.0 + - - +
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Residues in contact with HIS 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E ARG* 3.7 19.3 + - - -
30F ILE* 4.5 0.9 - - - -
45F THR* 3.8 12.6 - - + +
46F VAL 3.3 11.4 - - - +
47F ALA* 3.6 11.4 - - + -
217F SER* 3.1 27.4 - - - -
218F CYS 3.0 29.8 + - - +
219F ASP* 3.9 1.6 - - - +
220F LEU* 3.1 30.9 + - - +
255F ASP* 2.9 24.9 + - - +
256F ALA* 1.3 75.4 - - - +
258F VAL* 1.3 63.8 + - - +
259F TYR* 3.6 21.7 - + - -
600F UMP 2.8 22.4 + - - -
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Residues in contact with VAL 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F ILE* 4.5 11.7 - - + +
30F ILE* 3.7 28.5 - - + -
31F ILE* 4.7 4.9 - - + -
45F THR* 4.1 1.8 - - - -
46F VAL* 2.9 39.2 + - + +
220F LEU* 4.3 9.6 - - + +
221F GLY 5.5 1.8 - - - +
257F HIS* 1.3 77.0 - - - +
259F TYR* 1.3 76.0 + - - +
260F ARG* 4.5 0.2 - - - -
262F HIS* 4.1 3.4 - - + -
263F VAL* 4.1 16.6 - - + +
266F LEU* 3.5 33.7 - - + -
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Residues in contact with TYR 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E ARG* 3.1 22.4 + - - -
39F ASP* 3.4 19.1 - - - -
41F THR* 3.5 14.3 - - - +
43F THR* 2.9 20.0 - - - -
44F GLY 3.6 7.4 - - - -
45F THR* 3.6 6.3 - - + -
219F ASP* 3.4 31.4 + - - -
257F HIS* 3.6 9.6 - + - -
258F VAL* 1.3 76.9 - - - +
260F ARG* 1.3 60.0 + - - +
261F ASP* 3.4 15.3 - - - +
262F HIS* 2.8 39.1 + + + +
263F VAL* 3.4 5.5 + - - +
316F SER* 3.8 11.7 - - - -
600F UMP 2.7 29.0 + - - -
2601F CB3 3.4 14.1 + - - -
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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