Contacts of the helix formed by residues 243 - 249 (chain A) in PDB entry 5JQE
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 243 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ILE* 5.4 2.2 - - + -
222A TYR* 3.7 8.1 - - - +
226A GLU* 4.0 10.5 - - + +
239A ASN* 3.4 39.5 - - + +
240A GLY 3.1 6.1 + - - +
242A TRP* 1.3 79.1 - - - +
244A TRP* 1.3 65.3 + - + +
245A SER 3.3 1.2 + - - -
246A ASN* 3.7 8.9 + - - +
247A ILE* 3.1 28.6 + - + +
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Residues in contact with TRP 244 (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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126A SER* 6.1 0.6 - - - -
128A ILE* 4.0 13.7 - - + +
239A ASN 5.4 0.2 + - - -
240A GLY 3.5 16.8 + - - -
241A PRO* 3.5 31.4 - - + +
242A TRP 3.1 1.6 - - - -
243A ALA* 1.3 80.1 - - - +
245A SER* 1.3 57.1 + - - +
247A ILE* 3.4 7.7 + - + +
248A ASP* 2.9 36.6 + - - +
254A TYR* 4.2 6.5 - + - +
256A VAL* 3.9 18.9 - - + +
310A PRO* 6.5 0.9 - - + -
312A GLY* 5.5 4.0 - - - -
328A ARG* 3.5 77.4 - - + +
329A ILE* 4.0 16.4 - - + -
332A THR* 3.5 30.9 - - + +
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Residues in contact with SER 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A PRO 4.9 2.6 + - - -
242A TRP* 3.7 9.6 + - - -
243A ALA 3.3 1.0 - - - -
244A TRP* 1.3 79.2 - - - +
246A ASN* 1.3 69.9 + - - +
248A ASP* 3.3 20.3 + - - +
249A THR* 3.4 17.3 + - - +
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Residues in contact with ASN 246 (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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226A GLU* 4.5 24.0 - - - +
230A ASN* 3.7 5.4 + - - +
242A TRP 4.0 13.3 - - - +
243A ALA* 3.7 6.7 + - - +
244A TRP 3.4 0.2 - - - -
245A SER* 1.3 79.9 - - - +
247A ILE* 1.3 59.7 + - - +
249A THR* 3.3 17.9 + - - +
250A SER* 3.4 12.1 + - - -
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Residues in contact with ILE 247 (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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128A ILE* 3.9 14.6 - - + -
226A GLU* 5.0 2.5 - - + -
229A PHE* 3.9 20.6 - - + -
230A ASN* 3.2 32.5 - - - +
243A ALA* 3.1 22.2 - - + +
244A TRP* 3.6 10.8 - - + +
245A SER 3.2 0.2 - - - -
246A ASN* 1.3 75.3 - - + +
248A ASP* 1.3 67.1 + - - +
249A THR 3.3 0.4 - - - -
250A SER* 3.4 17.9 + - - -
251A LYS 3.8 3.6 + - - -
252A VAL* 4.1 7.4 - - + +
254A TYR* 3.4 50.6 - - + -
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Residues in contact with ASP 248 (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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244A TRP* 2.9 29.0 + - - +
245A SER* 3.3 12.0 + - - +
247A ILE* 1.3 77.8 - - - +
249A THR* 1.3 61.7 + - + +
251A LYS* 3.5 22.2 + - - +
254A TYR* 2.4 31.9 + - - -
328A ARG* 3.7 11.2 + - - -
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Residues in contact with THR 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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245A SER 3.4 12.6 + - - +
246A ASN* 3.3 16.1 + - - -
248A ASP* 1.3 73.9 - - + +
250A SER* 1.3 62.2 + - - +
251A LYS* 3.0 21.5 + - - +
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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