Contacts of the helix formed by residues 222 - 227 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A HIS 3.3 24.0 - - - -
88A TYR 3.3 17.5 - - - +
89A ALA* 3.6 7.0 - - - -
91D GLU* 3.1 26.2 + - - -
92D LEU* 4.1 0.8 - - - +
93D PHE* 4.6 0.7 - - - -
220D LYS 3.8 2.4 + - - -
221D MET* 1.3 70.7 - - - +
223D GLY* 1.3 63.2 + - - +
225D TYR* 3.0 18.1 + - - +
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Residues in contact with GLY 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ALA* 3.7 14.7 - - - +
223A GLY* 3.7 29.7 - - - +
89D ALA* 4.4 8.0 + - - +
216D THR* 5.6 0.7 - - - -
221D MET* 3.1 5.5 + - - +
222D GLY* 1.3 75.1 - - - +
224D ASN* 1.3 61.2 + - - +
225D TYR 3.1 1.4 + - - -
226D GLY* 4.0 3.3 + - - -
227D SER* 3.3 15.1 + - - -
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Residues in contact with ASN 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A TRP* 5.8 4.9 - - - -
210D ARG* 4.2 33.2 + - - +
211D ALA* 5.6 0.4 - - - +
216D THR* 2.9 41.4 + - - +
217D GLY* 3.9 8.9 - - - +
219D CYS 2.8 27.2 - - - +
221D MET* 3.2 16.2 + - - +
222D GLY 3.1 0.8 + - - -
223D GLY* 1.3 76.6 - - - +
225D TYR* 1.3 73.1 + - + +
227D SER* 3.6 11.0 + - - -
228D SER* 4.4 8.0 - - - -
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Residues in contact with TYR 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A TYR* 3.6 24.2 - + + -
173A VAL* 4.8 4.3 - - + -
93D PHE* 3.6 25.6 - + - -
210D ARG* 4.8 3.6 + - - -
219D CYS 4.1 3.8 + - - -
220D LYS* 3.5 18.7 - - - +
221D MET 3.3 25.6 - - - -
222D GLY* 3.0 8.8 + - - +
224D ASN* 1.3 91.5 - - + +
226D GLY* 1.3 65.7 + - - +
227D SER 3.2 2.2 - - - -
228D SER* 2.8 27.2 + - - +
229D LEU* 3.5 10.6 - - - +
258D THR* 4.2 16.8 - - + -
284D LEU* 4.3 1.7 - - - +
420D PLP 2.4 49.6 + - + +
2401D CBC 3.9 12.6 - + - -
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Residues in contact with GLY 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A TYR 2.7 26.0 + - - -
89A ALA* 3.9 14.8 - - - -
90A VAL* 4.6 4.4 - - - -
124A ARG 5.0 2.3 - - - +
125A ALA* 4.6 13.2 - - - +
221A MET* 5.3 4.2 - - - +
222D GLY 3.6 2.8 + - - -
223D GLY 4.0 2.0 + - - -
225D TYR* 1.3 75.3 - - - +
227D SER* 1.3 56.6 + - - +
228D SER 3.1 4.7 + - - -
229D LEU* 3.6 19.3 + - - +
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Residues in contact with SER 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ARG 5.8 2.5 - - - -
212A TRP* 5.9 3.9 - - - -
215A GLY* 6.0 1.6 - - - -
216A THR* 3.8 37.5 - - - +
221A MET* 5.3 4.5 - - - -
208D TYR* 6.2 0.7 - - - +
210D ARG 5.2 3.8 + - - -
223D GLY 3.3 19.0 + - - -
224D ASN* 3.6 11.1 + - - -
226D GLY* 1.3 71.2 - - - +
228D SER* 1.3 57.2 + - - +
229D LEU 3.7 0.4 - - - -
230D PHE* 5.0 5.2 + - - +
231D ALA* 5.3 2.8 + - - +
245D TRP* 4.6 5.6 - - - -
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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