Contacts of the strand formed by residues 249 - 256 (chain A) in PDB entry 2AYO
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 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A LYS* 4.0 19.8 + - - -
247A GLY 4.3 0.8 - - - -
248A VAL* 1.3 71.0 - - - +
250A PHE* 1.3 76.1 + - - +
268A LYS* 4.8 16.3 + - + +
269A GLU 3.3 3.4 - - - +
270A ASN* 2.8 24.0 + - - +
316A ILE* 3.7 0.9 - - - -
317A SER* 2.9 33.6 + - - +
318A ARG* 3.4 41.3 + - + +
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Residues in contact with PHE 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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248A VAL* 4.1 21.5 - - + -
249A GLU* 1.3 98.7 - - - +
251A GLU* 1.3 56.3 + - - +
252A THR* 5.7 1.1 - - + -
268A LYS* 2.7 40.1 - - - +
269A GLU* 2.6 41.4 + - + +
270A ASN 6.2 0.4 - - - -
271A GLN* 5.5 8.7 - - + -
274A LEU* 4.6 13.2 - - + -
293A LEU* 5.3 9.6 - - + -
314A SER* 4.2 26.5 - - - -
315A LYS 4.3 2.0 - - - -
316A ILE* 3.7 31.0 - - + -
317A SER* 3.5 7.8 - - - +
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Residues in contact with GLU 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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250A PHE* 1.3 75.5 - - - +
252A THR* 1.3 64.6 + - - +
253A THR* 5.4 10.0 - - + +
266A LYS* 6.0 6.3 - - + -
267A GLY 3.5 4.9 - - - +
268A LYS* 4.4 12.0 - - + -
313A SER 3.3 5.0 - - - +
314A SER* 3.3 2.3 - - - -
315A LYS* 3.1 42.6 + - + +
317A SER* 3.9 6.2 + - - +
359A THR* 3.6 28.3 + - - +
360A PRO* 4.8 3.8 - - - +
361A GLU* 3.4 18.9 - - - +
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Residues in contact with THR 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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250A PHE* 5.3 1.8 - - + -
251A GLU* 1.3 78.2 - - - +
253A THR* 1.3 62.4 + - - +
254A MET* 4.6 5.7 + - - +
265A THR 3.5 2.1 + - - +
266A LYS* 2.8 11.7 - - - +
267A GLY* 2.4 79.6 + - - +
268A LYS* 3.6 7.4 - - - +
269A GLU* 4.2 22.0 + - + +
312A LYS* 4.9 10.5 - - - +
313A SER 3.1 7.4 + - - -
314A SER* 4.2 11.1 + - - -
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Residues in contact with THR 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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251A GLU* 5.4 9.9 - - + +
252A THR* 1.3 77.2 + - - +
254A MET* 1.3 60.9 + - - +
255A LYS* 4.3 2.4 + - - +
264A VAL* 4.6 11.7 - - - -
265A THR 3.5 4.5 - - - -
266A LYS* 3.7 34.8 - - + +
311A ILE 3.9 0.5 - - - +
312A LYS* 3.6 0.3 - - - -
313A SER* 2.8 50.5 + - - +
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Residues in contact with MET 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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252A THR* 4.9 5.6 - - - +
253A THR* 1.3 75.8 - - - +
255A LYS* 1.3 58.8 + - - +
263A GLU 4.2 2.3 - - - +
264A VAL* 3.6 6.9 - - - +
265A THR* 3.0 48.5 + - - +
297A ILE* 3.7 25.6 - - - -
299A LYS* 2.9 43.5 - - - +
310A TYR* 4.2 13.5 - - + -
311A ILE 3.2 23.6 - - - +
312A LYS* 4.3 6.1 - - + -
4B PHE* 5.7 1.8 - - + -
64B GLU* 4.1 8.5 - - - +
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Residues in contact with LYS 255 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A THR* 5.8 1.8 - - - +
254A MET* 1.3 74.8 - - - +
256A CYS* 1.3 67.2 + - - +
262A GLU 5.4 1.1 - - - -
263A GLU 5.7 0.2 - - - -
264A VAL* 3.8 28.5 - - + +
310A TYR* 4.5 2.2 - - - -
311A ILE* 2.7 49.1 + - + +
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Residues in contact with CYS 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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255A LYS* 1.3 85.6 - - - +
257A THR* 1.3 60.2 + - - +
258A GLU* 2.9 54.8 + - - +
259A SER* 5.0 0.5 + - - -
261A GLU 6.0 0.4 - - - +
262A GLU* 3.9 31.1 + - + +
304A LEU* 4.1 9.2 - - - -
308A ALA* 4.7 1.8 - - - -
309A LEU 3.9 5.2 - - - -
310A TYR* 3.8 29.0 - - + -
311A ILE* 5.5 0.4 - - - +
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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