Contacts of the strand formed by residues 223 - 229 (chain C) in PDB entry 3THT
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 GLN 223 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178C HIS* 4.2 0.6 - - - +
179C PHE 2.9 28.5 + - - +
181C TYR* 3.9 32.8 - - + +
200C LEU* 3.9 2.5 - - - +
221C PRO* 3.8 0.7 - - - +
222C ASP* 1.3 87.1 + - - +
224C MET* 1.3 77.9 + - - +
225C THR* 3.6 22.3 + - - +
245C PHE* 4.0 19.1 - - + -
332C THR 4.4 0.2 - - - +
333C PHE* 3.4 2.3 - - - +
334C ARG* 2.7 62.7 + - - +
336C VAL* 4.0 7.6 - - + -
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Residues in contact with MET 224 (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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179C PHE* 2.8 47.4 + - + +
200C LEU* 3.7 10.9 - - + +
201C PRO* 3.6 38.1 - - + -
204C CYS* 3.8 14.6 - - - -
223C GLN* 1.3 84.1 + - - +
225C THR* 1.3 62.1 + - - +
226C ILE* 3.8 24.7 - - + -
331C PHE* 4.3 17.9 - - + -
332C THR 3.0 15.7 - - - +
333C PHE* 3.5 31.6 - - + -
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Residues in contact with THR 225 (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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176C VAL* 5.2 3.8 - - + -
177C LYS 3.8 2.7 - - - -
178C HIS* 3.3 50.0 - - + -
223C GLN* 3.6 12.7 + - - +
224C MET* 1.3 71.3 - - - +
226C ILE* 1.3 65.0 + - - +
227C ASN* 3.8 11.7 + - - +
330C SER 3.6 1.6 - - - +
332C THR* 2.9 35.5 + - - -
334C ARG* 3.0 31.5 + - - +
403C AKG 4.8 3.2 + - - -
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Residues in contact with ILE 226 (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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156C VAL* 3.9 19.1 - - + -
158C TRP* 5.4 7.2 - - + +
175C ARG 4.5 0.2 - - - -
176C VAL* 3.5 7.6 - - - +
177C LYS* 3.2 40.1 + - + +
179C PHE* 4.0 21.5 - - + -
224C MET* 3.8 17.0 - - + -
225C THR* 1.3 70.7 - - - +
227C ASN* 1.3 70.8 + - - +
228C GLN* 6.0 0.7 - - + -
329C THR* 3.4 15.0 - - + -
330C SER 3.1 3.8 - - - +
331C PHE* 3.3 51.4 - - + -
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Residues in contact with ASN 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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174C ARG* 2.7 33.7 - - - +
175C ARG 3.5 6.7 + - - +
176C VAL* 4.5 7.4 - - - +
225C THR* 3.8 14.0 + - - +
226C ILE* 1.3 83.0 - - - +
228C GLN* 1.3 59.7 + - - +
229C TYR* 3.2 31.6 + - + +
328C ARG 3.7 0.5 - - - +
329C THR* 3.1 9.9 - - - +
330C SER* 3.0 33.0 + - - +
403C AKG 3.5 30.1 + - - +
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Residues in contact with GLN 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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158C TRP* 3.2 39.6 - - + +
174C ARG* 3.3 11.4 - - - +
175C ARG* 3.0 61.3 + - + +
226C ILE* 6.0 0.7 - - + -
227C ASN* 1.3 74.9 - - - +
229C TYR* 1.3 59.9 + - - +
230C GLU* 2.7 33.1 + - - +
233C GLN* 3.6 5.1 + - - +
327C LEU* 3.2 27.5 - - + +
328C ARG 3.4 2.2 - - - -
329C THR* 4.2 12.6 - - + +
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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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174C ARG* 3.4 24.5 - - + -
227C ASN* 3.2 39.0 + - + +
228C GLN* 1.3 72.7 - - - +
230C GLU* 1.3 64.7 + - - +
231C PRO 3.6 0.2 - - - -
233C GLN* 3.9 13.5 - - - +
234C GLY* 3.5 34.3 - - - -
235C ILE* 4.0 8.3 - - + +
258C ILE* 5.0 5.4 - - + -
294C ILE* 3.7 10.2 - - + +
325C ARG* 6.5 0.4 - - - -
326C GLY 3.9 2.3 - - - +
327C LEU* 3.2 6.0 - - - +
328C ARG* 2.8 78.7 + - + +
330C SER* 3.6 2.0 - - - -
403C AKG 2.6 23.5 + - - +
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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