Contacts of the helix formed by residues 294 - 300 (chain B) in PDB entry 4EEM
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 LYS 294 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232B PHE* 4.4 7.6 - - + -
236B LEU* 3.7 32.3 - - + +
240B ASP* 5.8 4.2 + - - +
241B TYR 3.9 14.9 + - - +
242B THR* 2.9 27.2 + - + +
244B PHE* 4.0 20.6 - - + -
292B LEU 3.8 0.4 + - - -
293B SER* 1.3 71.3 - - - +
295B GLN* 1.3 58.1 + - - +
297B PHE* 3.1 4.3 + - - +
298B LEU* 2.9 51.9 + - + +
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Residues in contact with GLN 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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293B SER* 3.2 6.1 + - - +
294B LYS* 1.3 76.8 - - - +
296B GLN* 1.3 60.6 + - - +
298B LEU* 3.3 23.2 + - - +
299B THR* 2.8 50.2 + - - +
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Residues in contact with GLN 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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262B CYS* 5.3 0.3 - - - +
263B PHE 3.1 24.9 + - - +
264B SER* 3.2 19.2 + - - +
265B GLN* 3.4 7.4 - - - +
266B PRO* 3.5 17.1 - - + +
291B ALA 4.3 0.3 - - - +
292B LEU* 3.5 19.4 - - + -
293B SER* 2.9 38.9 + - - +
295B GLN* 1.3 76.9 - - - +
297B PHE* 1.3 63.1 + - - +
299B THR* 3.5 10.0 + - - -
300B ILE* 3.5 17.8 + - - +
321B LEU* 4.6 2.0 - - + +
326B MET* 3.5 28.2 - - + +
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Residues in contact with PHE 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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229B ASN* 3.2 23.6 - - - -
232B PHE* 3.3 56.5 - + + -
244B PHE* 5.4 1.1 - - + -
246B PHE* 3.7 23.8 - + - -
292B LEU* 4.2 13.4 - - + +
293B SER 3.0 12.7 + - - +
294B LYS 3.6 6.7 - - - +
296B GLN* 1.3 75.5 - - - +
298B LEU* 1.3 66.7 + - + +
300B ILE* 3.3 7.5 + - - +
302B GLY* 2.9 40.0 + - - -
303B PHE* 3.6 41.5 - + - -
371B LEU* 4.3 10.5 - - + -
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Residues in contact with LEU 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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232B PHE* 3.8 18.2 - - + -
294B LYS* 2.9 40.2 + - + +
295B GLN* 3.9 23.8 - - - +
297B PHE* 1.3 78.5 - - - +
299B THR* 1.3 56.9 + - - +
301B ASN* 2.9 20.9 + - - +
302B GLY 4.9 1.1 - - - +
371B LEU* 3.7 29.4 - - + -
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Residues in contact with THR 299 (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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295B GLN* 2.8 40.2 + - - +
296B GLN* 3.8 6.6 - - - -
297B PHE 3.3 0.4 - - - -
298B LEU* 1.3 76.2 - - - +
300B ILE* 1.3 58.3 + - - +
301B ASN 3.3 0.8 + - - -
324B ARG* 3.3 56.3 + - + +
326B MET* 4.4 9.1 - - + -
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Residues in contact with ILE 300 (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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292B LEU* 4.3 3.8 - - + -
296B GLN 3.5 5.1 + - - +
297B PHE 3.3 13.7 - - - +
298B LEU 3.2 0.2 - - - -
299B THR* 1.3 76.5 - - - +
301B ASN* 1.3 71.1 + - - +
302B GLY* 3.1 23.1 - - - +
303B PHE* 3.9 23.8 - - + -
317B ILE* 4.4 4.7 - - + -
320B ARG* 3.2 56.0 + - + +
321B LEU* 3.8 15.9 - - + -
324B ARG* 3.9 3.1 - - + -
326B MET* 3.8 24.5 - - + -
366B MET* 3.8 12.3 - - - +
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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