Contacts of the helix formed by residues 218 - 225 (chain B) in PDB entry 6I53
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 ILE 218 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B PRO* 3.4 34.5 - - + +
145B LEU* 3.7 31.4 - - + -
216B ARG 4.5 4.3 - - - +
217B ASN* 1.3 74.7 - - - +
219B GLY* 1.3 63.2 + - - +
220B TYR 3.2 2.9 - - - +
221B PHE* 3.9 11.2 - - + -
222B ILE* 3.3 36.0 + - + +
226B TYR* 5.8 2.2 - - + -
443B TRP* 4.2 19.1 - - + -
447B VAL* 6.0 1.1 - - + -
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Residues in contact with GLY 219 (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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217B ASN* 3.5 3.0 - - - +
218B ILE* 1.3 78.7 - - - +
220B TYR* 1.3 60.2 + - - +
222B ILE* 4.3 3.7 + - - +
223B LEU* 4.2 23.7 + - - +
291C SER* 3.5 33.9 - - - -
292C TYR* 4.5 3.0 + - - +
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Residues in contact with TYR 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B GLN* 5.7 1.3 - - + +
217B ASN 4.8 2.0 + - - +
218B ILE* 3.2 0.8 - - - +
219B GLY* 1.3 78.7 - - - +
221B PHE* 1.3 90.8 + + + +
222B ILE 3.3 0.7 + - - -
223B LEU* 3.3 5.0 + - - +
224B GLN* 3.0 69.4 + - + +
267B HIS* 5.8 1.6 + - - -
284C ARG* 3.3 51.8 + - + +
288C PRO 4.7 1.3 - - - -
289C LYS* 3.6 49.0 - - + +
290C VAL 3.3 16.8 - - - +
291C SER* 3.7 5.0 - - - +
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Residues in contact with PHE 221 (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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143B TYR* 3.2 35.0 - + - -
144B PRO* 3.6 31.2 - - + -
185B GLN* 3.4 28.7 - - - -
216B ARG* 3.9 7.6 - - - -
217B ASN 3.9 16.6 - - - -
218B ILE* 3.5 9.0 + - + +
220B TYR* 1.3 96.1 - + + +
222B ILE* 1.3 60.4 + - - +
224B GLN* 3.8 2.7 - - - -
225B THR* 2.8 39.2 + - + +
226B TYR* 3.0 23.0 + - + -
268B LEU* 5.2 6.3 - - + -
281B ILE* 4.3 11.9 - - + -
289C LYS* 6.1 2.2 - - - -
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Residues in contact with ILE 222 (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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218B ILE* 3.3 27.3 + - + +
219B GLY* 4.6 4.9 - - - +
220B TYR 3.3 0.8 - - - -
221B PHE* 1.3 78.1 - - - +
223B LEU* 1.3 69.5 + - + +
224B GLN 3.2 0.9 + - - -
226B TYR* 3.4 26.7 + - + -
227B MET* 2.8 47.2 + - + +
228B PRO* 3.7 0.2 - - - +
443B TRP* 3.9 20.0 - - + -
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Residues in contact with LEU 223 (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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219B GLY 4.2 13.4 + - - +
220B TYR 3.3 7.6 + - - +
222B ILE* 1.3 86.3 - - + +
224B GLN* 1.3 59.3 + - - +
227B MET* 4.7 10.5 - - + -
228B PRO* 3.9 10.6 - - - +
280C SER* 4.4 13.2 + - - -
284C ARG* 4.7 10.8 - - - +
292C TYR 4.3 7.6 - - - +
293C VAL* 3.8 30.1 - - + -
297C ASP* 4.1 25.4 - - + +
301C SER* 3.8 23.1 - - - +
304C PHE* 5.6 2.9 - - - -
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Residues in contact with GLN 224 (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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220B TYR* 3.0 61.2 + - + +
221B PHE* 4.3 2.7 - - - -
223B LEU* 1.3 80.0 - - - +
225B THR* 1.3 73.1 + - + +
228B PRO* 3.3 14.0 - - - +
264B ILE* 5.4 3.1 - - - +
267B HIS* 4.3 12.6 + - + -
268B LEU* 6.1 1.3 - - + -
280C SER* 4.5 3.2 + - - +
281C THR* 3.9 37.5 + - - +
284C ARG* 3.8 19.5 + - - +
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Residues in contact with THR 225 (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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221B PHE* 2.8 24.5 + - + +
224B GLN* 1.3 94.5 - - + +
226B TYR* 1.3 69.3 + - - +
227B MET 3.7 0.7 - - - -
228B PRO* 3.5 4.7 - - - +
229B SER* 3.3 25.3 + - - -
264B ILE* 4.9 13.8 - - + +
268B LEU* 4.3 20.6 - - + -
281B ILE* 3.4 34.4 - - + +
284B TYR* 5.9 0.2 - - - -
285B LEU* 4.5 12.1 - - + +
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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