Contacts of the strand formed by residues 245 - 259 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59B ALA* 4.9 1.5 - - + -
60B ASP* 4.5 14.2 + - - -
61B ASN* 4.9 7.6 + - - -
206B LYS* 4.1 28.2 + - + +
207B PRO 2.8 16.0 + - - +
208B LYS* 3.3 21.3 - - + +
209B LEU* 2.8 22.9 + - - -
244B THR* 1.3 74.6 - - - +
246B PRO* 1.3 93.7 - - - +
247B HIS 3.2 0.3 + - - -
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Residues in contact with PRO 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B LEU* 3.5 36.6 - - + +
59B ALA* 3.9 5.4 - - - +
61B ASN* 5.6 3.1 - - - +
208B LYS* 5.8 0.2 + - - -
209B LEU* 3.7 8.3 - - + +
235B THR* 4.6 5.6 - - + -
236B HIS* 3.6 32.3 - - + +
239B ALA* 3.6 25.0 - - + -
244B THR 3.8 1.6 - - - +
245B GLU* 1.3 106.3 - - - +
247B HIS* 1.3 57.8 + - - +
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Residues in contact with HIS 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B SER* 3.7 5.4 + - - -
58B LEU* 2.8 24.7 + - - +
59B ALA* 3.7 10.5 + - - +
196B SER* 5.5 4.7 - - - -
208B LYS* 3.7 46.7 + - + +
209B LEU 2.7 16.5 + - - +
210B SER* 3.5 18.2 - - - +
246B PRO* 1.3 75.0 - - - +
248B GLU* 1.3 73.1 + - + +
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Residues in contact with GLU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PHE* 5.5 1.2 - - - +
55B ARG* 2.6 51.9 + - - +
56B PHE 3.5 16.8 - - - +
57B SER* 5.0 1.3 - - - -
58B LEU* 4.1 8.7 - - - +
209B LEU 3.7 0.4 + - - -
210B SER* 3.2 16.9 + - - +
211B CYS 2.9 24.9 + - - -
247B HIS* 1.3 97.7 + - + +
249B PHE* 1.3 66.5 + - - +
250B ILE* 3.8 11.6 - - + +
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Residues in contact with PHE 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B PHE 3.8 0.3 - - - +
55B ARG* 3.5 2.8 - - - -
56B PHE* 2.9 52.6 + + + +
58B LEU* 4.0 22.0 - - + +
211B CYS* 3.3 18.2 - - + +
213B MET* 3.8 17.0 - - + -
227B ASN 4.5 2.7 - - - -
228B ILE* 3.8 35.0 - - + -
231B TYR* 3.5 30.5 - - + -
232B ALA* 4.7 7.2 - - + -
248B GLU* 1.3 75.1 - - - +
250B ILE* 1.3 77.7 + - - +
251B LEU* 3.8 31.0 - - + -
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Residues in contact with ILE 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PHE* 4.2 10.5 - - + -
50A ALA* 4.0 16.8 - - + -
252A GLN* 5.5 2.0 - - - +
53B SER* 3.8 22.2 - - - +
54B PHE 3.2 11.7 - - - +
55B ARG* 3.8 30.1 - - + +
210B SER* 4.8 0.2 - - - -
211B CYS 2.7 24.0 + - - +
212B LEU* 3.2 21.5 - - + -
213B MET 2.8 26.2 + - - -
248B GLU* 3.8 26.2 - - + +
249B PHE* 1.3 85.7 - - - +
251B LEU* 1.3 64.6 + - - +
252B GLN* 4.2 0.7 - - + +
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Residues in contact with LEU 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B SER* 3.3 5.9 - - - -
54B PHE* 2.9 45.4 + - + +
56B PHE* 5.3 0.2 - - + -
213B MET* 3.4 38.4 - - + +
215B GLN* 4.0 16.2 - - + +
224B VAL* 4.6 3.4 - - + -
227B ASN* 5.0 0.2 - - + -
228B ILE* 3.7 33.9 - - + +
249B PHE* 3.8 16.7 - - + -
250B ILE* 1.3 74.0 - - - +
252B GLN* 1.3 69.9 + - - +
253B MET* 4.0 26.1 + - + +
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Residues in contact with GLN 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A SER* 4.7 7.5 + - - -
212A LEU* 3.6 14.5 - - + +
250A ILE* 5.5 2.0 - - - +
252A GLN* 3.5 35.3 - - + +
50B ALA* 4.0 3.3 - - - +
51B PRO 3.3 14.7 + - - +
53B SER* 3.2 31.6 - - - +
212B LEU* 4.7 7.5 - - + +
213B MET 2.9 10.8 + - - +
214B TYR* 3.4 30.5 - - + -
215B GLN 2.9 25.8 + - - -
250B ILE* 4.2 1.2 - - + +
251B LEU* 1.3 75.0 - - - +
253B MET* 1.3 79.3 + - - +
