Contacts of the strand formed by residues 215 - 225 (chain A) in PDB entry 2ADU
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 ALA 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A ILE 3.6 21.8 - - - +
209A LYS 3.9 9.4 - - - +
210A GLU* 3.1 3.1 - - - +
211A ASN* 2.6 33.0 + - + +
212A GLY 3.4 8.1 - - - +
213A LEU 3.4 0.8 - - - -
214A ASN* 1.3 82.0 - - - +
216A GLY* 1.3 59.1 + - - +
255A HIS* 3.4 12.1 - - - -
256A ILE* 3.7 14.4 - - + -
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Residues in contact with GLY 216 (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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208A ILE* 3.7 20.2 - - - +
210A GLU* 4.1 12.3 - - - -
212A GLY 4.9 1.6 - - - -
215A ALA* 1.3 74.8 - - - +
217A LEU* 1.3 66.0 + - - +
254A THR* 3.5 4.7 - - - -
255A HIS* 3.1 39.1 + - - +
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Residues in contact with LEU 217 (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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201A GLU* 3.8 14.6 - - + -
204A SER* 3.0 37.7 - - - +
205A ARG* 3.8 47.1 - - + +
208A ILE* 4.8 0.2 - - + -
210A GLU* 4.4 7.4 + - - +
216A GLY* 1.3 76.8 - - - +
218A ALA* 1.3 63.4 + - - +
219A PHE 3.4 2.3 + - - +
253A GLY 3.6 9.6 - - - +
255A HIS* 3.9 5.9 + - - -
413A LEU* 4.3 7.4 - - - +
414A ALA 5.1 0.2 - - - +
419A TRP* 3.5 43.9 - - + -
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Residues in contact with ALA 218 (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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216A GLY 3.8 2.4 + - - -
217A LEU* 1.3 73.4 - - - +
219A PHE* 1.3 66.8 + - + +
253A GLY 3.0 21.2 + - - -
254A THR 4.1 7.0 - - - +
255A HIS* 4.0 8.7 - - + -
260A ILE* 3.5 42.1 - - + +
338A ILE* 5.6 2.4 - - - +
413A LEU* 3.8 13.5 - - - +
414A ALA* 3.7 17.9 + - - +
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Residues in contact with PHE 219 (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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217A LEU* 3.4 3.3 - - - +
218A ALA* 1.3 88.2 - - + +
220A PRO* 1.3 96.3 - - + +
221A THR* 3.8 0.7 + - - -
251A ASP* 3.4 10.3 - - - -
252A PHE* 3.4 25.6 - - - +
253A GLY* 3.4 31.1 + - - +
260A ILE* 4.6 0.4 - - + -
262A ASP* 3.2 32.5 - - + -
338A ILE* 3.7 31.4 - - + -
414A ALA* 3.9 16.6 - - + -
419A TRP* 3.1 13.7 - - - -
906A R20 3.7 28.3 - + + -
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Residues in contact with PRO 220 (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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201A GLU* 4.7 0.2 - - - +
219A PHE* 1.3 112.0 - - + +
221A THR* 1.3 60.4 + - - +
222A GLY 3.1 6.8 + - - -
233A THR* 4.3 2.5 - - + -
251A ASP 3.5 0.3 - - - +
382A HIS* 3.7 30.3 + - + +
414A ALA* 3.9 17.3 - - + +
415A PHE* 3.3 33.2 - - - +
416A CYS* 3.6 21.1 - - + +
419A TRP* 3.2 13.4 - - + -
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Residues in contact with THR 221 (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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196A ILE* 5.9 0.2 - - + -
197A CYS* 3.7 24.8 + - + -
200A LEU* 3.7 35.8 - - + +
201A GLU* 2.9 39.3 + - - +
219A PHE 5.2 0.5 + - - -
220A PRO* 1.3 70.5 - - - +
222A GLY* 1.3 71.8 + - - +
223A CYS 3.5 1.2 + - - -
233A THR* 2.8 25.8 + - - -
250A ILE* 4.7 7.6 - - + -
251A ASP 3.7 3.8 - - - -
252A PHE* 4.2 12.1 - - + +
419A TRP* 4.6 0.2 - - - -
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Residues in contact with GLY 222 (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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220A PRO 3.1 4.7 + - - -
221A THR* 1.3 76.9 - - - +
223A CYS* 1.3 59.0 + - - +
224A SER* 3.7 2.7 - - - -
231A HIS 5.5 2.7 - - - -
232A TYR 3.4 13.5 - - - -
249A LYS 2.9 7.0 - - - +
250A ILE* 3.2 4.9 - - - -
251A ASP* 2.7 43.2 + - - -
382A HIS* 4.7 7.0 - - - -
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Residues in contact with CYS 223 (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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193A MET* 3.6 25.4 - - + -
196A ILE* 5.6 1.3 - - + -
197A CYS* 3.6 29.6 - - - -
221A THR* 4.3 0.7 - - + -
222A GLY* 1.3 74.6 - - - +
224A SER* 1.3 67.8 + - - +
225A LEU* 3.4 10.7 + - - +
232A TYR* 2.9 28.1 + - - -
234A PRO* 3.7 10.1 - - - -
248A CYS* 3.5 17.1 - - - -
249A LYS 3.0 8.7 - - - -
250A ILE* 4.1 9.6 - - + -
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Residues in contact with SER 224 (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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222A GLY* 4.9 1.4 - - - -
223A CYS* 1.3 76.0 + - - +
225A LEU* 1.3 58.1 + - - +
228A CYS* 3.3 21.1 - - - -
229A ALA 3.6 15.9 - - - -
230A ALA* 3.1 28.6 - - - -
231A HIS 3.6 0.7 + - - -
232A TYR* 3.2 24.7 + - - -
248A CYS* 3.5 1.2 - - - -
249A LYS* 3.0 35.9 + - - -
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Residues in contact with LEU 225 (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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193A MET* 3.6 23.6 - - + -
223A CYS 3.5 17.9 - - - +
224A SER* 1.3 72.9 - - - +
226A ASN* 1.3 75.8 + - - +
227A ASN* 3.2 2.6 + - - +
228A CYS* 2.9 30.0 + - - +
232A TYR* 4.5 9.6 - - + -
240A THR* 3.8 29.2 - - + -
242A LEU* 4.0 11.0 - - + -
246A ASP* 4.2 17.3 - - + +
247A ILE 3.7 0.7 - - - -
248A CYS* 3.7 21.8 - - + -
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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