Contacts of the strand formed by residues 226 - 233 (chain C) in PDB entry 3H3B
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 ALA 226 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172C LYS* 3.9 23.6 - - + -
173C LYS 3.6 7.4 - - - +
174C ASN* 3.3 24.9 - - - +
224C ASP 3.4 2.6 + - - -
225C SER* 1.3 76.3 - - - +
227C VAL* 1.3 65.8 + - - +
228C TYR* 3.6 9.4 - - + -
249C SER* 3.6 2.3 + - - -
250C VAL 2.8 31.2 + - - -
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Residues in contact with VAL 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C VAL 3.8 0.3 - - - +
172C LYS* 3.7 0.7 - - - -
173C LYS* 2.8 40.5 + - + +
226C ALA* 1.3 76.9 - - - +
228C TYR* 1.3 67.7 + - - +
229C TYR* 3.6 33.2 - - + +
246C GLN 5.5 0.2 - - - +
247C GLY* 4.1 2.9 - - - -
248C THR 3.6 19.5 - - - +
249C SER* 4.4 15.9 - - - +
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Residues in contact with TYR 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C GLN* 2.8 25.4 + - - +
154C ILE* 3.8 19.1 - - + -
170C TRP* 5.3 0.9 - - + -
171C VAL 3.4 5.6 - - - -
172C LYS* 3.7 32.3 + - + +
182C ILE* 3.6 29.4 - - + -
198C PHE* 5.4 2.7 - + - -
201C LYS* 6.1 0.3 - - - +
215C MET* 3.7 10.3 - - + -
217C LEU* 3.9 21.8 - - + +
224C ASP* 2.7 39.8 + - - +
226C ALA* 3.6 20.6 - - + -
227C VAL* 1.3 75.2 - - - +
229C TYR* 1.3 58.3 + - - +
247C GLY* 3.4 1.2 - - - -
248C THR 2.8 27.3 + - - +
250C VAL* 3.7 23.1 - - + -
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Residues in contact with TYR 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C GLN* 3.3 16.3 + - - -
48C GLN 4.3 1.9 + - - -
49C SER* 3.5 27.6 - - - -
50C PRO* 3.9 11.2 - - + -
140C GLN* 3.6 2.5 - - - +
170C TRP* 3.2 12.4 - - - -
171C VAL* 2.8 42.4 + - + +
173C LYS* 3.7 26.7 - - + +
227C VAL* 3.6 23.5 - - + +
228C TYR* 1.3 75.9 - - - +
230C CYS* 1.3 60.7 + - - +
231C VAL* 4.1 2.9 - - + -
244C TRP* 3.6 37.5 - + + -
245C GLY 3.4 18.6 - - - -
246C GLN 3.9 3.1 + - - -
247C GLY* 3.7 15.7 - - - -
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Residues in contact with CYS 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C LEU* 3.8 11.2 - - + +
140C GLN* 3.3 24.5 + - - +
156C CYS* 2.0 53.4 - - + -
168C ILE* 4.0 10.3 - - + -
169C ASN 3.2 4.5 - - - -
170C TRP* 3.8 13.7 - - + -
229C TYR* 1.3 71.4 - - - +
231C VAL* 1.3 65.4 + - - +
245C GLY 2.9 26.3 + - - -
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Residues in contact with VAL 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C LEU* 4.3 2.5 - - - -
168C ILE* 3.6 3.7 - - - -
169C ASN* 2.7 48.6 + - - +
171C VAL* 4.0 15.5 - - + -
229C TYR* 4.2 2.5 - - + -
230C CYS* 1.3 80.0 - - - +
232C ARG* 1.3 63.1 + - - +
241C MET* 3.6 34.3 - - + -
242C ASP 4.5 0.4 - - - +
243C TYR 3.5 13.7 - - - +
244C TRP* 3.5 51.6 - - + +
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Residues in contact with ARG 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C VAL* 3.6 17.4 - - - +
138C LEU* 3.8 11.3 - - + +
161C TYR* 3.3 55.6 - - - +
166C TYR* 3.4 49.1 + - + -
167C PHE 3.5 7.2 - - - +
168C ILE* 4.8 1.3 - - + -
169C ASN* 4.1 0.2 - - - -
231C VAL* 1.3 72.5 - - - +
233C SER* 1.3 59.7 + - - +
238C GLU* 4.6 7.7 + - - -
241C MET* 3.1 4.6 - - - -
242C ASP* 2.8 65.1 + - - +
243C TYR* 3.0 36.3 + - + +
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Residues in contact with SER 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C TRP* 4.1 10.7 - - - -
166C TYR* 3.4 10.6 - - - +
167C PHE* 2.8 46.0 + - - +
169C ASN* 3.0 20.1 + - - -
184C HIS* 4.8 0.2 - - - -
232C ARG* 1.3 74.8 - - - +
234C GLY* 1.3 59.7 + - - +
239C TYR 3.6 17.2 + - - -
240C ALA 3.6 10.8 - - - -
241C MET* 3.8 9.9 - - - -
242C ASP* 4.6 2.0 - - - -
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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