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Residues in contact with MET 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A LEU* 3.9 2.3 - - - +
26B LEU* 3.8 12.6 - - + -
50B ALA* 3.3 13.5 - - - -
51B PRO* 4.0 10.7 + - + +
52B PRO 6.1 0.4 - - - +
53B SER* 5.4 0.6 - - - +
54B PHE* 3.4 44.6 - - + -
214B TYR* 4.3 2.9 - - - -
215B GLN 3.5 4.3 - - - -
218B CYS* 3.5 26.0 - - - -
220B LEU* 4.4 4.3 - - + -
224B VAL* 4.2 20.6 - - + -
251B LEU* 4.0 17.2 + - + +
252B GLN* 1.3 95.8 + - - +
254B GLY* 1.3 61.8 + - - +
256B ALA* 3.8 28.5 - - + -
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Residues in contact with GLY 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A GLN* 3.5 8.3 - - - -
212A LEU* 4.8 0.2 - - - -
48B LEU 3.5 0.2 - - - +
49B PHE* 3.4 16.7 - - - -
50B ALA* 2.9 22.2 + - - -
51B PRO* 4.0 1.0 - - - +
214B TYR* 3.4 21.1 + - - -
215B GLN 2.8 12.9 + - - -
216B ARG 3.8 0.7 - - - -
218B CYS* 4.3 0.2 - - - -
253B MET* 1.3 73.7 - - - +
255B ASP* 1.3 58.8 + - - +
256B ALA 3.0 8.1 + - - -
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Residues in contact with ASP 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A THR 4.8 1.0 - - - +
166A ASP 5.1 1.2 - - - +
167A ARG* 3.5 31.9 + - + +
192A GLN* 4.1 6.6 - - - +
194A PHE* 3.6 27.5 - - + -
37B ARG* 4.5 8.7 + - - -
45B THR* 5.4 0.2 + - - -
47B ALA* 3.7 11.3 - - - +
48B LEU 4.2 2.7 - - - -
49B PHE* 4.0 5.9 - - - -
216B ARG 2.8 18.4 + - - +
217B SER* 4.3 1.3 - - - -
218B CYS* 2.9 26.1 + - - -
254B GLY* 1.3 70.5 - - - +
256B ALA* 1.3 58.2 + - - +
257B HIS* 2.9 31.6 + - - +
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Residues in contact with ALA 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LEU* 4.6 0.7 - - + -
30B ILE* 3.8 10.7 - - + +
47B ALA* 3.3 2.1 - - - -
48B LEU* 3.0 39.6 + - + +
51B PRO* 4.0 18.8 - - + -
218B CYS* 4.0 7.4 - - - -
220B LEU* 4.0 8.1 - - + -
253B MET* 3.8 27.8 - - + -
254B GLY 3.0 1.8 + - - -
255B ASP* 1.3 71.4 + - - +
257B HIS* 1.3 59.4 + - - +
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Residues in contact with HIS 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ARG* 3.7 19.7 + - - -
30B ILE* 4.5 1.1 - - - -
45B THR* 3.8 11.4 - - + +
46B VAL 3.2 12.6 - - - +
47B ALA* 3.6 11.9 - - + -
217B SER* 3.1 27.1 - - - -
218B CYS 3.1 26.8 + - - +
219B ASP* 3.9 0.8 - - - -
220B LEU* 3.1 30.7 + - - +
255B ASP* 2.9 24.8 + - - +
256B ALA* 1.3 74.4 - - - +
258B VAL* 1.3 64.6 + - - +
259B TYR* 3.6 21.4 - + - -
400B UMP 2.6 23.7 + - - -
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Residues in contact with VAL 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ILE* 4.5 11.7 - - + +
30B ILE* 3.8 26.5 - - + -
31B ILE* 4.7 5.6 - - + -
45B THR* 4.2 2.0 - - - -
46B VAL* 2.9 40.1 + - + +
219B ASP* 5.6 0.2 - - - -
220B LEU* 4.3 9.6 - - + +
221B GLY 5.5 2.0 - - - +
257B HIS* 1.3 78.3 - - - +
259B TYR* 1.3 73.9 + - - +
260B ARG* 3.6 0.3 + - - -
262B HIS* 4.1 3.4 - - + -
263B VAL* 4.1 16.8 - - + +
266B LEU* 3.6 32.5 - - + -
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Residues in contact with TYR 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ARG* 3.1 22.1 + - - -
39B ASP* 3.4 19.3 + - - -
41B THR* 3.6 12.6 - - - +
43B THR* 3.0 20.2 - - - -
44B GLY 3.6 2.7 - - - -
45B THR* 3.6 10.8 - - + -
219B ASP* 3.4 30.7 - - - -
257B HIS* 3.6 11.4 - + - -
258B VAL* 1.3 79.0 - - - +
260B ARG* 1.3 66.4 + - - +
261B ASP* 3.4 15.5 - - - +
262B HIS* 2.9 32.8 + + + +
263B VAL* 3.4 5.2 + - - +
316B SER* 3.8 11.7 - - - -
400B UMP 2.6 29.8 + - - -
2401B CB3 3.3 15.6 + - - -
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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