Contacts of the strand formed by residues 225 - 229 (chain B) in PDB entry 2INU
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 225 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200B GLY* 5.7 2.0 - - - -
201B LYS 3.2 4.8 + - - +
202B THR* 3.0 31.1 - - + +
203B GLY 3.0 23.4 + - - -
223B LEU* 3.7 4.1 - - - +
224B GLU* 1.3 102.8 + - + +
226B ALA* 1.3 61.0 + - - +
228B ILE* 3.9 13.6 - - + +
247B ASN* 3.6 23.7 + - - -
250B GLU* 2.8 31.4 + - - +
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Residues in contact with ALA 226 (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 THR* 4.6 0.4 - - - -
203B GLY* 3.3 3.6 + - - -
204B ILE 3.0 26.2 + - - +
220B PHE* 3.7 15.6 - - + -
223B LEU* 4.1 11.3 - - - +
225B HIS* 1.3 75.0 - - - +
227B LEU* 1.3 62.0 + - + +
242B ILE* 3.4 26.5 - - + -
245B CYS* 3.8 12.3 - - - -
247B ASN 2.9 13.8 + - - +
248B CYS 3.3 12.1 + - - +
250B GLU* 5.4 0.2 + - - -
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Residues in contact with LEU 227 (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 ILE* 3.4 38.8 - - + +
215B ILE* 4.3 24.5 - - + -
220B PHE* 4.5 11.7 - - + -
226B ALA* 1.3 79.8 - - + +
228B ILE* 1.3 67.8 + - - +
229B VAL* 3.9 21.1 - - + -
237B VAL* 4.2 26.5 - - + -
242B ILE* 5.5 2.7 - - + -
248B CYS 2.9 14.0 + - - +
249B VAL* 4.2 22.0 - - + -
250B GLU* 2.9 26.2 + - - +
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Residues in contact with ILE 228 (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 THR* 4.2 5.4 - - + +
204B ILE 3.0 7.4 + - - +
205B GLU* 3.3 39.6 - - + +
206B VAL* 2.7 31.7 + - - +
225B HIS* 3.9 30.5 - - + +
227B LEU* 1.3 79.9 - - - +
229B VAL* 1.3 67.5 + - - +
230B ARG* 4.8 2.2 - - + +
250B GLU* 3.4 33.0 - - + +
252B THR* 4.4 15.5 - - + +
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Residues in contact with VAL 229 (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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206B VAL* 3.8 21.1 - - + -
210B ASN* 3.8 21.3 - - - +
213B PHE* 5.4 0.9 - - + -
215B ILE* 5.6 2.5 - - + -
227B LEU* 3.9 24.2 - - + -
228B ILE* 1.3 81.2 - - - +
230B ARG* 1.3 60.9 + - - +
231B GLY 4.0 0.2 + - - -
232B ALA* 3.7 25.1 - - + +
235B LEU* 4.1 18.6 - - + -
250B GLU 2.8 11.5 + - - -
251B LEU* 3.3 36.3 - - + +
252B THR* 3.3 2.9 + - - +
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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