Contacts of the helix formed by residues 368 - 377 (chain C) in PDB entry 3QN3
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 368 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119C ARG* 4.0 7.2 - - - +
366C GLU 3.3 5.3 + - - +
367C ASP* 1.3 70.7 + - - +
369C PHE* 1.3 63.6 + - - +
370C ILE 3.2 2.7 - - - -
371C ALA* 2.9 19.2 + - - +
372C ASP* 3.6 7.5 + - - +
394C ALA* 3.5 30.1 - - + +
395C LYS* 4.1 11.9 - - - -
398C ARG* 3.7 19.1 - - + -
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Residues in contact with PHE 369 (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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115C MET* 3.4 51.4 - - + -
118C ALA* 4.6 4.0 - - + -
119C ARG* 3.3 21.7 - - + +
129C LEU* 3.5 25.1 - - + -
133C LEU* 4.0 19.3 - - + -
333C PRO* 6.1 0.9 - - + -
339C ILE* 3.7 27.4 - - + -
367C ASP* 2.9 17.5 + - - +
368C ALA* 1.3 75.8 - - - +
370C ILE* 1.3 62.8 + - + +
372C ASP* 3.1 7.1 + - - +
373C PHE* 2.9 56.2 + + - -
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Residues in contact with ILE 370 (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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38C PRO* 6.2 3.6 - - + -
333C PRO* 4.3 22.7 - - + -
358C MET* 3.4 17.5 - - + +
359C SER* 3.7 15.9 - - - +
360C HIS* 3.6 32.3 - - + +
364C GLU* 4.9 4.0 - - - +
367C ASP 5.1 0.2 + - - -
368C ALA 3.1 0.2 + - - -
369C PHE* 1.3 85.9 - - + +
371C ALA* 1.3 59.5 + - - +
373C PHE* 3.9 6.7 - - + -
374C ALA* 2.9 26.0 + - - +
382C ILE* 4.0 7.5 - - + +
383C LYS 4.5 0.4 - - - +
384C THR* 3.7 26.0 - - - +
395C LYS* 3.8 22.7 - - + -
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Residues in contact with ALA 371 (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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368C ALA 2.9 12.8 + - - +
370C ILE* 1.3 79.7 - - - +
372C ASP* 1.3 64.9 + - - +
373C PHE 3.3 0.3 + - - -
374C ALA* 3.3 2.1 + - - +
375C VAL* 3.3 24.3 + - - +
382C ILE* 4.1 7.2 - - - -
395C LYS* 3.7 29.8 - - + +
398C ARG* 3.8 16.2 - - + -
399C LEU* 3.8 17.4 - - + +
402C ILE* 4.5 1.3 - - - -
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Residues in contact with ASP 372 (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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119C ARG* 5.3 1.4 + - - -
129C LEU* 3.5 28.5 - - + +
130C TYR* 3.2 38.1 + - - +
133C LEU* 5.0 0.7 - - + -
368C ALA 3.6 6.6 + - - +
369C PHE* 3.1 8.8 + - - +
371C ALA* 1.3 78.1 - - - +
373C PHE* 1.3 57.1 + - - +
375C VAL 3.3 1.2 + - - -
376C ALA* 2.9 26.8 + - - +
398C ARG* 2.8 51.1 + - - +
402C ILE* 4.0 4.7 - - - +
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Residues in contact with PHE 373 (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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133C LEU* 3.9 20.4 - - + +
333C PRO* 4.2 10.8 - - + -
339C ILE* 3.6 30.1 - - + -
342C THR* 3.6 30.7 - - + -
343C MET* 3.7 23.8 - - + -
358C MET* 3.9 20.2 - - + -
369C PHE* 2.9 32.6 + + + +
370C ILE* 3.7 8.3 - - - +
371C ALA 3.2 0.2 - - - -
372C ASP* 1.3 77.8 - - - +
374C ALA* 1.3 62.6 + - - +
376C ALA* 3.2 2.9 + - + -
377C LEU* 3.1 47.7 + - + +
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Residues in contact with ALA 374 (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 ILE 4.4 2.9 - - - +
142C PRO* 4.1 22.0 - - + -
358C MET* 3.8 17.0 - - + +
370C ILE 2.9 17.9 + - - +
371C ALA 3.7 4.0 - - - +
373C PHE* 1.3 76.5 - - - +
375C VAL* 1.3 61.5 + - - +
377C LEU 3.6 0.2 + - - -
378C ASN* 3.2 2.8 + - - -
379C THR* 3.0 46.8 + - - +
380C GLY 4.6 0.5 + - - -
381C GLN 4.5 0.4 - - - +
382C ILE* 4.2 5.8 - - + -
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Residues in contact with VAL 375 (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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130C TYR* 3.9 26.5 - - + -
138C ALA* 3.6 3.8 - - - +
139C SER* 4.0 18.2 - - - +
140C ILE 3.7 22.0 - - - +
141C LEU* 3.9 13.5 - - + -
142C PRO* 4.0 2.2 - - + -
371C ALA 3.3 13.2 + - - +
372C ASP 3.9 5.2 - - - +
373C PHE 3.3 0.2 - - - -
374C ALA* 1.3 71.0 - - - +
376C ALA* 1.3 66.9 + - - +
377C LEU 3.1 1.8 - - - -
378C ASN* 3.0 20.6 + - - +
399C LEU* 3.8 21.3 - - + -
402C ILE* 4.1 15.5 - - + -
406C SER* 5.5 1.1 - - - -
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Residues in contact with ALA 376 (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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137B ASN* 5.2 1.7 + - - -
130C TYR* 3.5 10.7 - - - +
133C LEU* 3.4 33.4 - - + -
134C GLY* 3.4 19.8 - - - +
138C ALA* 3.8 17.1 - - - +
372C ASP 2.9 18.8 + - - +
373C PHE* 3.2 7.8 + - + +
375C VAL* 1.3 77.7 - - - +
377C LEU* 1.3 65.4 + - + +
378C ASN* 3.6 3.6 + - - -
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Residues in contact with LEU 377 (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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137B ASN* 3.5 43.3 - - + +
133C LEU 4.9 0.7 - - - +
343C MET* 3.9 16.2 - - + -
346C VAL* 3.9 38.1 - - + -
350C GLN* 3.2 17.5 + - - +
358C MET* 4.3 7.4 - - + -
373C PHE* 3.1 42.4 + - + +
376C ALA* 1.3 83.2 - - + +
378C ASN* 1.3 74.3 + - - +
379C THR* 3.0 9.7 + - + -
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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