Contacts of the helix formed by residues 237 - 244 (chain A) in PDB entry 1JD7
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 SER 237 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A THR* 3.2 11.4 + - - +
236A GLY* 1.3 73.4 - - - -
238A LEU* 1.3 63.7 + - - +
239A ALA 2.9 2.9 - - - -
240A TRP* 2.9 55.9 + - - -
365A THR 4.3 5.0 + - - -
366A ASN* 2.7 35.3 + - - -
367A ASN* 3.5 4.7 - - - -
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Residues in contact with LEU 238 (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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232A THR* 4.6 1.8 - - + +
233A PHE* 3.4 55.0 - - + -
236A GLY 4.2 0.2 - - - -
237A SER* 1.3 72.3 - - - +
239A ALA* 1.3 63.1 + - - +
240A TRP 3.0 0.4 - - - -
241A LEU* 2.9 32.2 + - + +
361A TRP* 4.0 1.7 - - - -
366A ASN 3.1 8.0 + - - +
367A ASN* 3.2 21.5 + - - +
369A ILE* 3.7 30.9 - - + +
381A ILE* 3.9 28.3 - - + +
383A LYS* 4.0 19.3 - - + -
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Residues in contact with ALA 239 (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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237A SER* 2.9 3.7 - - - -
238A LEU* 1.3 77.9 - - - +
240A TRP* 1.3 62.9 + - + +
241A LEU 3.1 1.5 + - - -
242A SER* 3.5 20.7 + - - -
361A TRP* 4.6 0.7 - - - -
363A ASP* 3.5 39.3 - - + +
365A THR* 3.7 18.6 - - - +
366A ASN 3.0 15.1 + - - +
369A ILE* 4.0 2.0 - - - +
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Residues in contact with TRP 240 (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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231A ASN* 6.2 0.4 - - - -
232A THR* 4.2 13.5 - - + -
235A ASN 4.8 2.2 - - - -
236A GLY* 3.4 25.6 - - - -
237A SER* 2.9 43.8 + - - +
239A ALA* 1.3 78.7 - - + +
241A LEU* 1.3 55.7 + - - +
242A SER* 3.2 4.3 - - - -
243A ASN* 3.3 18.9 - - - +
248A TRP* 3.1 32.1 - + + -
365A THR 5.4 1.8 + - - -
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Residues in contact with LEU 241 (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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229A LEU* 4.2 5.4 - - + -
232A THR* 3.9 22.4 - - + +
233A PHE* 4.1 12.6 - - + -
238A LEU* 2.9 42.2 + - + +
240A TRP* 1.3 75.3 - - - +
242A SER* 1.3 62.9 + - - +
243A ASN 3.0 4.8 + - - -
244A PHE* 3.1 50.4 + - + +
248A TRP* 4.0 5.6 - - + -
290A PHE* 3.7 35.2 - - + -
294A TYR* 3.7 7.6 + - - -
361A TRP* 3.7 8.2 - - + -
369A ILE* 5.1 0.9 - - + -
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Residues in contact with SER 242 (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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239A ALA 3.5 11.3 + - - -
240A TRP 3.2 0.9 + - - -
241A LEU* 1.3 77.7 - - - +
243A ASN* 1.3 67.3 + - - +
244A PHE 3.6 0.2 - - - -
294A TYR* 3.7 8.3 + - - -
358A VAL* 5.2 4.5 - - - +
361A TRP* 3.5 49.5 - - - +
363A ASP* 5.1 0.7 - - - -
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Residues in contact with ASN 243 (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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240A TRP 3.3 16.8 - - - +
242A SER* 1.3 84.9 + - - +
244A PHE* 1.3 65.3 + - - +
247A GLY* 3.6 26.1 + - - -
248A TRP* 3.2 21.0 + - - +
294A TYR* 3.6 2.2 - - - -
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Residues in contact with PHE 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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225A TYR* 3.5 42.4 - + - -
228A GLU* 4.0 4.5 - - + -
229A LEU* 3.8 34.1 - - + -
241A LEU* 3.1 39.6 + - + +
243A ASN* 1.3 78.7 - - - +
245A GLY* 1.3 61.0 + - - +
246A GLU* 4.3 2.1 + - - +
247A GLY 4.9 0.3 + - - -
248A TRP* 3.7 28.0 - + - +
250A PHE* 3.5 24.5 - + - -
290A PHE* 3.8 16.6 - + + -
294A TYR* 2.8 36.5 + + + -
296A TYR* 4.9 0.5 - - - -
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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