Contacts of the helix formed by residues 79 - 86 (chain A) in PDB entry 1R9G
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 CYS 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A PRO 4.3 3.6 - - - +
47A GLY* 4.6 13.2 - - - +
78A THR* 1.3 71.5 - - - +
80A ALA* 1.3 66.7 + - - +
82A LEU* 2.7 28.9 + - - +
83A ILE 3.7 1.6 + - - -
134A ILE 3.9 15.0 - - - -
135A ARG* 4.6 8.5 - - - -
137A PRO* 3.7 16.7 - - - +
167A CYS 3.0 14.4 + - - -
168A SER 4.2 12.3 - - - +
169A PHE 4.1 3.4 + - - +
170A HIS* 3.3 44.0 - - + +
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Residues in contact with ALA 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLY* 3.2 5.4 - - - -
47A GLY 2.9 40.8 - - - +
48A GLU 4.1 0.9 - - - -
49A SER* 3.7 20.5 - - - +
52A MSE 5.6 1.6 - - - -
79A CYS* 1.3 83.4 - - - +
81A GLY* 1.3 61.8 + - - +
83A ILE* 2.9 27.5 + - - +
84A ILE* 3.3 14.2 + - + +
106A ARG* 5.4 0.7 - - - +
137A PRO* 4.6 0.9 - - - +
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Residues in contact with GLY 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU* 3.3 27.4 - - - +
46A GLY* 3.2 9.6 - - - -
52A MSE 4.9 0.2 - - - -
77A GLY* 3.7 8.1 - - - -
78A THR 2.7 20.7 + - - -
80A ALA* 1.3 70.7 - - - +
82A LEU* 1.3 61.2 + - - -
84A ILE* 3.3 10.1 + - - +
85A LEU* 3.1 23.4 + - - +
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A GLY* 3.6 18.7 - - - +
79A CYS 2.7 19.4 + - - +
81A GLY* 1.3 70.8 - - - -
83A ILE* 1.3 60.5 + - - +
85A LEU* 3.2 4.2 + - + -
86A ALA* 3.0 28.4 + - + +
100A LEU* 3.9 28.9 - - + -
102A VAL* 4.4 5.8 - - + -
104A VAL* 4.2 16.2 - - + -
137A PRO* 4.7 4.7 - - + +
139A ILE* 4.1 26.5 - - + -
166A GLY* 4.2 11.0 - - - -
167A CYS 4.0 22.4 - - - +
168A SER* 4.1 12.1 - - - +
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Residues in contact with ILE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A SER* 3.5 37.9 - - - +
80A ALA* 2.9 15.3 + - - +
82A LEU* 1.3 78.1 - - - +
84A ILE* 1.3 64.9 + - + +
85A LEU 3.3 0.2 + - - -
86A ALA 3.3 14.2 + - - +
88A GLU* 3.9 19.0 - - + +
96A HIS* 3.5 24.5 - - + +
104A VAL* 4.2 16.6 - - + -
105A GLU 5.6 0.2 - - - -
106A ARG* 4.0 25.1 - - + +
137A PRO* 4.2 30.5 - - + -
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Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU* 4.8 7.0 - - + -
49A SER* 4.3 16.6 - - - +
52A MSE 3.3 37.9 - - + +
53A ARG* 4.6 11.9 - - - +
56A ILE* 5.0 12.3 - - + -
65A LEU* 5.5 2.2 - - + -
80A ALA* 3.3 11.8 + - + +
81A GLY 3.6 6.3 - - - +
83A ILE* 1.3 78.6 - - + +
85A LEU* 1.3 59.9 + - - +
96A HIS* 3.0 35.8 - - + +
97A LEU* 3.0 50.5 + - + +
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU* 5.0 6.7 - - + -
75A MSE 3.8 27.4 - - + +
76A PHE 4.4 0.2 - - - -
77A GLY* 3.6 27.4 - - - +
81A GLY 3.1 15.5 + - - +
82A LEU* 3.8 4.9 - - - +
84A ILE* 1.3 77.6 - - - +
86A ALA* 1.3 53.1 + - - +
97A LEU* 4.2 12.1 - - + -
98A GLY 3.5 0.2 + - - -
99A LEU* 2.8 45.4 + - + -
100A LEU* 3.0 31.3 + - + +
164A PHE* 3.9 15.3 - - + -
165A LEU 4.0 7.2 - - - +
166A GLY* 5.4 0.4 - - - -
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Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A LEU* 3.0 18.1 + - + +
83A ILE 3.3 10.2 + - - +
84A ILE 4.0 1.0 - - - +
85A LEU* 1.3 77.8 - - - +
87A LYS* 1.3 67.0 + - - +
96A HIS* 4.4 7.3 + - - +
98A GLY* 3.0 20.8 + - - -
100A LEU* 3.5 10.1 - - + +
102A VAL* 3.4 33.7 - - + +
104A VAL* 3.8 11.4 - - + -
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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