Contacts of the strand formed by residues 220 - 226 (chain B) in PDB entry 1H4R
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 ASN 220 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B LYS 4.8 7.4 + - - +
101B TYR* 5.4 7.3 - - - -
218B GLY 4.1 7.6 + - - -
219B VAL* 1.3 73.6 - - - +
221B TYR* 1.3 58.4 + - - +
222B PHE* 3.5 24.1 - - + -
234B LEU 3.4 1.4 - - - +
235B GLY* 3.3 3.1 - - - -
236B VAL* 2.9 55.0 + - + +
237B ASP* 4.9 0.4 - - - +
299B LEU* 3.7 32.3 - - + +
303B ASN* 4.4 8.7 - - - +
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Residues in contact with TYR 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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130B LYS 5.7 0.2 - - - -
215B GLU 4.5 0.2 + - - -
216B MET* 3.4 39.0 - - + +
219B VAL* 3.5 39.3 - - + +
220B ASN* 1.3 70.3 - - - +
222B PHE* 1.3 75.2 + - - +
233B LEU* 4.2 15.7 - - + -
234B LEU 3.3 6.5 - - - -
244B TYR* 3.8 25.2 + + - -
249B ARG* 2.6 68.9 + - + +
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Residues in contact with PHE 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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220B ASN* 3.5 31.9 - - + -
221B TYR* 1.3 80.0 - - - +
223B ALA* 1.3 66.0 + - - +
224B ILE* 3.5 2.0 + - + +
233B LEU* 3.3 8.9 - - - +
234B LEU* 2.8 48.8 + - + +
236B VAL* 4.1 15.5 - - + -
292B VAL* 3.5 26.7 - - + -
295B LEU* 3.9 20.9 - - + -
296B ILE* 3.8 36.3 - - + -
299B LEU* 3.8 23.1 - - + -
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Residues in contact with ALA 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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222B PHE* 1.3 73.1 - - - +
224B ILE* 1.3 63.6 + - - +
231B GLU* 5.1 8.1 - - - +
232B LEU 3.7 7.4 - - - +
233B LEU* 4.0 9.5 - - + +
286B ASN 4.6 0.2 - - - +
287B SER* 4.3 13.0 + - - -
288B SER 5.5 0.7 + - - -
292B VAL* 6.0 1.1 - - - +
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Residues in contact with ILE 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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222B PHE* 3.9 5.2 - - + +
223B ALA* 1.3 80.4 - - - +
225B ARG* 1.3 64.1 + - - +
226B ASN* 6.0 0.2 - - - -
231B GLU* 3.4 10.5 - - - +
232B LEU* 2.9 53.1 + - + +
233B LEU 4.2 2.7 - - - -
234B LEU* 3.9 33.7 - - + +
243B ILE* 4.3 15.7 - - + -
283B PHE* 5.1 1.1 - - + -
285B PHE* 3.5 46.4 - - + -
286B ASN 3.3 12.8 - - - +
287B SER* 4.5 5.6 - - - -
296B ILE* 5.4 1.1 - - + -
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Residues in contact with ARG 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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224B ILE* 1.3 81.5 - - - +
226B ASN* 1.3 68.8 + - - +
229B GLY* 4.0 15.9 + - - +
230B THR 3.1 10.5 - - - +
231B GLU* 2.6 36.7 + - - +
285B PHE* 3.4 5.3 - - - -
286B ASN* 2.8 41.9 + - + +
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Residues in contact with ASN 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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224B ILE* 6.2 0.2 - - + -
225B ARG* 1.3 79.2 - - - +
227B LYS* 1.3 63.8 + - - +
228B LYS* 3.0 34.5 + - - +
229B GLY* 2.9 19.1 + - - -
230B THR* 3.0 44.8 + - - +
232B LEU* 3.6 27.1 - - + +
283B PHE* 4.8 11.8 - - + -
284B LYS 4.2 10.5 - - - +
285B PHE* 4.4 2.0 - - - -
286B ASN* 5.1 2.6 - - - +
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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