Contacts of the helix formed by residues 84 - 91 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78F ARG* 3.7 24.0 + - - +
79F GLN 4.0 3.6 - - - +
80F TYR* 3.5 24.3 - - + -
81F GLN* 2.7 40.9 + - - +
83F ASN* 1.3 78.5 - - - +
85F LEU* 1.3 64.3 + - - +
87F ASP* 3.1 19.4 + - - +
88F LEU* 3.1 13.8 + - - +
152F ILE* 5.7 0.2 - - + -
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Residues in contact with LEU 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F GLN 3.6 2.0 + - - +
82F GLU* 2.8 18.9 + - + +
84F ASP* 1.3 77.2 - - - +
86F PRO* 1.3 67.7 - - + +
87F ASP 3.1 0.3 + - - -
88F LEU* 3.2 13.2 + - + +
89F ILE* 3.0 37.1 + - + +
97F LEU* 5.6 1.6 - - + -
123F ALA* 5.0 2.5 - - + -
125F ILE* 3.6 34.3 - - + -
152F ILE* 3.3 32.7 - - + +
154F VAL* 4.5 10.8 - - + -
160F THR* 3.8 20.9 - - + -
163F MSE 3.8 15.5 - - + -
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Residues in contact with PRO 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F GLU 3.6 4.3 - - - +
83F ASN* 3.1 19.1 - - - +
85F LEU* 1.3 96.3 - - + +
87F ASP* 1.3 60.7 + - - +
89F ILE* 3.5 5.8 + - + +
90F ALA* 3.0 25.9 + - - +
163F MSE 4.7 23.6 - - + -
167F GLU* 6.0 2.6 - - + +
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Residues in contact with ASP 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F ASN 4.8 6.0 + - - +
84F ASP* 3.1 10.3 + - - +
86F PRO* 1.3 78.2 - - - +
88F LEU* 1.3 67.4 + - - +
90F ALA* 3.0 18.4 + - - +
91F SER* 3.1 14.7 + - - -
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Residues in contact with LEU 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F TYR* 4.3 29.6 - - + +
84F ASP 3.1 13.1 + - - +
85F LEU* 3.2 11.6 + - + +
87F ASP* 1.3 75.1 - - - +
89F ILE* 1.3 65.9 + - + +
91F SER* 2.9 28.3 + - - +
92F LEU* 3.7 23.9 - - + +
97F LEU* 5.9 1.3 - - + -
122F HIS* 4.4 10.1 - - + +
123F ALA* 3.7 29.8 - - + -
150F PRO* 4.4 5.2 - - + -
152F ILE* 4.1 15.9 - - + -
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Residues in contact with ILE 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F LEU* 3.0 33.9 + - + +
86F PRO* 3.8 4.9 - - + +
88F LEU* 1.3 80.2 - - + +
90F ALA* 1.3 63.8 + - - +
92F LEU* 3.2 28.3 + - + +
95F PRO* 4.4 5.8 - - + -
97F LEU* 4.2 13.9 - - + -
163F MSE 4.2 11.0 - - - -
164F LEU* 3.4 33.7 - - + -
167F GLU* 4.2 17.7 - - + +
169F ILE* 3.9 23.1 - - + -
190F ARG* 4.0 16.8 + - - +
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Residues in contact with ALA 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F PRO 3.0 15.3 + - - +
87F ASP* 3.0 18.1 + - - +
89F ILE* 1.3 80.4 - - - +
91F SER* 1.3 58.0 + - - +
92F LEU 3.3 4.3 + - - +
167F GLU* 6.1 1.1 - - - -
190F ARG* 5.7 1.1 + - - +
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Residues in contact with SER 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F ASP 3.1 10.1 + - - -
88F LEU* 2.9 21.7 + - - +
89F ILE 3.2 0.2 - - - -
90F ALA* 1.3 75.2 - - - +
92F LEU* 1.3 70.8 + - - +
93F ASP 4.2 0.9 + - - -
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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