Contacts of the helix formed by residues 230 - 234 (chain M) in PDB entry 2JA7
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 ARG 230 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21M LEU* 4.8 2.0 - - - +
212M LYS 5.9 0.2 + - - -
216M VAL* 5.8 5.7 - - - +
219M PHE* 3.3 26.9 - - + -
224M PHE* 3.8 0.6 - - - -
225M ASN 4.5 0.4 - - - -
226M GLU* 3.5 35.5 + - - +
229M SER* 1.3 72.9 - - - +
231M PRO* 1.3 74.9 - - + +
232M GLU* 3.2 40.2 + - + +
233M TRP* 2.6 58.5 + - + +
234M MET 4.2 0.2 + - - -
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Residues in contact with PRO 231 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102M VAL* 5.1 5.2 - - + -
211M PHE* 3.6 26.7 - - + -
214M ILE* 5.1 6.5 - - + -
219M PHE* 3.4 35.4 - - + -
222M LEU* 5.9 2.7 - - + -
224M PHE* 3.1 51.2 - - + -
230M ARG* 1.3 80.8 - - - +
232M GLU* 1.3 51.9 + - - +
233M TRP 2.7 12.3 + - - -
234M MET* 2.8 29.5 + - + +
235M ILE* 4.4 1.2 + - - +
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Residues in contact with GLU 232 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208M LEU* 4.4 11.8 - - + +
211M PHE* 3.9 26.6 + - + +
212M LYS* 4.1 37.4 - - + +
219M PHE* 3.5 13.5 - - - -
230M ARG* 2.8 47.6 + - + -
231M PRO* 1.3 77.6 - - - +
233M TRP* 1.3 74.4 + - + +
234M MET 3.4 0.2 - - - -
235M ILE* 3.9 19.2 + - - +
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Residues in contact with TRP 233 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M LEU* 4.1 22.7 - - + +
22M PHE 3.6 9.4 - - - +
23M SER* 2.8 44.6 - - - +
24M PRO* 3.3 18.2 - - + +
25M GLU* 4.4 5.0 + - - -
95M PHE* 5.2 1.0 - - - -
226M GLU 4.5 1.8 - - - -
227M VAL 3.9 16.6 - - - -
228M PHE 3.8 4.0 - - - -
229M SER* 3.5 19.5 - - - -
230M ARG* 2.6 78.8 + - + +
231M PRO 2.7 1.0 + - - -
232M GLU* 1.3 83.6 + - + +
234M MET* 1.3 58.3 + - - +
235M ILE 2.9 15.1 + - - +
236M LEU* 4.3 3.6 - - - +
1211N ASN* 4.2 13.3 - - - +
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Residues in contact with MET 234 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M LEU* 4.5 8.5 - - + -
92M HIS* 3.3 27.1 + - - +
95M PHE* 3.4 38.4 - - + -
98M LYS* 4.0 25.1 - - + -
99M ILE* 3.5 24.5 - - + +
102M VAL* 4.2 16.2 - - + -
211M PHE* 4.5 5.6 - - + -
224M PHE* 3.0 37.9 - - + -
231M PRO* 2.8 26.4 + - + +
233M TRP* 1.3 77.8 - - - +
235M ILE* 1.3 59.0 + - + +
236M LEU* 4.4 0.9 - - - -
1414M ALA* 5.2 3.1 - - - -
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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