Contacts of the strand formed by residues 245 - 259 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A ALA* 4.9 1.1 - - + -
60A ASP* 4.4 14.7 + - - -
61A ASN* 4.8 7.3 + - - -
206A LYS* 4.2 29.3 + - + +
207A PRO 2.8 15.4 + - - +
208A LYS* 3.4 22.6 - - + +
209A LEU* 2.8 23.7 + - - -
244A THR* 1.3 73.3 - - - +
246A PRO* 1.3 93.3 - - - +
247A HIS 3.3 0.2 + - - -
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Residues in contact with PRO 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU* 3.6 36.3 - - + +
59A ALA* 3.9 5.7 - - - +
61A ASN* 5.6 2.9 - - - +
208A LYS* 5.8 0.5 + - - -
209A LEU* 3.7 7.4 - - + +
235A THR* 4.5 5.8 - - + -
236A HIS* 3.6 31.2 - - + +
239A ALA* 3.6 24.4 - - + -
244A THR 3.9 1.3 - - - +
245A GLU* 1.3 106.4 - - - +
247A HIS* 1.3 59.3 + - - +
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Residues in contact with HIS 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A SER* 3.7 6.1 + - - -
58A LEU* 2.9 23.1 + - - +
59A ALA* 3.7 11.6 + - + +
196A SER* 5.5 4.9 - - - -
208A LYS* 3.7 46.1 + - + +
209A LEU 2.7 17.4 + - - +
210A SER* 3.5 18.2 - - - +
246A PRO* 1.3 76.2 - - - +
248A GLU* 1.3 75.1 + - + +
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Residues in contact with GLU 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ARG* 2.6 51.9 + - - +
56A PHE 3.5 15.9 - - - +
57A SER* 5.0 1.3 - - - -
58A LEU* 4.1 9.2 - - - +
209A LEU 3.7 0.4 + - - -
210A SER* 3.2 15.9 + - - +
211A CYS 3.0 24.3 + - - -
247A HIS* 1.3 97.1 + - + +
249A PHE* 1.3 65.5 + - - +
250A ILE* 3.8 12.2 - - + +
49B PHE* 5.4 0.7 - - - +
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Residues in contact with PHE 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A PHE 3.8 0.3 - - - +
55A ARG* 3.5 1.9 - - - -
56A PHE* 2.8 54.3 + + + +
58A LEU* 4.0 21.5 - - + -
211A CYS* 3.3 20.4 - - + -
213A MET* 3.8 16.4 - - + -
227A ASN 4.6 3.1 - - - -
228A ILE* 3.9 34.3 - - + -
231A TYR* 3.5 29.4 - + + -
232A ALA* 4.7 6.7 - - + -
248A GLU* 1.3 75.4 - - - +
250A ILE* 1.3 78.7 + - - +
251A LEU* 3.8 30.5 - - + -
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Residues in contact with ILE 250 (chain A).
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* 3.8 22.0 - - - +
54A PHE 3.2 10.1 - - - +
55A ARG* 3.8 31.4 - - + +
210A SER* 4.8 0.2 - - - -
211A CYS 2.8 22.1 + - - +
212A LEU* 3.2 23.2 - - + -
213A MET 2.8 27.0 + - - -
248A GLU* 3.8 26.5 - - + +
249A PHE* 1.3 85.8 - - - +
251A LEU* 1.3 64.1 + - - +
252A GLN* 4.2 0.7 - - + -
49B PHE* 4.3 9.6 - - + -
50B ALA* 4.0 16.6 - - + +
252B GLN* 5.5 1.6 - - - +
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Residues in contact with LEU 251 (chain A).
