Contacts of the helix formed by residues 293 - 298 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B LEU* 3.4 23.6 - - + -
152B GLU* 2.6 31.8 + - - -
157B ILE* 3.6 17.5 - - + -
160B LYS* 3.2 36.7 - - + +
161B ILE* 3.9 29.6 - - + -
291B ALA* 2.7 12.3 + - - +
292B PRO* 1.3 97.3 - - + +
294B PRO* 1.3 82.6 - - + +
295B ILE* 3.8 17.7 - - + -
296B PHE* 3.2 22.1 + + + +
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Residues in contact with PRO 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B MET* 3.4 30.3 - - + +
146B ALA* 6.3 1.1 - - + -
147B LEU* 5.7 4.9 - - + +
150B GLU* 6.0 2.7 - - - +
293B TYR* 1.3 94.4 - - + +
295B ILE* 1.3 59.8 + - + +
297B ALA* 2.6 41.7 + - + +
298B ILE* 3.9 3.5 + - - +
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Residues in contact with ILE 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B SER* 3.5 15.3 - - - +
143B MET* 3.6 24.1 - - + +
144B LEU* 3.5 41.3 - - + +
147B LEU* 4.7 14.1 - - + -
293B TYR* 3.8 11.2 - - + -
294B PRO* 1.3 78.2 - - + +
296B PHE* 1.3 95.1 + - + +
297B ALA 2.8 6.9 + - - -
298B ILE* 3.0 29.0 + - + +
301B GLY* 5.2 1.0 - - - -
302B PRO* 4.3 20.6 - - + +
303B LYS* 5.0 0.5 + - - -
306B ILE* 4.8 2.2 - - + -
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Residues in contact with PHE 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B LEU* 6.0 1.3 - - + -
161B ILE* 3.8 23.3 - - + -
287B LEU* 3.6 51.8 - - + +
288B LYS* 3.7 12.6 - - - +
291B ALA* 4.1 7.0 - - - -
292B PRO* 4.1 14.4 - - + -
293B TYR* 3.2 29.6 + + + +
294B PRO 2.9 3.4 + - - -
295B ILE* 1.3 91.2 - - + +
297B ALA* 1.3 58.4 + - - +
302B PRO 3.9 16.6 - - - -
303B LYS* 3.4 25.9 - - + +
306B ILE* 3.6 40.6 - - + -
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B LYS* 3.6 18.8 + - - +
291B ALA* 5.1 9.0 - - + -
293B TYR 4.1 1.3 + - - +
294B PRO* 2.6 26.3 + - + +
296B PHE* 1.3 72.4 - - - +
298B ILE* 1.3 63.9 + - + +
299B LYS 3.2 3.1 + - - -
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Residues in contact with ILE 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B GLY* 3.3 33.4 - - - +
139B HIS* 3.6 32.3 - - + +
140B SER* 3.6 14.8 - - - -
143B MET* 3.1 38.4 - - + -
294B PRO 4.3 2.5 - - - +
295B ILE* 3.0 19.8 + - + +
297B ALA* 1.3 76.2 - - + +
299B LYS* 1.3 68.7 + - - +
301B GLY* 3.1 14.2 + - - +
303B LYS* 3.1 14.6 + - - -
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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