Contacts of the helix formed by residues 222 - 227 (chain G) in PDB entry 2ABJ
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 222 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91G GLU* 3.1 26.2 + - - -
92G LEU* 4.1 1.0 - - - +
93G PHE* 4.6 0.9 - - - -
220G LYS 3.8 2.4 + - - -
221G MET* 1.3 71.9 - - - +
223G GLY* 1.3 61.8 + - - +
225G TYR* 3.0 17.7 + - - +
87J HIS 3.3 24.7 - - - -
88J TYR 3.3 16.8 - - - -
89J ALA* 3.3 7.3 - - - +
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Residues in contact with GLY 223 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89G ALA* 4.4 8.8 + - - +
216G THR* 5.6 0.4 - - - -
221G MET* 3.1 5.3 + - - +
222G GLY* 1.3 75.2 - - - +
224G ASN* 1.3 62.7 + - - +
225G TYR 3.2 0.9 + - - -
226G GLY* 4.1 3.2 + - - -
227G SER* 3.3 14.2 + - - -
89J ALA* 3.6 14.7 - - - +
223J GLY* 3.7 29.6 - - - +
226J GLY* 6.5 0.4 - - - -
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Residues in contact with ASN 224 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210G ARG* 4.3 29.9 + - - +
211G ALA* 5.8 0.4 - - - +
216G THR* 2.8 41.9 + - - +
217G GLY* 4.0 8.4 - - - +
219G CYS 2.8 27.4 - - - +
221G MET* 3.3 16.9 + - - +
222G GLY 3.1 0.8 + - - -
223G GLY* 1.3 77.0 - - - +
225G TYR* 1.3 72.3 + - + +
227G SER* 3.4 11.5 + - - -
228G SER* 3.4 10.4 + - - -
212J TRP* 5.8 4.9 - - - -
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Residues in contact with TYR 225 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93G PHE* 3.6 26.2 - + - -
210G ARG* 4.8 3.1 + - - -
219G CYS 4.1 3.8 + - - -
220G LYS* 3.6 16.9 - - - +
221G MET 3.3 24.9 - - - -
222G GLY* 3.0 8.4 + - - +
224G ASN* 1.3 91.8 - - + +
226G GLY* 1.3 65.9 + - - +
227G SER 3.2 2.2 - - - -
228G SER* 3.0 26.2 + - - -
229G LEU* 3.5 11.3 - - - +
258G THR* 4.1 17.5 - - + -
284G LEU* 4.4 1.6 - - - +
420G PLP 2.4 46.6 + - + +
3401G CBC 3.9 12.6 - + - -
88J TYR* 3.5 25.1 - + + -
173J VAL* 4.7 5.8 - - + +
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Residues in contact with GLY 226 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222G GLY 3.6 2.4 + - - -
223G GLY 4.1 2.4 + - - -
225G TYR* 1.3 75.9 - - - +
227G SER* 1.3 57.1 + - - +
228G SER 3.1 4.7 + - - -
229G LEU* 3.6 20.4 + - - +
88J TYR 2.7 24.9 + - - -
89J ALA* 3.8 14.8 - - - -
90J VAL* 4.6 4.5 - - - -
124J ARG 4.9 2.3 - - - +
125J ALA* 4.6 13.0 - - - +
221J MET* 5.4 4.3 - - - +
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Residues in contact with SER 227 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210G ARG 5.2 4.7 + - - -
223G GLY 3.3 18.9 + - - -
224G ASN* 3.4 13.3 + - - -
226G GLY* 1.3 72.1 - - - +
228G SER* 1.3 56.6 + - - +
229G LEU 3.7 0.2 - - - -
230G PHE* 4.9 5.8 + - - +
231G ALA* 5.2 2.8 + - - +
245G TRP* 4.6 7.6 - - - -
124J ARG 5.8 2.0 - - - -
212J TRP* 5.9 3.7 - - - -
215J GLY* 6.3 0.9 - - - -
216J THR* 3.7 36.8 - - - +
221J MET* 5.5 4.2 - - - -
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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