Contacts of the strand formed by residues 220 - 226 (chain A) in PDB entry 3U8Z
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A LYS 4.7 7.7 + - - +
101A TYR* 5.6 6.7 - - - -
218A GLY 4.1 8.6 + - - -
219A VAL* 1.3 71.9 - - - +
221A TYR* 1.3 60.9 + - - +
222A PHE* 3.6 23.0 - - + -
234A LEU 3.1 5.4 - - - +
235A GLY* 3.3 1.4 - - - -
236A VAL* 2.9 54.7 + - + +
299A LEU* 3.7 31.4 - - + +
303A ASN* 4.6 6.5 - - - +
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Residues in contact with TYR 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A GLU 4.5 0.3 + - - -
216A MET* 3.3 39.1 - - + +
219A VAL* 3.6 32.0 - - + +
220A ASN* 1.3 70.4 - - - +
222A PHE* 1.3 74.5 + - - +
233A LEU* 4.3 11.2 - - + -
234A LEU 3.2 5.4 - - - -
244A TYR* 3.6 36.9 + + - -
249A ARG* 2.6 71.6 + - + +
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Residues in contact with PHE 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ASN* 3.6 31.9 - - + -
221A TYR* 1.3 79.0 - - - +
223A ALA* 1.3 66.2 + - - +
224A ILE* 3.5 1.9 + - + +
233A LEU* 3.3 7.5 - - - -
234A LEU* 2.8 42.3 + - + +
236A VAL* 4.0 16.4 - - + -
287A SER* 5.6 0.2 - - - +
292A VAL* 3.5 28.3 - - + -
295A LEU* 4.3 17.9 - - + -
296A ILE* 3.6 37.0 - - + -
299A LEU* 3.6 23.8 - - + -
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Residues in contact with ALA 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A PHE* 1.3 71.2 - - - +
224A ILE* 1.4 63.8 + - - +
232A LEU 3.8 5.8 - - - +
233A LEU* 4.1 10.1 - - + +
287A SER* 4.0 15.4 + - - -
288A SER 5.3 0.5 + - - -
128B ASP 3.7 20.2 - - - +
129B GLU* 3.5 29.7 - - + +
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Residues in contact with ILE 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A PHE* 3.8 11.4 - - + +
223A ALA* 1.4 79.4 - - - +
225A ARG* 1.3 56.7 + - - +
232A LEU* 2.8 68.6 + - + +
233A LEU 3.9 7.2 - - - +
234A LEU* 3.9 9.0 - - + +
243A ILE* 4.1 22.0 - - + -
283A PHE* 4.4 1.1 - - + -
285A PHE* 3.5 49.6 - - + -
286A ASN 3.3 11.2 - - - +
287A SER* 4.5 6.7 - - - -
296A ILE* 5.4 0.9 - - + -
129B GLU* 2.8 15.3 + - - +
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Residues in contact with ARG 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ILE* 1.3 76.5 - - - +
226A ASN* 1.3 65.4 + - - +
229A GLY* 3.5 29.2 - - - +
230A THR 3.3 6.3 - - - +
231A GLU* 3.2 30.2 + - + -
285A PHE* 3.4 4.6 - - - -
286A ASN* 2.7 57.6 + - + +
288A SER* 5.1 5.1 + - - -
126B ILE* 3.9 11.7 + - - +
127B LEU* 2.6 45.2 + - - +
129B GLU* 3.5 18.5 + - - +
138B SER* 4.7 10.1 + - - -
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Residues in contact with ASN 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ARG* 1.3 77.5 - - - +
227A LYS* 1.3 58.5 + - - +
228A LYS* 2.9 25.7 + - - +
229A GLY* 2.9 27.7 + - - -
230A THR* 3.0 37.5 + - - +
232A LEU* 3.9 22.5 - - + +
253A LYS* 6.2 0.2 - - - +
270A GLU* 5.1 1.3 - - - -
283A PHE* 4.5 11.3 - - + -
284A LYS 4.0 13.5 - - - +
285A PHE* 4.4 3.1 - - - +
286A ASN* 5.4 1.6 - - - +
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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