Contacts of the helix formed by residues 230 - 237 (chain B) in PDB entry 1M7X
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 THR 230 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228B VAL* 3.6 5.8 + - + +
229B GLN* 1.3 73.8 - - - +
231B GLU* 1.3 64.1 + - - +
232B GLU* 3.6 21.8 + - - +
233B ARG* 3.2 49.6 + - - +
234B LYS* 3.1 27.4 + - - +
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Residues in contact with GLU 231 (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 GLN 4.3 2.8 - - - +
230B THR* 1.3 71.8 - - - +
232B GLU* 1.3 69.9 + - - +
234B LYS* 3.3 35.0 + - - +
235B LYS* 2.9 33.1 + - - +
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Residues in contact with GLU 232 (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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232A GLU* 4.8 21.3 - - + +
230B THR* 3.1 23.7 - - - +
231B GLU* 1.3 89.4 + - - +
233B ARG* 1.3 59.5 + - + +
235B LYS* 3.3 8.0 + - - +
236B ALA* 2.9 27.9 + - - +
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Residues in contact with ARG 233 (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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227B VAL* 4.2 10.1 - - - +
228B VAL 3.4 22.2 + - - -
229B GLN* 3.7 18.3 + - + +
230B THR* 3.2 34.5 + - - +
232B GLU* 1.3 80.5 - - + +
234B LYS* 1.3 67.5 + - - +
236B ALA* 3.3 4.6 + - - -
237B ASN* 3.4 7.3 + - - -
326B HIS* 3.4 56.2 + - + +
330B LEU 5.0 0.9 - - - +
331B ASN* 2.8 41.0 - - - +
398B GLY* 4.6 2.6 + - - -
400B ASP* 3.0 23.9 + - - +
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Residues in contact with LYS 234 (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 GLN* 3.3 38.7 + - + +
230B THR 3.1 17.5 + - - +
231B GLU* 3.3 33.0 + - - +
232B GLU 3.3 0.2 - - - -
233B ARG* 1.3 76.0 - - - +
235B LYS* 1.3 64.1 + - - +
237B ASN* 3.1 18.4 + - - +
238B GLN* 3.5 11.4 + - - +
451B SER* 3.3 22.3 + - - +
452B GLY* 3.6 26.1 - - - +
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Residues in contact with LYS 235 (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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327A ALA 5.4 5.5 + - - -
231B GLU 2.9 19.3 + - - +
232B GLU* 3.5 7.0 - - - +
234B LYS* 1.3 72.8 - - - +
236B ALA* 1.3 61.0 + - - +
237B ASN 3.0 4.5 - - - -
238B GLN* 3.0 41.9 + - - +
240B ASP* 5.9 0.7 - - - +
241B ALA* 3.6 10.3 - - + +
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Residues in contact with ALA 236 (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 GLU 2.9 17.4 + - - +
233B ARG 3.6 0.2 - - - +
234B LYS 3.2 0.4 - - - -
235B LYS* 1.3 75.5 - - - +
237B ASN* 1.3 60.6 + - - +
238B GLN 3.5 0.2 - - - -
241B ALA* 3.9 8.8 - - - +
242B PRO 4.7 1.4 - - - +
243B ILE* 3.7 13.3 - - - +
282B THR* 5.7 4.9 - - - +
283B HIS* 3.2 19.7 + - + +
331B ASN* 3.5 28.7 - - - +
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Residues in contact with ASN 237 (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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233B ARG 3.4 3.0 + - - +
234B LYS 3.1 11.4 + - - +
235B LYS 3.0 0.8 - - - -
236B ALA* 1.3 79.0 - - - +
238B GLN* 1.3 59.0 + - - +
239B PHE* 5.3 0.2 - - - -
243B ILE* 4.0 4.0 - - - +
283B HIS* 2.8 31.9 - - - -
331B ASN* 2.9 16.5 + - - +
400B ASP* 3.0 28.6 - - - +
401B ALA* 4.8 2.6 - - - +
452B GLY 3.3 14.9 - - - +
454B VAL* 3.7 30.4 - - + +
456B MET* 5.7 0.2 - - - +
478B TRP* 5.6 0.5 - - - -
479B TYR* 3.0 26.2 + - - -
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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