Contacts of the strand formed by residues 233 - 237 (chain B) in PDB entry 1IAX
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 HIS 233 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ILE* 3.6 38.3 + - + -
12A LEU* 3.8 10.5 - - - +
138B LEU* 3.6 32.8 + - + +
145B PHE* 4.8 1.8 - - + -
200B LYS* 3.0 21.6 + - + +
201B GLY* 3.0 3.2 - - - -
202B LEU* 2.8 28.1 + - - -
227B THR* 4.1 3.7 + - - -
231B ASN 5.2 0.9 - - - -
232B ILE* 1.3 74.8 - - - +
234B LEU* 1.3 60.4 + - - +
235B VAL* 3.9 0.4 - - - -
268B ASP 3.5 5.1 + - - -
269B LEU* 3.2 28.3 - - + +
271B HIS* 2.7 37.9 - - + +
294B ASN* 4.9 0.6 + - - -
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Residues in contact with LEU 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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202B LEU* 3.5 31.2 - - + -
204B LEU* 4.2 8.3 - - + -
220B LEU* 5.1 3.1 - - + +
223B VAL* 4.3 8.3 - - + -
224B LEU* 3.9 30.3 - - + +
227B THR* 3.7 18.4 - - + +
232B ILE 3.8 0.4 + - - -
233B HIS* 1.3 73.0 - - - +
235B VAL* 1.3 62.5 + - - +
236B CYS* 3.8 19.6 - - - -
253B ILE* 3.9 30.7 - - + -
269B LEU 2.6 12.7 + - - +
270B VAL* 3.7 3.8 - - + +
271B HIS 3.1 25.8 + - - +
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Residues in contact with VAL 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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134B ILE* 4.1 17.0 - - + -
138B LEU* 3.8 27.8 - - + -
145B PHE* 4.0 17.0 - - + -
202B LEU 2.8 12.5 + - - +
203B ILE* 3.1 29.5 - - + +
204B LEU* 2.7 32.7 + - - +
233B HIS* 4.9 1.1 - - + -
234B LEU* 1.3 73.8 - - - +
236B CYS* 1.3 59.5 + - - +
271B HIS* 3.4 11.7 - - + +
273B VAL* 4.2 23.6 - - + -
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Residues in contact with CYS 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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204B LEU* 3.9 11.2 - - + +
206B ASN* 5.8 4.0 - - + -
220B LEU* 5.0 7.9 - - - -
234B LEU* 3.8 23.8 - - - -
235B VAL* 1.3 73.4 - - - +
237B ASP* 1.3 55.0 + - - +
238B GLU* 3.4 26.6 + - + +
253B ILE* 3.5 37.9 - - + -
271B HIS 2.8 13.8 + - - +
272B ILE* 3.4 2.9 - - + -
273B VAL 2.7 31.6 + - - -
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Residues in contact with ASP 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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131B ASN* 2.8 33.0 + - - +
155B PHE* 3.9 15.0 - - + -
203B ILE* 4.0 6.2 - - + +
204B LEU 2.8 22.1 + - - +
205B THR* 3.2 17.7 - - + +
206B ASN 2.8 27.7 + - - +
207B PRO 4.4 0.5 - - - +
235B VAL 3.8 0.4 + - - -
236B CYS* 1.3 68.1 - - - +
238B GLU* 1.3 55.0 + - - +
239B ILE* 3.2 31.3 + - - +
273B VAL* 3.8 16.0 - - - +
501B PLP 4.3 8.3 + - - -
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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