Contacts of the helix formed by residues 307 - 317 (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 GLY 307 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304B THR* 4.2 1.4 + - - -
305B HIS* 3.2 22.9 + - - -
306B ALA* 1.3 76.9 - - - +
308B ALA* 1.3 59.4 + - - -
309B GLY 3.3 2.5 - - - -
311B SER* 2.7 34.1 + - - +
330B GLN* 3.1 20.9 - - - -
333B ASN* 4.4 0.2 - - - -
502B UDP 3.6 8.0 + - - -
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ILE* 6.6 0.4 - - + -
196B LEU* 5.1 2.6 - - - +
307B GLY* 1.3 73.5 - - - +
309B GLY* 1.3 62.2 + - - +
311B SER* 3.9 4.0 - - - -
312B GLN* 3.5 20.3 + - - +
333B ASN* 3.8 15.2 - - - +
502B UDP 3.3 6.3 + - - +
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Residues in contact with GLY 309 (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* 5.0 4.3 - - - -
308B ALA* 1.3 76.5 - - - +
310B GLY* 1.3 63.0 + - - -
312B GLN* 3.4 8.9 + - - +
313B GLU* 3.1 38.2 + - - +
502B UDP 2.8 22.0 + - - -
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Residues in contact with GLY 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B GLN* 4.1 11.4 - - - -
302B PHE* 3.5 15.8 - - - -
304B THR* 4.5 8.7 - - - -
305B HIS* 5.4 0.9 - - - -
307B GLY 3.4 2.4 + - - -
309B GLY* 1.3 70.8 - - - +
311B SER* 1.3 65.2 + - - +
313B GLU* 4.0 12.0 + - - -
314B GLY* 3.0 20.4 + - - -
321B MET* 4.4 0.5 - - - +
502B UDP 2.8 20.3 + - - -
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Residues in contact with SER 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LEU* 3.9 22.2 - - - -
306B ALA* 3.2 24.0 + - - +
307B GLY 2.7 28.9 + - - +
308B ALA* 3.9 4.0 - - - -
310B GLY* 1.3 72.8 - - - +
312B GLN* 1.3 61.2 + - - +
314B GLY* 3.5 1.2 + - - -
315B LEU* 3.2 26.0 + - - +
321B MET* 4.1 6.3 - - - +
333B ASN* 3.9 8.7 - - - +
337B LEU* 3.8 20.7 - - - +
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Residues in contact with GLN 312 (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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193B PRO* 3.9 27.3 - - + +
196B LEU* 4.5 4.7 - - + -
213B ALA* 3.6 26.6 - - + +
215B GLN* 3.1 27.4 + - - +
308B ALA 3.5 10.4 + - - +
309B GLY* 3.4 11.4 + - - +
310B GLY 3.3 0.2 - - - -
311B SER* 1.3 78.6 - - - +
313B GLU* 1.3 67.4 + - - +
315B LEU* 3.3 6.5 + - - +
316B ALA* 2.8 33.5 + - - +
380B MET* 3.2 19.4 - - - +
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Residues in contact with GLU 313 (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* 3.1 7.2 + - - +
218B ARG* 2.7 23.7 + - - +
292B GLN* 3.0 19.1 + - - +
293B LEU* 4.5 15.3 - - + -
296B LEU* 3.7 15.2 - - + +
309B GLY 3.1 20.5 + - - +
310B GLY* 3.7 2.4 - - - +
312B GLN* 1.3 89.0 - - - +
314B GLY* 1.3 52.9 + - - +
316B ALA* 3.9 2.9 - - - -
317B THR* 2.7 39.9 + - - +
502B UDP 2.6 44.1 + - - -
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Residues in contact with GLY 314 (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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296B LEU* 4.2 1.9 - - - +
302B PHE* 4.1 11.9 - - - -
310B GLY 3.0 12.4 + - - -
312B GLN 3.3 0.2 - - - -
313B GLU* 1.3 75.7 - - - +
315B LEU* 1.3 60.3 + - - +
317B THR* 3.2 5.8 + - - -
318B ALA 3.2 2.9 + - - -
319B THR* 2.8 32.6 + - - +
321B MET* 3.8 26.2 - - - -
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Residues in contact with LEU 315 (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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193B PRO* 4.8 3.4 - - + -
195B ALA* 4.5 6.3 - - + -
196B LEU* 3.9 24.5 - - + -
311B SER 3.2 17.9 + - - +
312B GLN* 3.6 5.8 - - - +
314B GLY* 1.3 76.8 - - - +
316B ALA* 1.3 57.6 + - - +
317B THR 3.1 0.2 - - - -
318B ALA* 3.0 18.4 + - - +
321B MET* 3.7 17.5 - - + +
337B LEU* 3.7 15.5 - - + -
340B LEU* 4.3 7.2 - - + -
342B VAL* 3.8 22.4 - - + -
373B LEU* 3.8 11.9 - - + +
376B ILE* 3.6 23.5 - - + +
377B GLN* 3.8 15.1 + - - +
380B MET* 3.6 14.6 - - - -
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Residues in contact with ALA 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B LEU* 6.2 1.8 - - + -
312B GLN* 2.8 29.2 + - - +
313B GLU* 4.0 5.2 - - - +
314B GLY 3.3 0.2 - - - -
315B LEU* 1.3 72.8 - - - +
317B THR* 1.3 62.0 + - + +
318B ALA 3.4 0.4 - - - -
377B GLN* 3.3 20.9 + - - +
380B MET* 3.7 24.7 - - + -
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Residues in contact with THR 317 (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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293B LEU* 4.2 11.7 - - + -
296B LEU* 3.5 22.9 + - + +
297B ARG* 3.6 41.7 - - + +
313B GLU 2.7 22.3 + - - +
314B GLY* 3.2 5.0 + - - -
316B ALA* 1.3 81.1 - - + +
318B ALA* 1.3 69.6 + - - +
319B THR* 2.8 22.3 + - - -
377B GLN* 3.3 9.5 + - - +
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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