Contacts of the helix formed by residues 291 - 298 (chain B) in PDB entry 4M83
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 PRO 291 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B GLU* 4.1 31.0 - - + +
222B GLY 4.5 2.7 - - - +
223B GLY 4.0 18.6 - - - +
224B TRP* 4.1 8.1 - - + -
287B HIS* 6.2 1.1 - - + -
289B TRP* 4.7 5.5 - - + +
290B VAL* 1.3 85.5 - - + +
292B GLN* 1.3 59.9 + - - +
293B LEU 3.5 2.0 - - - -
294B ALA* 3.2 15.3 + - + -
295B ILE* 2.8 41.0 + - + +
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Residues in contact with GLN 292 (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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221B GLU* 4.6 1.0 + - - -
235B LEU* 3.8 10.8 - - + -
237B SER* 2.8 30.2 + - - -
239B GLY* 5.2 0.6 + - - -
290B VAL* 2.8 15.5 + - + +
291B PRO* 1.3 69.0 - - - +
293B LEU* 1.3 62.4 + - - +
295B ILE* 3.4 0.7 + - - +
296B LEU* 2.8 38.7 + - + +
302B PHE* 3.2 29.8 - - - -
310B GLY* 4.1 6.5 - - - -
313B GLU* 3.0 17.8 + - - +
502B UDP 3.2 48.9 + - + +
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Residues in contact with LEU 293 (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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215B GLN* 4.8 4.5 - - - +
218B ARG* 3.6 50.6 - - + +
221B GLU* 5.0 2.5 + - - +
291B PRO 3.5 0.4 - - - -
292B GLN* 1.3 78.1 - - - +
294B ALA* 1.3 63.2 + - - +
296B LEU* 3.2 4.1 + - + +
297B ARG* 3.0 66.3 + - - +
313B GLU* 4.5 19.7 - - + -
316B ALA* 6.2 1.8 - - + -
317B THR* 4.2 19.1 - - + -
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Residues in contact with ALA 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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221B GLU* 6.4 0.2 - - + -
222B GLY 4.1 5.2 - - - +
223B GLY* 3.9 26.7 - - - -
224B TRP* 4.2 5.3 - - - +
291B PRO* 3.2 23.8 + - + +
293B LEU* 1.3 80.3 - - - +
295B ILE* 1.3 61.4 + - - +
297B ARG* 3.9 14.0 + - - +
298B GLN* 3.6 20.4 + - - +
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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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224B TRP* 3.4 58.6 - - + +
233B VAL* 4.8 5.8 - - + -
235B LEU* 3.9 28.0 - - + -
265B VAL* 4.0 18.2 - - + -
287B HIS* 5.6 1.1 - - + -
290B VAL* 3.8 27.4 - - + -
291B PRO* 2.8 23.2 + - + +
292B GLN 3.9 2.5 - - - +
294B ALA* 1.3 75.7 - - - +
296B LEU* 1.3 59.4 + - - +
298B GLN 2.7 32.4 - - - +
299B ALA* 3.7 1.9 - - + +
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Residues in contact with LEU 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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235B LEU* 3.9 14.4 - - + -
292B GLN* 2.8 37.6 + - + +
293B LEU* 3.2 4.2 + - - +
295B ILE* 1.3 69.8 - - - +
297B ARG* 1.3 67.1 + - - +
298B GLN 3.0 2.5 + - - -
299B ALA* 3.5 11.2 + - + +
302B PHE* 3.4 51.4 - - + -
313B GLU* 3.7 34.5 - - + +
317B THR* 3.5 13.4 - - + +
319B THR* 3.3 29.1 + - + +
503B MG 4.1 0.7 - - - -
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Residues in contact with ARG 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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218B ARG* 5.3 4.8 - - - +
293B LEU* 3.0 58.7 + - + +
294B ALA* 4.2 11.3 - - - +
295B ILE 3.3 0.4 - - - -
296B LEU* 1.3 75.2 - - - +
298B GLN* 1.3 57.4 + - + +
317B THR* 3.6 24.3 - - + +
503B MG 2.6 22.5 - - - -
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Residues in contact with GLN 298 (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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224B TRP* 2.5 47.3 - - + +
225B GLN* 4.2 2.8 - - - -
226B ARG* 3.9 29.6 - - - +
233B VAL* 4.1 0.9 - - - +
294B ALA 3.6 15.4 - - - +
295B ILE 2.7 15.7 + - - +
296B LEU 3.0 0.2 - - - -
297B ARG* 1.3 79.5 - - + +
299B ALA* 1.3 58.0 + - - +
503B MG 3.6 2.7 - - - -
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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