Contacts of the strand formed by residues 230 - 234 (chain A) in PDB entry 2ABQ
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 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A PHE* 4.6 0.7 - - - -
226A ALA* 3.3 2.1 - - - +
227A SER* 2.7 44.5 + - - +
228A ALA 3.4 0.6 - - - -
229A GLU* 1.3 81.4 - - - +
231A MSE 1.3 62.1 + - - +
232A PHE* 5.1 5.6 - - - -
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Residues in contact with MSE 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A ILE* 3.7 35.7 - - - +
203A VAL* 4.1 6.3 - - + -
204A GLN* 3.3 33.4 - - + +
207A ILE* 5.4 2.5 - - + -
224A LEU* 3.8 16.6 - - + -
225A PHE 3.3 6.7 - - - +
226A ALA* 3.5 30.3 - - + -
227A SER 5.3 2.9 - - - +
230A GLY* 1.3 75.4 - - - +
232A PHE* 1.3 68.9 + - - +
304A LYS* 3.7 8.2 - - - +
305A GLU* 3.0 37.9 + - + +
306A GLY* 4.0 8.5 - - - -
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Residues in contact with PHE 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A LEU* 3.2 8.1 - - - +
225A PHE* 3.0 52.7 + + + +
227A SER* 6.0 0.4 - - - -
230A GLY* 5.1 1.6 - - - -
231A MSE 1.3 83.3 - - - +
233A HIS* 1.3 70.0 + - - +
234A VAL* 3.8 17.2 - - + +
266A GLU* 3.7 29.6 - - + -
269A VAL* 3.5 36.1 - - + -
270A PRO* 5.5 0.9 - - + -
302A ILE* 4.0 19.7 - - + -
303A LYS 3.2 14.8 - - - +
304A LYS* 4.0 13.9 - - + -
305A GLU* 4.0 4.3 - - - -
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Residues in contact with HIS 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A ILE* 3.9 22.8 - - + +
221A ASP 3.5 24.4 + - - -
222A GLY* 3.7 3.6 - - - -
223A ALA 3.2 12.4 + - - -
224A LEU* 4.7 0.7 - - - +
232A PHE* 1.3 73.5 - - - +
234A VAL* 1.3 101.4 + - - +
235A ASN* 2.8 27.8 + - - -
301A THR 4.5 6.7 - - - -
302A ILE* 3.4 3.1 - - - -
303A LYS* 2.6 54.4 + - + +
305A GLU* 3.5 20.0 - - - +
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Residues in contact with VAL 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ALA* 2.7 36.0 + - - +
225A PHE* 6.1 0.2 - - + -
232A PHE* 3.8 17.7 - - + -
233A HIS* 1.3 99.5 - - - +
235A ASN* 1.3 72.2 + - - +
269A VAL* 4.3 11.4 - - + -
270A PRO* 5.1 5.2 - - + -
273A VAL* 4.7 17.0 - - + +
298A LEU* 4.2 15.9 - - + -
301A THR* 3.9 13.9 - - - +
302A ILE* 3.2 25.6 - - + -
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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