Contacts of the helix formed by residues 245 - 248 (chain B) in PDB entry 2EZT
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 TYR 245 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244B THR* 1.3 70.9 - - - +
246B PRO* 1.4 75.3 - - + +
248B LYS* 2.9 21.1 + - + +
261B SER* 3.6 8.8 - - - +
265B VAL* 3.4 24.5 - - + +
392B ILE* 3.9 18.3 - - + +
398B ASN* 2.9 55.8 + - + +
401B ALA* 5.3 0.4 - - + +
402B ASN* 3.4 24.2 - - + -
413B HIS* 3.6 18.3 + + - -
414B ILE 5.8 0.2 - - - -
415B THR* 3.8 21.4 - - + +
1615B FAD 2.9 41.9 + + + +
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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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221B ILE* 3.7 21.0 - - + +
244B THR* 3.6 9.9 - - - +
245B TYR* 1.4 99.2 - - + +
247B ALA* 1.3 54.8 + - - +
248B LYS 3.2 1.6 - - - +
250B ILE* 5.4 0.3 - - - +
413B HIS* 3.2 27.4 + - + +
417B ASN* 3.6 39.9 - - - +
1615B FAD 3.7 33.4 - - - +
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Residues in contact with ALA 247 (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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219B TYR* 3.8 10.1 + - + +
220B GLY* 3.7 25.6 - - - -
221B ILE* 3.8 6.3 - - - +
243B SER* 3.6 16.3 + - - -
244B THR* 3.1 23.0 + - - +
245B TYR 3.1 1.2 - - - -
246B PRO* 1.3 75.1 - - - +
248B LYS* 1.3 66.4 + - - +
249B GLY 3.4 0.3 + - - -
250B ILE* 3.2 29.8 + - + +
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Residues in contact with LYS 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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244B THR 3.5 3.4 + - - +
245B TYR* 2.9 18.2 + - + +
246B PRO 3.6 1.6 - - - +
247B ALA* 1.3 79.5 - - - +
249B GLY* 1.3 61.0 + - - +
250B ILE* 3.5 2.6 + - - +
253B ASP* 3.0 42.4 + - - +
258B TYR* 3.8 16.4 - - + +
267B GLN* 4.6 2.6 - - - +
401B ALA 3.5 11.0 - - - -
402B ASN* 2.6 48.6 + - + +
403B ARG 4.7 1.8 + - - -
405B LEU* 3.0 20.0 + - - -
407B LEU* 3.8 20.2 - - + -
413B HIS* 2.7 31.5 + - + +
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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