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* 3.3 5.1 - - - -
54A PHE* 2.9 47.1 + - + +
213A MET* 3.4 38.6 - - + +
215A GLN* 4.1 17.3 - - + +
224A VAL* 4.5 3.8 - - + -
227A ASN* 4.9 0.2 - - + -
228A ILE* 3.7 32.8 - - + +
249A PHE* 3.8 16.2 - - + -
250A ILE* 1.3 74.4 - - - +
252A GLN* 1.3 68.7 + - - +
253A MET* 4.0 26.7 + - + +
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Residues in contact with GLN 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ALA* 4.0 3.3 - - - +
51A PRO 3.3 15.0 + - - +
53A SER* 3.2 31.1 - - - +
212A LEU* 4.6 7.4 - - + +
213A MET 3.0 9.8 + - - +
214A TYR* 3.4 31.0 - - + -
215A GLN 2.9 25.1 + - - -
250A ILE* 4.2 1.4 - - + +
251A LEU* 1.3 74.2 - - - +
253A MET* 1.3 79.9 + - - +
53B SER* 4.6 8.3 + - - -
212B LEU* 3.7 14.3 - - + +
250B ILE* 5.5 1.4 - - - +
252B GLN* 3.5 35.2 - - + +
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Residues in contact with MET 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 3.8 19.1 - - + -
50A ALA* 3.3 13.9 - - - -
51A PRO* 4.3 15.5 + - + -
52A PRO 5.9 0.9 + - - +
53A SER* 5.4 0.4 - - - +
54A PHE* 3.4 44.4 - - + -
214A TYR* 4.3 3.4 - - - -
215A GLN 3.5 3.6 - - - -
218A CYS* 3.5 26.7 - - - -
220A LEU* 4.4 4.9 - - + -
224A VAL* 4.2 19.3 - - + -
251A LEU* 4.0 17.7 + - + +
252A GLN* 1.3 96.0 + - - +
254A GLY* 1.3 60.4 + - - +
256A ALA* 3.9 15.9 - - + -
212B LEU* 3.9 2.1 - - - +
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Residues in contact with GLY 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU 3.6 0.2 - - - +
49A PHE* 3.4 15.0 - - - -
50A ALA* 2.9 24.1 + - - -
51A PRO* 4.0 0.9 - - - +
214A TYR* 3.4 20.8 + - - -
215A GLN 2.8 14.0 + - - -
218A CYS* 4.3 0.2 - - - -
253A MET* 1.3 73.8 - - - +
255A ASP* 1.3 59.0 + - - +
256A ALA 3.1 7.6 + - - -
192B GLN* 3.5 8.7 - - - -
212B LEU* 4.8 0.4 - - - -
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Residues in contact with ASP 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ARG* 4.6 8.1 + - - -
47A ALA* 3.7 7.3 - - - +
48A LEU 4.2 2.9 - - - -
49A PHE* 4.0 5.2 - - - -
216A ARG 2.8 18.3 + - - +
217A SER* 4.3 3.8 - - - -
218A CYS* 2.8 28.1 + - - -
254A GLY* 1.3 69.0 - - - -
256A ALA* 1.3 58.5 + - - +
257A HIS* 2.8 35.4 + - - +
165B THR 4.8 1.7 - - - +
166B ASP 5.1 1.0 - - - +
167B ARG* 3.6 27.7 + - + +
192B GLN* 4.2 7.0 - - - +
194B PHE* 3.5 28.3 - - + -
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Residues in contact with ALA 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 4.6 0.4 - - + -
30A ILE* 3.8 11.7 - - + +
47A ALA* 3.3 1.6 - - - -
48A LEU* 3.0 39.5 + - + +
51A PRO* 4.0 19.3 - - + -
218A CYS* 4.0 7.4 - - - -
220A LEU* 4.0 9.4 - - + -
253A MET* 3.9 26.0 - - + -
254A GLY 3.1 2.0 + - - -
255A ASP* 1.3 70.3 + - - +
257A HIS* 1.3 59.5 + - - +
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Residues in contact with HIS 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ILE* 4.5 0.9 - - - -
45A THR* 3.8 13.2 - - + +
46A VAL 3.3 12.8 - - - +
47A ALA* 3.6 10.8 - - + -
217A SER* 3.1 26.9 - - - -
218A CYS 3.0 27.4 + - - +
219A ASP* 3.9 1.2 - - - -
220A LEU* 3.1 30.9 + - - +
255A ASP* 2.8 21.2 + - - +
256A ALA* 1.3 74.2 - - - +
258A VAL* 1.3 63.9 + - - +
259A TYR* 3.6 21.2 - + - -
350A UMP 2.8 23.3 + - - -
167B ARG* 3.7 20.2 + - - -
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Residues in contact with VAL 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ILE* 4.4 11.7 - - + +
30A ILE* 3.8 26.5 - - + -
31A ILE* 4.6 5.8 - - + -
45A THR* 4.2 2.0 - - - -
46A VAL* 2.9 40.4 + - + +
219A ASP* 5.6 0.2 - - - -
220A LEU* 4.3 10.1 - - + +
221A GLY 5.5 1.3 - - - +
257A HIS* 1.3 77.7 - - - +
259A TYR* 1.3 75.4 + - - +
262A HIS* 4.2 2.2 - - + -
263A VAL* 4.1 18.4 - - + -
266A LEU* 3.6 32.3 - - + -
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Residues in contact with TYR 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ASP* 3.5 19.3 - - - -
41A THR* 3.6 13.5 - - - +
43A THR* 3.0 20.0 - - - -
44A GLY 3.7 2.2 - - - -
45A THR* 3.6 11.2 - - + -
219A ASP* 3.4 32.5 - - - -
257A HIS* 3.6 10.1 - + - -
258A VAL* 1.3 76.6 - - - +
260A ARG* 1.3 60.9 + - - +
261A ASP* 3.2 15.9 - - - +
262A HIS* 2.9 38.3 + + + +
263A VAL* 3.5 5.5 + - - +
316A SER* 3.8 11.9 - - - -
350A UMP 2.6 29.8 + - - -
2351A CB3 3.3 14.0 + - - -
167B ARG* 3.1 21.1 + - - -
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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