Contacts of the helix formed by residues 293 - 298 (chain D) in PDB entry 1M6X
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 293 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D LEU* 3.1 34.1 - - + -
152D GLU* 2.9 29.4 + - - -
157D ILE* 3.6 14.4 - - + +
160D LYS* 3.2 30.6 - - + +
161D ILE* 3.9 29.8 - - + -
291D ALA* 2.7 13.9 + - - +
292D PRO* 1.3 98.6 - - + +
294D PRO* 1.3 81.4 - - + +
295D ILE* 3.8 18.2 - - + -
296D PHE* 3.3 19.2 + + + +
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Residues in contact with PRO 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D MET* 3.7 36.4 - - + +
146D ALA* 6.2 1.6 - - + -
147D LEU* 5.6 5.8 - - + +
293D TYR* 1.3 95.2 - - + +
295D ILE* 1.3 72.1 + - + +
297D ALA* 2.6 28.5 + - + +
298D ILE* 3.9 2.4 + - - +
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Residues in contact with ILE 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D SER* 3.2 48.9 - - - +
143D MET* 3.7 17.9 - - + +
144D LEU* 4.1 7.9 - - + +
147D LEU* 4.4 13.7 - - + -
293D TYR* 3.8 11.0 - - + -
294D PRO* 1.3 78.1 - - + +
296D PHE* 1.3 93.9 + - + +
297D ALA 2.8 6.9 + - - -
298D ILE* 3.0 31.1 + - + +
301D GLY* 5.2 1.2 - - - -
302D PRO* 4.3 23.1 - - + +
303D LYS* 4.9 1.0 + - - -
306D ILE* 5.0 6.5 - - + -
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Residues in contact with PHE 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D LEU* 5.6 0.9 - - + -
161D ILE* 3.8 28.3 - - + -
287D LEU* 3.6 50.5 - - + +
288D LYS* 3.7 24.9 - - - +
291D ALA* 4.1 4.9 - - - -
292D PRO* 4.1 11.2 - - + -
293D TYR* 3.6 27.8 - + + +
294D PRO 2.9 1.6 + - - -
295D ILE* 1.3 91.7 - - + +
297D ALA* 1.3 57.9 + - - +
298D ILE 3.5 0.2 - - - -
302D PRO 3.9 16.6 - - - -
303D LYS* 3.8 15.6 - - + +
306D ILE* 3.5 41.3 - - + -
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Residues in contact with ALA 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288D LYS* 3.5 18.3 + - - +
291D ALA* 5.1 9.0 - - + -
293D TYR 4.2 1.7 + - - +
294D PRO* 2.6 25.5 + - + +
296D PHE* 1.3 71.7 - - - +
298D ILE* 1.3 64.8 + - + +
299D LYS* 3.2 2.9 + - - +
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Residues in contact with ILE 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D HIS* 3.7 28.7 - - + +
140D SER* 3.5 35.7 - - - +
143D MET* 3.5 34.3 - - + -
294D PRO 4.3 3.6 - - - +
295D ILE* 3.0 20.3 + - + +
297D ALA* 1.3 75.6 - - + +
299D LYS* 1.3 75.1 + - - +
301D GLY* 3.0 11.8 + - - -
303D LYS* 3.3 13.2 + - - -
26J G 3.6 0.2 + - - -
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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