Contacts of the helix formed by residues 346 - 354 (chain C) in PDB entry 6P19
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 TYR 346 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C PHE* 4.7 2.9 - + + -
192C ASP* 3.4 49.9 - - + +
194C LEU* 3.8 17.9 - - + -
225C PHE* 4.7 0.2 - - - -
340C ASP 5.4 4.5 + - - -
344C GLY* 2.8 43.5 + - - +
345C PRO* 1.3 82.3 - - + +
347C ILE* 1.3 64.0 + - + +
348C SER 3.2 1.1 - - - -
349C GLU* 3.2 3.8 + - - +
350C THR* 2.9 33.1 + - - +
433C ILE* 4.0 25.4 - - + -
436C ARG* 3.4 49.4 + - + +
437C ASN* 4.7 7.8 - - + +
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Residues in contact with ILE 347 (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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194C LEU* 4.3 12.6 - - + -
207C THR* 4.5 8.9 - - + +
210C LEU* 6.5 1.1 - - + -
220C ILE* 3.7 29.6 - - + -
221C LEU* 5.9 0.2 - - - -
224C PHE* 3.6 41.3 - - + -
225C PHE* 3.7 23.0 - - + -
344C GLY 5.1 0.9 - - - +
346C TYR* 1.3 78.7 - - + +
348C SER* 1.3 56.7 + - - +
350C THR* 2.7 22.3 + - - +
351C LEU* 2.9 17.4 + - - +
429C MET* 5.6 4.0 - - + -
433C ILE* 3.7 33.2 - - + -
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Residues in contact with SER 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C LEU* 5.2 0.9 - - - -
225C PHE* 3.4 20.2 - - - -
296C VAL* 5.5 4.3 - - - -
314C ASN* 3.3 32.4 + - - +
336C LEU* 4.5 10.3 - - - -
345C PRO* 3.6 27.4 - - - +
347C ILE* 1.3 76.6 - - - +
349C GLU* 1.3 57.0 + - - -
351C LEU 3.3 0.2 + - - -
352C ARG* 2.9 31.3 + - - +
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Residues in contact with GLU 349 (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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191C LYS* 5.3 2.6 - - - +
193C ASN* 2.9 37.8 + - - +
345C PRO* 3.6 17.0 - - + +
346C TYR 3.2 9.2 + - - +
348C SER* 1.3 83.6 + - - +
350C THR* 1.3 57.0 + - - +
352C ARG* 3.2 10.8 + - + +
353C VAL* 2.9 37.4 + - - +
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Residues in contact with THR 350 (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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193C ASN* 3.7 13.2 - - + -
194C LEU* 3.3 47.1 - - + +
195C PHE* 5.8 0.7 - - + -
205C PRO* 4.7 3.9 - - + +
206C ALA 5.2 2.9 - - - -
207C THR* 3.4 21.3 + - - +
346C TYR 2.9 15.4 + - - +
347C ILE* 2.7 25.8 + - - -
349C GLU* 1.3 72.4 - - - +
351C LEU* 1.3 60.6 + - - +
353C VAL* 3.5 9.8 - - + +
354C ASP* 2.9 31.9 + - - +
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Residues in contact with LEU 351 (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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207C THR* 4.3 11.8 - - + +
211C ARG* 3.4 29.2 - - - +
217C THR* 3.9 25.6 - - + -
220C ILE* 4.4 17.5 - - + -
221C LEU* 4.1 16.8 - - + -
314C ASN* 3.5 32.3 - - + +
347C ILE 2.9 17.0 + - - +
350C THR* 1.3 76.8 + - - +
352C ARG* 1.3 61.9 + - - +
354C ASP* 3.6 17.7 + - + +
356C THR 5.9 0.4 - - - +
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Residues in contact with ARG 352 (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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296C VAL* 3.4 10.7 - - - +
314C ASN* 2.6 47.5 + - + +
315C MET* 3.3 19.4 - - - +
316C GLU* 3.1 35.3 + - - +
348C SER* 2.9 22.4 + - - +
349C GLU* 3.2 12.5 + - + +
351C LEU* 1.3 79.2 - - - +
353C VAL* 1.3 60.3 + - - +
354C ASP 3.4 4.5 + - - +
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Residues in contact with VAL 353 (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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193C ASN* 5.4 6.7 - - + +
195C PHE* 5.7 6.7 - - + -
205C PRO* 5.0 10.1 - - + +
349C GLU* 2.9 34.0 + - - +
350C THR* 3.5 16.4 - - + +
352C ARG* 1.3 75.6 - - + +
354C ASP* 1.3 65.7 + - - +
355C PRO* 3.3 9.9 - - - +
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Residues in contact with ASP 354 (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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205C PRO* 3.5 21.8 - - + +
207C THR* 2.4 26.8 + - - +
208C ILE* 4.0 8.2 + - - +
211C ARG* 5.1 3.7 + - - -
350C THR 2.9 18.5 + - - +
351C LEU* 3.7 18.5 - - + +
352C ARG 3.2 4.3 - - - +
353C VAL* 1.3 76.7 - - - +
355C PRO* 1.3 71.4 - - - +
356C THR* 3.3 36.4 + - - +
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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