Contacts of the strand formed by residues 328 - 334 (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 ARG 328 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C ASN 3.7 0.7 - - - +
228C GLN* 3.4 3.6 - - - -
229C TYR* 2.8 67.1 + - + +
251C SER* 5.2 2.0 - - - -
253C SER* 3.1 30.1 + - - +
254C LEU 3.6 8.3 - - - +
255C GLY* 4.7 0.2 - - - -
256C SER* 3.3 25.6 - - - +
258C ILE* 3.6 31.8 - - + +
260C MET* 4.5 0.6 - - - +
274C LEU* 3.9 16.0 - - - +
294C ILE* 3.4 6.2 - - - +
326C GLY 4.4 2.2 - - - +
327C LEU* 1.3 77.2 - - - +
329C THR* 1.3 68.3 + - - +
330C SER* 3.2 13.8 + - - -
403C AKG 2.6 43.4 + - - -
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Residues in contact with THR 329 (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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153C LEU* 3.7 28.3 - - + +
156C VAL* 5.0 5.8 - - + -
158C TRP* 5.7 3.9 - - + +
226C ILE* 3.4 28.7 - - + -
227C ASN 3.1 6.7 - - - +
228C GLN* 4.2 13.6 - - + +
253C SER* 4.1 0.2 - - - -
254C LEU* 2.7 46.0 + - - +
255C GLY* 4.7 0.2 - - - -
327C LEU* 4.9 5.4 - - - +
328C ARG* 1.3 79.5 + - - +
330C SER* 1.3 60.4 + - - +
331C PHE* 3.5 13.7 - - + -
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Residues in contact with SER 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C THR 3.6 1.0 - - - +
226C ILE* 3.1 3.5 - - - -
227C ASN* 3.0 31.7 + - - +
229C TYR* 3.6 6.6 - - - -
251C SER* 5.2 1.8 - - - -
252C LEU 3.2 9.0 - - - -
328C ARG* 3.2 39.5 + - - +
329C THR* 1.3 73.7 - - - +
331C PHE* 1.3 71.9 + - - +
332C THR* 3.9 1.1 - - - -
403C AKG 3.2 23.0 - - - +
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Residues in contact with PHE 331 (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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152C LEU* 3.9 32.3 - - + -
153C LEU* 5.3 0.4 - - - -
155C SER* 4.9 4.0 - - - -
156C VAL* 3.9 12.8 - - + -
201C PRO* 6.2 0.7 - - + -
204C CYS* 5.4 2.7 - - + -
224C MET* 4.3 17.5 - - + -
225C THR 3.8 4.3 - - - -
226C ILE* 3.3 46.7 - - + -
251C SER* 3.5 0.8 - - - -
252C LEU* 2.9 44.1 + - + -
254C LEU* 4.1 18.2 - - + -
329C THR* 3.5 14.4 - - + -
330C SER* 1.3 81.4 - - - +
332C THR* 1.3 61.2 + - - +
333C PHE* 3.2 30.3 - + + -
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Residues in contact with THR 332 (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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223C GLN* 4.4 0.9 - - - +
224C MET* 3.0 5.2 - - - -
225C THR* 2.9 49.2 + - - -
227C ASN* 4.6 0.3 + - - -
240C ASP* 4.9 0.7 - - - +
249C ILE* 4.0 15.3 - - + -
250C VAL 3.2 17.7 - - - +
251C SER* 3.2 16.7 + - - +
282C MET* 6.0 0.7 - - + -
330C SER* 4.6 1.2 + - - -
331C PHE* 1.3 73.6 - - - +
333C PHE* 1.3 61.4 + - - +
334C ARG* 3.9 24.7 + - + +
403C AKG 3.3 27.3 + - + +
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Residues in contact with PHE 333 (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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200C LEU* 5.0 4.5 - - + -
204C CYS* 3.9 33.7 - - + -
207C PHE* 6.4 0.2 - - + -
208C LEU* 3.8 30.5 - - + -
211C TRP* 5.6 6.5 - - - -
221C PRO* 3.9 22.6 - - + +
223C GLN 3.4 4.0 - - - -
224C MET* 3.5 26.0 - - + -
248C GLU 4.5 1.9 - - - +
249C ILE* 3.9 2.8 - - - -
250C VAL* 3.1 48.2 + - + +
252C LEU* 4.5 11.9 - - + -
279C LEU* 5.7 0.7 - - + -
331C PHE* 3.2 38.8 - + + -
332C THR* 1.3 72.1 - - - +
334C ARG* 1.3 63.8 + - - +
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Residues in contact with ARG 334 (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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178C HIS* 5.5 1.4 - - - -
221C PRO* 4.2 4.5 - - - -
222C ASP 3.5 2.1 + - - -
223C GLN* 2.7 51.1 + - - +
225C THR* 3.0 31.6 + - - +
240C ASP* 3.3 25.2 + - - -
245C PHE* 3.4 51.7 - - + -
248C GLU 5.5 1.3 - - - -
249C ILE* 3.6 27.4 - - + +
332C THR* 3.9 15.6 - - + +
333C PHE* 1.3 79.8 - - - +
335C LYS* 1.3 60.1 + - - +
336C VAL 4.0 0.2 - - - -
403C AKG 3.1 26.7 + - - -
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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