Contacts of the helix formed by residues 67 - 74 (chain C) in PDB entry 3Q29
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 67 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C GLU* 3.4 44.8 + - - +
46C GLU* 5.4 5.8 + - - +
63C TRP* 3.7 13.9 - - + +
64C ALA 3.6 1.0 + - - -
65C HIS 3.1 0.8 - - - -
66C ASP* 1.3 81.2 + - - +
68C PHE* 1.3 64.2 + - + +
69C GLY 3.2 2.9 + - - -
70C GLY* 3.5 4.6 + - - -
71C TYR* 3.3 41.6 + - + -
337C MET* 5.7 0.4 - - + -
338C SER* 3.3 36.8 + - - +
341C TRP* 3.9 22.5 - - + +
342C TYR 5.5 0.2 - - - +
2D GLC 2.9 43.1 + - - +
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Residues in contact with PHE 68 (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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61C ILE* 3.6 25.6 - - + -
63C TRP* 3.6 34.8 - - + -
64C ALA 3.7 11.4 - - - -
65C HIS* 3.1 14.6 + - - +
67C ARG* 1.3 78.7 - - - +
69C GLY* 1.3 60.0 + - - +
70C GLY 3.4 0.2 - - - -
71C TYR* 3.4 16.7 + + - +
72C ALA* 2.8 30.9 + - - +
77C LEU* 3.5 21.6 - - + +
98C VAL* 6.0 0.2 - - + -
105C ILE* 3.6 19.2 - - + +
106C ALA* 3.5 22.0 - - + -
264C SER* 3.6 13.0 - - - -
266C GLY* 3.3 28.5 - - - -
333C ASN* 5.6 0.7 - - + -
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Residues in contact with GLY 69 (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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67C ARG 3.2 0.2 - - - -
68C PHE* 1.3 76.5 - - - +
70C GLY* 1.3 59.1 + - - +
73C GLN* 2.8 31.5 + - - +
100C TYR* 3.6 29.3 - - - -
333C ASN* 2.8 31.7 + - - +
335C PRO* 4.3 2.7 - - - -
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Residues in contact with GLY 70 (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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66C ASP 5.2 0.2 + - - -
67C ARG 3.5 7.0 + - - -
68C PHE 3.4 0.2 - - - -
69C GLY* 1.3 74.2 - - - +
71C TYR* 1.3 65.2 + - - +
73C GLN* 3.3 3.3 + - - +
74C SER* 3.2 25.8 + - - -
76C LEU* 5.6 0.2 - - - -
333C ASN 3.9 3.0 + - - -
334C ILE 4.6 0.6 + - - -
335C PRO* 3.8 26.9 - - - +
338C SER* 6.3 2.0 - - - -
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Residues in contact with TYR 71 (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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45C GLU* 2.7 38.5 + - - +
48C PHE* 3.7 33.2 - + + -
49C PRO* 4.0 22.0 - - + +
61C ILE* 3.7 16.0 - - + +
63C TRP* 5.4 2.1 - - + -
67C ARG* 3.3 33.0 - - + +
68C PHE* 3.5 24.0 - + - +
69C GLY 3.2 0.4 - - - -
70C GLY* 1.3 78.1 - - - +
72C ALA* 1.3 62.2 + - - +
74C SER 3.1 7.1 + - - -
76C LEU* 2.9 40.0 + - + +
77C LEU* 3.5 20.6 - - + -
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Residues in contact with ALA 72 (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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68C PHE 2.8 21.3 + - - +
71C TYR* 1.3 73.0 - - - +
73C GLN* 1.3 56.1 + - - +
75C GLY* 2.7 24.9 + - - +
76C LEU 4.6 0.4 - - - +
77C LEU* 4.0 12.0 - - + +
100C TYR* 3.6 25.8 - - + -
105C ILE* 3.8 25.1 - - + -
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Residues in contact with GLN 73 (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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326A GLN* 3.2 38.3 + - - +
327A LYS* 4.8 6.2 - - - +
69C GLY 2.8 18.7 + - - +
70C GLY* 3.4 7.2 - - - +
72C ALA* 1.3 74.9 - - - +
74C SER* 1.3 57.9 + - - +
75C GLY 3.5 2.1 + - - -
100C TYR* 3.5 21.2 + - - +
101C ASN* 3.8 12.7 + - - +
335C PRO* 3.8 21.7 - - + +
382C ALA* 3.6 32.0 - - + +
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Residues in contact with SER 74 (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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70C GLY 3.2 10.9 + - - -
71C TYR 3.1 2.8 + - - -
72C ALA 3.1 1.2 - - - -
73C GLN* 1.3 76.3 - - - +
75C GLY* 1.3 63.4 + - - +
76C LEU* 3.1 36.0 + - - +
381C LYS 3.0 25.3 + - - -
382C ALA* 3.9 9.8 - - - -
384C GLU 4.5 9.2 - - - +
385C GLY* 4.0 5.1 - - - -
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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