Contacts of the helix formed by residues 277 - 282 (chain A) in PDB entry 1JWL
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 277 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A HIS* 4.8 8.5 + - + -
78A GLN* 5.9 2.5 - - - +
276A THR* 1.3 75.5 - - - +
278A ASP* 1.3 69.2 + - - +
279A SER 3.3 0.3 + - - -
280A SER* 3.3 19.4 + - - -
281A CYS* 5.6 0.2 - - - -
221B SER* 5.3 8.8 - - - -
222B ALA* 5.4 3.5 - - - +
223B MET* 6.0 2.3 - - - +
248B GLN* 5.9 0.9 - - - +
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Residues in contact with ASP 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A THR* 3.3 7.5 + - - +
277A GLU* 1.3 79.9 - - - +
279A SER* 1.3 65.8 + - - +
281A CYS* 2.8 19.1 + - - +
282A TYR* 3.4 27.3 - - + +
222B ALA* 4.1 16.6 + - - +
248B GLN* 3.4 40.9 + - - +
251B LEU* 4.0 11.1 - - + +
278B ASP* 4.5 11.6 - - - +
282B TYR* 4.5 5.7 + - - -
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Residues in contact with SER 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ASP* 3.3 28.0 - - - -
275A ASP* 3.4 1.5 + - - -
276A THR* 2.5 30.9 + - - -
278A ASP* 1.3 77.0 - - - +
280A SER* 1.3 55.8 + - - +
281A CYS 3.1 4.6 + - - -
282A TYR* 3.4 25.2 + - - +
286A LEU* 3.2 29.4 + - - -
288A THR* 4.8 0.7 - - - -
326A ARG* 2.8 25.6 + - - -
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Residues in contact with SER 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A THR 5.3 0.2 - - - -
277A GLU 3.3 14.9 + - - -
278A ASP 2.9 1.2 + - - -
279A SER* 1.3 79.2 + - - +
281A CYS* 1.3 66.4 + - - +
282A TYR 3.6 0.7 - - - -
285A PRO* 3.9 11.6 - - - +
326A ARG* 3.7 31.6 - - - +
223B MET* 4.4 10.3 - - - +
255B ARG* 3.3 21.5 + - - -
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Residues in contact with CYS 281 (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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277A GLU 5.6 0.2 - - - -
278A ASP 2.8 10.8 + - - +
280A SER* 1.3 92.2 - - - +
282A TYR* 1.3 65.7 + - - +
283A ILE* 3.8 4.0 - - - +
222B ALA* 4.1 18.4 - - + -
223B MET* 3.8 37.7 - - - -
226B PHE* 4.2 5.6 - - - -
251B LEU* 3.8 15.2 - - + +
252B GLY* 4.4 10.1 - - - -
255B ARG* 3.4 32.0 - - + +
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Residues in contact with TYR 282 (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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247A ASP 3.9 24.7 + - - -
248A GLN* 4.2 13.2 + - - +
251A LEU* 3.8 43.9 - - + +
254A MET* 4.4 9.0 - - + -
276A THR* 4.4 4.9 + - - -
278A ASP* 3.4 33.6 - - + +
279A SER* 3.4 23.6 + - - +
280A SER 3.6 0.4 - - - -
281A CYS* 1.3 82.2 - - - +
283A ILE* 1.3 56.9 + - - +
284A PRO* 2.5 35.4 - - - +
285A PRO* 2.7 7.3 - - - +
286A LEU* 3.8 26.7 - - + +
251B LEU* 4.1 15.9 - - + -
255B ARG* 4.2 1.0 - - - +
278B ASP* 4.5 3.8 + - - -
282B TYR* 5.4 1.1 - + - -
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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