Contacts of the strand formed by residues 232 - 239 (chain D) in PDB entry 2I62
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 THR 232 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230D GLY 3.6 3.5 + - - -
231D TYR* 1.3 73.4 - - - +
233D ILE* 1.3 68.5 + - - +
234D GLU* 3.2 12.3 + - + +
258D GLY* 4.2 0.4 - - - -
259D ARG* 2.8 46.8 + - + +
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Residues in contact with ILE 233 (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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241C GLN* 5.7 0.9 - - - +
223D ARG* 3.7 44.6 - - + +
226D VAL* 3.8 25.6 - - + -
227D GLU* 3.7 23.2 + - + +
231D TYR 3.7 1.8 + - - -
232D THR* 1.3 73.7 - - - +
234D GLU* 1.3 60.7 + - - +
235D GLN 3.4 29.2 - - - +
236D PHE* 4.0 21.1 - - + -
256D LEU* 4.9 4.3 - - + -
257D VAL 3.6 7.2 - - - +
258D GLY* 4.3 1.3 - - - -
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Residues in contact with GLU 234 (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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54D ALA* 4.7 7.1 - - - +
55D VAL* 5.2 0.3 - - - +
193D PHE* 3.3 22.3 - - - -
232D THR* 3.2 17.5 + - + +
233D ILE* 1.3 75.2 - - - +
235D GLN* 1.3 74.5 + - + +
257D VAL* 2.8 17.2 + - + +
259D ARG* 2.7 47.8 + - + +
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Residues in contact with GLN 235 (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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48D LYS* 4.7 6.2 + - - +
49D ILE* 3.7 27.5 + - + +
53D GLY* 5.8 3.2 - - - -
54D ALA* 5.5 6.1 - - - +
55D VAL* 4.4 10.3 - - - +
233D ILE* 3.4 9.0 - - - +
234D GLU* 1.3 91.0 + - + +
236D PHE* 1.3 62.4 + - - +
237D GLU* 5.5 6.7 - - + +
255D SER 4.6 0.2 - - - -
256D LEU* 3.2 4.2 - - - -
257D VAL* 2.9 54.1 + - + +
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Residues in contact with PHE 236 (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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238C VAL 4.5 3.6 - - - +
240C SER* 3.4 33.7 + - - +
219D TRP* 3.5 58.6 - + + -
222D VAL* 4.3 1.8 - - + -
223D ARG* 4.1 17.3 - - + -
233D ILE* 4.0 21.3 - - + -
235D GLN* 1.3 75.7 - - - +
237D GLU* 1.3 81.4 + - - +
238D VAL* 4.1 7.6 - - + -
254D PHE* 3.9 25.1 - + + -
255D SER 3.4 4.7 - - - -
256D LEU* 3.7 33.7 - - + -
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Residues in contact with GLU 237 (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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41C HIS* 5.5 7.4 + - - -
237C GLU* 3.5 21.8 - - - +
238C VAL 4.0 11.9 - - - +
45D ASN* 3.6 25.1 - - - +
235D GLN* 5.5 5.6 - - + +
236D PHE* 1.3 87.5 + - - +
238D VAL* 1.3 65.3 + - - +
239D ILE 4.1 0.2 - - - -
254D PHE* 3.2 7.8 - - - +
255D SER* 2.9 36.5 + - - +
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Residues in contact with VAL 238 (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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219C TRP* 3.9 34.1 - - + -
236C PHE* 4.6 6.6 - - + +
237C GLU* 4.1 14.4 - - - +
238C VAL* 3.7 42.6 + - + +
45D ASN* 5.3 0.5 + - - -
200D LEU* 4.0 6.1 - - + -
219D TRP* 4.1 17.9 - - + -
236D PHE* 4.1 18.8 - - + -
237D GLU* 1.3 80.1 + - - +
239D ILE* 1.3 68.5 + - - +
240D SER* 3.9 4.4 + - - +
253D LEU 3.5 9.2 - - - +
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Residues in contact with ILE 239 (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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38D ILE* 5.1 3.6 - - + +
41D HIS* 3.8 26.2 - - + +
42D LEU* 3.5 44.4 - - + +
45D ASN* 3.6 29.4 - - + +
238D VAL* 1.3 74.5 - - - +
240D SER* 1.3 59.2 + - - +
241D GLN* 3.3 19.5 - - + +
252D GLY* 2.9 8.0 - - - -
253D LEU* 2.7 61.1 + - + +
254D PHE* 5.0 7.0 - - - -
255D SER* 5.2 0.7 - - - +
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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