Contacts of the helix formed by residues 73 - 80 (chain C) in PDB entry 3GZN
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 SER 73 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ARG* 4.6 21.3 - - - +
71C GLN 3.2 7.4 + - - -
72C VAL* 1.3 89.3 - - - +
74C GLY* 1.3 64.4 + - - +
75C GLU* 3.4 13.2 + - - +
76C ASP* 2.9 39.6 + - - +
77C ALA 3.4 2.1 + - - -
88C ILE* 3.9 4.6 - - - +
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Residues in contact with GLY 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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129A ARG* 5.7 0.6 - - - +
73C SER* 1.3 73.2 - - - +
75C GLU* 1.3 60.2 + - - +
77C ALA* 3.3 9.9 + - - +
78C GLY 3.4 3.1 + - - -
88C ILE* 3.8 22.8 - - - +
34D TRP* 3.0 22.3 + - - -
35D GLU* 3.4 22.2 - - - -
36D GLY* 4.2 0.9 - - - -
37D ARG* 4.2 0.9 - - - -
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Residues in contact with GLU 75 (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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73C SER* 3.4 14.1 - - - +
74C GLY* 1.3 72.4 - - - +
76C ASP* 1.3 67.7 + - - +
77C ALA 3.2 0.4 - - - -
78C GLY* 3.1 10.2 + - - +
79C ASN 3.4 5.2 + - - -
36D GLY* 3.0 25.0 + - - +
37D ARG 4.4 0.7 - - - +
39D ASN* 2.8 41.3 + - + +
40D HIS* 3.3 37.8 + - + +
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Residues in contact with ASP 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C THR* 5.1 7.3 + - - -
71C GLN 4.0 1.7 - - - +
72C VAL* 4.2 1.6 - - + -
73C SER* 2.9 39.1 + - - +
74C GLY 3.3 0.2 - - - -
75C GLU* 1.3 82.0 - - - +
77C ALA* 1.3 60.5 + - - +
78C GLY 3.3 0.7 + - - -
79C ASN* 3.4 6.2 - - - +
80C ASN* 3.3 27.7 + - - +
83C LEU* 4.0 16.8 - - + -
92C ARG* 2.8 41.9 + - - -
496C GLU* 5.5 1.2 - - - +
40D HIS* 4.9 4.9 - - - -
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Residues in contact with ALA 77 (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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72C VAL* 4.3 3.5 - - + +
73C SER 3.4 7.2 + - - +
74C GLY 3.3 11.3 + - - +
75C GLU 3.2 0.4 - - - -
76C ASP* 1.3 77.6 - - - +
78C GLY* 1.3 60.9 + - - +
79C ASN 3.8 0.2 + - - -
80C ASN 3.9 11.8 - - - +
83C LEU* 4.3 14.5 - - - +
84C GLN* 3.8 25.8 - - - +
88C ILE* 4.1 10.1 - - + -
34D TRP* 3.8 24.5 - - + -
37D ARG* 5.7 0.2 + - - -
90D LEU* 5.2 2.1 - - - +
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Residues in contact with GLY 78 (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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74C GLY 3.4 5.0 + - - -
75C GLU 3.1 5.7 + - - -
76C ASP 3.1 1.6 - - - -
77C ALA* 1.3 79.9 - - - +
79C ASN* 1.3 58.1 + - - +
80C ASN 3.6 0.2 - - - -
34D TRP* 4.6 0.2 - - - -
37D ARG* 3.2 40.4 + - - +
38D TRP* 4.5 7.7 - - - -
40D HIS* 5.1 0.7 - - - -
90D LEU* 3.5 26.6 - - - +
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Residues in contact with ASN 79 (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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47C ALA* 3.2 25.4 + - - +
75C GLU 3.4 6.4 + - - +
76C ASP* 3.4 12.3 - - - +
77C ALA 3.5 0.2 - - - -
78C GLY* 1.3 76.5 - - - +
80C ASN* 1.3 60.0 + - - +
496C GLU* 2.7 47.1 + - - +
498C HIS* 2.5 42.6 + - + +
40D HIS* 3.4 29.3 + - + +
90D LEU* 4.4 5.8 - - - +
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Residues in contact with ASN 80 (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 ALA 3.4 6.7 + - - -
46C THR* 3.1 35.2 + - - +
47C ALA* 3.5 3.1 - - - +
50C THR* 2.8 25.4 + - - +
76C ASP 3.3 16.9 + - - +
77C ALA 3.9 8.7 - - - +
78C GLY 3.6 0.2 - - - -
79C ASN* 1.3 82.4 + - - +
81C PHE* 1.3 60.6 + - - +
82C PHE* 2.7 30.6 + - - +
83C LEU* 3.7 33.2 - - + +
498C HIS* 4.6 0.4 - - - -
90D LEU* 4.2 10.0 - - - +
136D VAL* 5.9 0.3 - - - +
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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