Contacts of the helix formed by residues 248 - 255 (chain A) in PDB entry 3OPY
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 248 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A TYR* 1.3 76.9 - - + +
249A GLY* 1.3 64.2 + - - +
251A THR* 2.6 37.0 + - - +
259A MET* 5.0 11.2 - - + -
279A ILE 3.0 13.8 + - - +
280A GLY* 3.5 21.7 + - - -
281A THR 3.1 19.4 + - - +
282A ALA* 3.3 13.3 - - + +
363B ALA* 6.1 0.2 - - - +
365B SER* 4.5 14.7 + - - -
366B HIS 5.2 1.2 + - - -
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Residues in contact with GLY 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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216A ILE* 4.3 9.8 - - - +
217A THR 3.5 18.3 + - - -
218A SER* 4.3 9.6 - - - -
246A CYS* 3.6 23.2 + - - +
247A TYR 3.6 0.8 - - - +
248A GLU* 1.3 75.2 - - - +
250A TYR* 1.3 61.5 + - - -
251A THR 3.4 0.2 + - - -
252A GLY 3.5 5.9 + - - -
253A LEU* 4.5 0.2 - - - +
280A GLY 3.4 9.5 + - - -
282A ALA* 3.9 10.7 - - - +
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Residues in contact with TYR 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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216A ILE* 3.7 19.3 - - + -
218A SER* 3.6 27.9 + - - -
249A GLY* 1.3 69.9 - - - -
251A THR* 1.4 54.0 + - + +
253A LEU* 3.0 20.3 + - + +
254A VAL* 2.8 37.1 + - - +
282A ALA* 4.9 3.4 + - - +
283A ARG 5.9 1.8 - - - +
284A CYS* 4.5 15.7 - - + -
287A PHE* 3.6 66.6 - + + -
308A LEU* 5.0 2.7 - - + -
310A VAL* 3.3 19.1 - - + +
316A SER* 2.7 31.7 + - - -
319A GLY* 5.0 1.8 - - - -
320A ALA* 3.3 13.9 + - - +
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Residues in contact with THR 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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248A GLU* 2.6 28.4 + - - +
250A TYR* 1.4 74.5 - - + +
252A GLY* 1.3 55.9 + - - +
254A VAL* 3.3 5.3 + - - +
255A LYS* 2.8 45.0 + - - +
259A MET* 5.3 1.4 - - - -
282A ALA* 3.8 20.3 - - + +
283A ARG 4.5 11.2 - - - +
285A LYS* 6.1 1.3 - - + +
286A GLU* 3.9 24.7 - - - +
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Residues in contact with GLY 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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246A CYS* 3.4 7.2 - - - -
247A TYR 3.1 24.9 + - - -
248A GLU 3.4 0.2 + - - -
249A GLY 3.5 0.4 + - - -
250A TYR 3.3 0.6 - - - -
251A THR* 1.3 81.8 + - - +
253A LEU* 1.4 56.5 + - - +
256A GLY* 3.0 26.6 - - - -
259A MET* 3.3 26.7 - - - +
260A LEU* 3.5 4.0 - - - +
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Residues in contact with LEU 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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214A ALA* 5.4 2.0 - - + -
216A ILE* 5.2 1.6 - - + -
246A CYS* 3.1 25.5 - - + -
250A TYR* 3.0 32.1 + - + +
252A GLY* 1.4 74.4 - - - +
254A VAL* 1.4 55.9 + - - +
256A GLY 3.8 0.2 + - - -
260A LEU* 4.5 12.6 - - + -
287A PHE* 4.3 3.6 - - + -
296A ALA* 3.3 32.3 - - + +
299A ASN* 2.6 29.3 + - + +
300A MET* 3.9 24.2 - - + +
305A ILE* 6.4 0.2 - - + -
308A LEU* 4.1 33.9 - - + -
323A PHE* 4.5 7.0 - - + -
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Residues in contact with VAL 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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250A TYR 2.8 19.1 + - - +
251A THR* 3.9 6.5 - - - +
253A LEU* 1.4 78.1 - - - +
255A LYS* 1.4 54.9 + - + +
256A GLY 3.2 1.3 - - - -
286A GLU* 5.0 17.5 - - + +
287A PHE* 4.1 27.1 - - + +
292A GLY* 3.4 35.4 - - - +
295A GLN* 4.1 16.4 - - + +
296A ALA* 4.1 4.5 - - + +
299A ASN* 2.8 16.9 + - - +
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Residues in contact with LYS 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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251A THR* 2.8 37.0 + - - +
252A GLY 3.7 1.1 - - - -
254A VAL* 1.4 70.8 - - + +
256A GLY* 1.3 61.6 + - - +
257A GLY* 3.0 5.9 + - - -
259A MET* 3.8 36.6 - - + +
286A GLU* 6.1 0.9 - - - +
299A ASN* 4.1 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