Contacts of the helix formed by residues 84 - 92 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78H ARG* 3.6 28.3 + - - +
79H GLN 4.6 0.7 - - - +
80H TYR* 3.8 24.1 - - + -
81H GLN* 2.8 36.2 + - - +
83H ASN* 1.3 83.9 - - - +
85H LEU* 1.3 66.8 + - - +
86H PRO 3.4 0.7 - - - -
87H ASP* 3.0 13.0 + - + +
88H LEU* 2.8 23.1 + - - +
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Residues in contact with LEU 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81H GLN 3.8 2.4 + - - -
82H GLU* 3.2 15.0 + - + +
84H ASP* 1.3 76.5 - - - +
86H PRO* 1.3 62.2 - - + +
88H LEU* 2.9 14.6 + - + +
89H ILE* 2.7 46.0 + - + +
97H LEU* 5.7 1.1 - - + -
123H ALA* 4.9 1.6 - - + -
125H ILE* 3.9 26.0 - - + -
152H ILE* 3.2 32.6 - - + +
154H VAL* 4.6 9.9 - - + -
160H THR* 3.8 22.7 - - + -
163H MSE 3.5 24.2 - - + -
164H LEU* 4.8 0.2 - - + -
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Residues in contact with PRO 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82H GLU 3.8 6.1 - - - +
83H ASN* 3.7 12.1 - - - +
84H ASP 3.7 2.7 - - - -
85H LEU* 1.3 94.1 - - + +
87H ASP* 1.3 60.6 + - - +
89H ILE* 3.7 8.8 - - + +
90H ALA* 2.8 31.9 + - - +
163H MSE 4.3 21.1 - - + -
167H GLU* 5.5 2.8 - - + +
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Residues in contact with ASP 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83H ASN 4.9 3.7 + - - +
84H ASP* 3.0 14.2 + - + +
86H PRO* 1.3 79.5 - - - +
88H LEU* 1.3 67.9 + - - +
90H ALA* 3.5 7.4 + - - +
91H SER* 3.2 20.8 + - - -
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Residues in contact with LEU 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80H TYR* 4.5 21.5 - - + +
84H ASP 2.8 13.2 + - - +
85H LEU* 3.2 13.2 - - + +
87H ASP* 1.3 76.3 - - - +
89H ILE* 1.3 64.9 + - + +
91H SER* 2.6 28.0 + - - +
92H LEU* 2.8 25.5 - - + +
97H LEU* 5.8 1.8 - - + -
122H HIS* 4.6 11.0 - - + +
123H ALA* 3.4 33.2 - - + -
150H PRO* 4.7 6.1 - - + -
152H ILE* 4.1 15.7 - - + -
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Residues in contact with ILE 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85H LEU* 2.7 27.9 + - + +
86H PRO* 3.8 4.0 - - + +
88H LEU* 1.3 76.9 - - + +
90H ALA* 1.3 62.9 + - - +
92H LEU* 3.2 29.1 + - + +
95H PRO* 4.2 5.3 - - + +
97H LEU* 4.6 10.8 - - + -
163H MSE 3.8 25.1 - - + -
164H LEU* 3.5 33.0 - - + -
167H GLU* 4.1 20.6 - - + +
169H ILE* 3.9 23.8 - - + -
190H ARG* 4.1 11.7 + - - +
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Residues in contact with ALA 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86H PRO 2.8 22.9 + - - +
87H ASP* 3.9 9.6 - - - +
88H LEU 3.2 0.2 - - - -
89H ILE* 1.3 75.6 - - - +
91H SER* 1.3 60.6 + - - +
92H LEU 3.6 3.8 + - - +
167H GLU* 5.2 6.7 - - - +
190H ARG* 5.8 0.9 - - - +
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Residues in contact with SER 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87H ASP 3.2 11.6 + - - -
88H LEU* 2.6 27.4 + - - +
90H ALA* 1.3 78.7 - - - +
92H LEU* 1.3 68.2 + - - +
93H ASP 4.1 1.0 + - - -
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Residues in contact with LEU 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88H LEU* 2.8 50.7 + - + +
89H ILE* 3.2 12.0 + - + +
90H ALA 4.2 4.0 - - - +
91H SER* 1.3 89.6 + - - +
93H ASP* 1.3 60.0 + - - +
94H GLN 4.4 0.7 - - - +
95H PRO* 3.9 22.0 - - + -
97H LEU* 5.6 1.6 - - + -
122H HIS* 3.6 46.2 - - + +
190H ARG* 3.2 22.2 + - - -
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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