Contacts of the helix formed by residues 248 - 256 (chain A) in PDB entry 5E63
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 LYS 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A LEU* 3.4 28.4 - - + +
222A GLY* 3.1 22.5 + - - +
223A CYS* 3.9 8.7 - - + -
244A ASP* 2.7 41.2 + - - +
246A GLN 3.5 0.2 - - - -
247A GLY* 1.3 86.5 - - - +
249A ILE* 1.3 65.3 + - + +
250A ILE 3.6 0.7 - - - -
251A PRO* 3.7 3.0 - - - +
252A PHE* 3.2 23.6 + - - +
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Residues in contact with ILE 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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202A PHE* 4.0 25.6 - - + -
221A LEU* 4.2 21.1 - - + -
223A CYS* 3.7 22.9 - - - -
239A VAL* 4.1 13.0 - - + -
244A ASP 3.1 11.0 + - - +
245A ILE* 3.9 20.6 - - + +
248A LYS* 1.3 75.8 - - - +
250A ILE* 1.3 70.9 + - - +
252A PHE* 3.2 3.7 + - - +
253A PHE* 3.2 43.8 + - + -
269A TRP* 4.0 24.2 - - + -
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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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245A ILE* 2.9 25.2 + - + +
246A GLN* 4.4 8.1 - - - +
249A ILE* 1.3 77.3 - - - +
251A PRO* 1.3 73.0 - - + +
254A HIS* 3.1 10.1 + - + +
266A TYR* 2.7 31.9 + - - +
269A TRP* 3.6 25.8 - - + -
270A CYS* 3.7 28.5 - - + +
273A ALA* 3.8 28.9 - - + -
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Residues in contact with PRO 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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246A GLN 3.2 26.9 - - - +
247A GLY* 3.5 15.3 - - - +
248A LYS 3.7 10.8 - - - +
249A ILE 3.7 1.6 - - - -
250A ILE* 1.3 93.8 - - + +
252A PHE* 1.3 63.2 + - - +
254A HIS* 3.5 7.7 + - + +
255A GLN* 3.3 24.1 + - - +
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Residues in contact with PHE 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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169A PRO* 3.6 42.6 - - + -
172A LEU* 3.6 24.9 - - + -
173A ALA 4.4 0.2 - - - -
220A TYR* 4.0 14.8 - + - -
221A LEU* 4.1 14.6 - - + -
248A LYS 3.2 19.6 + - - +
249A ILE* 3.2 7.8 + - - +
251A PRO* 1.3 74.4 - - - +
253A PHE* 1.3 96.7 + + + +
255A GLN* 3.1 4.5 + - - -
256A TYR* 2.8 50.3 + + + +
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Residues in contact with PHE 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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172A LEU* 4.2 7.2 - - + -
173A ALA* 4.2 8.3 - - - -
176A VAL* 3.8 14.8 - - + -
182A PHE* 4.3 7.4 - + - -
202A PHE* 3.6 37.2 - + - -
221A LEU* 5.4 1.8 - - + -
249A ILE* 3.2 38.8 + - + -
252A PHE* 1.3 107.5 - + + +
254A HIS* 1.3 63.9 + - - +
256A TYR 3.3 20.8 - - - +
257A LYS* 3.4 14.9 - - - +
258A ILE* 3.6 31.5 + - + -
263A TYR* 5.4 0.2 - - - -
266A TYR* 3.5 29.6 + + + -
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Residues in contact with HIS 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 ILE* 3.1 16.3 + - + +
251A PRO* 3.6 9.2 - - + +
253A PHE* 1.3 76.9 - - - +
255A GLN* 1.3 68.8 + - + +
257A LYS* 2.8 40.9 + - - +
266A TYR* 3.1 16.4 + - - +
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Residues in contact with GLN 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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170A PHE* 4.6 6.1 - - - -
251A PRO 3.3 9.8 + - - +
252A PHE* 3.1 4.4 + - - +
254A HIS* 1.3 85.0 - - + +
256A TYR* 1.3 99.5 + - + +
257A LYS* 3.6 6.9 + - - +
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Residues in contact with TYR 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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169A PRO* 3.3 45.1 - - + +
170A PHE* 3.7 36.6 - + + -
173A ALA* 3.6 18.2 - - + +
252A PHE* 2.8 43.6 + + + +
253A PHE* 3.3 19.8 - - - +
255A GLN* 1.3 102.5 + - + +
257A LYS* 1.3 64.3 + - - +
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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