Contacts of the helix formed by residues 84 - 92 (chain C) in PDB entry 1GZ0
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 ASP 84 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78C ARG* 4.1 15.8 + - - +
79C GLN 3.8 3.8 - - - +
80C TYR* 3.1 25.8 - - + -
81C GLN* 2.8 42.8 + - - +
83C ASN* 1.3 78.8 - - - +
85C LEU* 1.3 65.3 + - - +
86C PRO 3.3 0.4 - - - -
87C ASP* 3.1 12.4 + - + +
88C LEU* 3.1 21.2 + - - +
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Residues in contact with LEU 85 (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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81C GLN 3.8 2.4 + - - -
82C GLU* 3.3 14.5 + - + +
84C ASP* 1.3 78.0 - - - +
86C PRO* 1.3 70.9 - - + +
88C LEU* 3.1 14.5 + - + +
89C ILE* 3.1 36.8 + - + +
97C LEU* 5.6 2.5 - - + -
123C ALA* 5.2 3.4 - - + -
125C ILE* 3.6 32.5 - - + -
152C ILE* 3.4 32.9 - - + +
154C VAL* 4.6 7.6 - - + -
160C THR* 3.8 13.2 - - + +
163C MSE 3.6 24.0 - - + -
164C LEU* 4.5 0.7 - - + -
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Residues in contact with PRO 86 (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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82C GLU 3.9 2.9 - - - +
83C ASN* 3.2 19.7 - - - +
85C LEU* 1.3 95.6 - - + +
87C ASP* 1.3 64.9 + - - +
89C ILE* 3.4 5.8 + - + +
90C ALA* 3.2 20.3 + - - +
163C MSE 4.3 29.8 - - + -
167C GLU* 6.4 0.9 - - + -
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Residues in contact with ASP 87 (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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83C ASN 5.0 4.2 - - - +
84C ASP* 3.1 10.8 + - + +
86C PRO* 1.3 83.9 - - - +
88C LEU* 1.3 61.7 + - - +
90C ALA* 3.4 11.3 - - - +
91C SER* 3.3 18.7 + - - -
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Residues in contact with LEU 88 (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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80C TYR* 3.9 40.2 - - + +
84C ASP 3.1 12.0 + - - +
85C LEU* 3.1 13.0 + - + +
87C ASP* 1.3 74.5 - - - +
89C ILE* 1.3 66.7 + - + +
91C SER* 2.5 31.7 + - - +
92C LEU* 3.3 25.7 - - + +
97C LEU* 6.1 1.6 - - + -
122C HIS* 4.7 6.7 - - + +
123C ALA* 4.2 23.8 - - + -
150C PRO* 4.9 4.3 - - + -
152C ILE* 4.3 11.7 - - + -
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Residues in contact with ILE 89 (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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85C LEU* 3.1 23.4 + - + +
86C PRO* 3.7 7.2 - - + +
88C LEU* 1.3 77.4 - - + +
90C ALA* 1.3 63.3 + - - +
92C LEU* 3.1 33.3 + - + +
95C PRO* 4.2 3.9 - - + +
97C LEU* 4.4 11.7 - - + -
163C MSE 4.1 14.6 - - - -
164C LEU* 3.3 34.3 - - + -
167C GLU* 4.6 15.0 - - + +
169C ILE* 3.9 26.2 - - + -
190C ARG* 4.1 15.6 + - - +
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Residues in contact with ALA 90 (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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86C PRO 3.2 13.2 + - - +
87C ASP* 3.4 18.4 - - - +
88C LEU 3.1 0.6 - - - -
89C ILE* 1.3 79.4 - - - +
91C SER* 1.3 58.6 + - - +
92C LEU 3.6 2.8 + - - +
167C GLU* 6.2 0.2 - - - -
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Residues in contact with SER 91 (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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87C ASP 3.3 7.6 + - - -
88C LEU* 2.5 29.2 + - - +
90C ALA* 1.3 79.2 - - - +
92C LEU* 1.3 68.7 + - - +
93C ASP* 3.8 5.5 + - - +
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Residues in contact with LEU 92 (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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88C LEU* 3.3 35.9 + - + +
89C ILE* 3.1 23.2 + - + +
90C ALA 4.5 2.4 - - - +
91C SER* 1.3 92.2 - - - +
93C ASP* 1.3 67.1 + - - +
94C GLN 4.5 0.4 - - - +
95C PRO* 3.7 21.1 - - + +
97C LEU* 5.1 3.6 - - + -
122C HIS* 3.8 44.0 - - + +
190C ARG* 3.4 15.8 + - - -
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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