Contacts of the helix formed by residues 94 - 105 (chain A) in PDB entry 2OG9
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 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A ASP* 3.2 28.3 + - - +
92A PRO 4.3 0.7 - - - -
93A SER* 1.3 78.7 - - - +
95A ILE* 1.3 63.2 + - - +
96A ALA 3.5 2.2 - - - -
97A LYS* 2.9 47.9 + - + -
98A LEU* 3.0 24.8 + - - +
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Residues in contact with ILE 95 (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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92A PRO 3.5 17.5 - - - +
93A SER 3.0 9.3 + - - +
94A ASP* 1.3 72.2 - - - +
96A ALA* 1.3 63.4 + - - +
98A LEU* 3.3 3.6 + - - +
99A TRP* 3.0 21.0 + - - +
123A ASP* 3.2 25.9 - - - +
126A LEU* 3.8 40.5 - - + +
127A TRP* 3.4 47.3 - - + +
130A LYS* 4.0 19.1 - - - +
296A THR* 3.5 3.6 - - - +
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Residues in contact with ALA 96 (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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94A ASP 3.5 0.2 - - - -
95A ILE* 1.3 78.4 - - - +
97A LYS* 1.3 63.8 + - - +
99A TRP* 3.1 10.6 + - - +
100A ASP* 3.0 29.7 + - - +
296A THR* 4.3 19.5 + - + +
300A LYS* 5.6 6.5 - - - +
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Residues in contact with LYS 97 (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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90A GLU* 4.1 20.2 + - - -
91A ASP* 4.9 5.8 - - - +
94A ASP* 2.9 46.3 + - + +
95A ILE 3.3 0.2 - - - -
96A ALA* 1.3 79.3 - - - +
98A LEU* 1.3 62.0 - - - +
100A ASP* 3.3 10.9 + - - +
101A LYS* 2.9 25.3 + - + +
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Residues in contact with LEU 98 (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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15A ILE* 4.1 7.2 - - + -
87A LEU* 4.0 22.0 - - + -
90A GLU* 3.5 44.0 - - + +
91A ASP 3.5 22.4 - - - +
92A PRO* 4.3 2.0 - - + -
94A ASP 3.0 18.5 + - - +
95A ILE 3.7 3.8 - - - +
96A ALA 3.3 0.2 - - - -
97A LYS* 1.3 79.5 - - - +
99A TRP* 1.3 66.0 + - - +
101A LYS* 3.7 14.0 - - + +
102A LEU* 3.0 30.9 + - + +
126A LEU* 3.9 25.6 - - + -
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Residues in contact with TRP 99 (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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95A ILE 3.0 13.9 + - - +
96A ALA* 3.3 13.5 - - - +
98A LEU* 1.3 75.9 - - - +
100A ASP* 1.3 75.0 + - - +
102A LEU* 3.9 2.5 - - - +
103A CYS* 3.0 47.5 + - + +
111A ARG* 4.5 14.6 - - + -
116A THR* 3.8 35.9 - - + -
119A ILE* 3.4 29.4 - - + +
123A ASP* 3.6 23.8 - - + +
292A VAL 4.7 1.8 - - - -
293A GLY* 2.8 24.3 + - - -
296A THR* 4.3 7.0 - - + -
297A PRO* 3.7 26.5 - - + +
300A LYS* 5.4 8.3 - - - -
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Residues in contact with ASP 100 (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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96A ALA* 3.0 18.4 + - - +
97A LYS* 3.5 11.4 - - - +
99A TRP* 1.3 94.8 - - - +
101A LYS* 1.3 60.4 + - - +
103A CYS* 3.2 3.9 + - - +
104A TRP* 2.8 48.8 + - + +
300A LYS* 5.0 7.4 + - - -
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Residues in contact with LYS 101 (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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86A ALA* 2.7 42.0 + - + +
88A ILE 5.2 1.8 + - - -
90A GLU* 2.7 35.1 + - - +
97A LYS* 2.9 17.9 + - + +
98A LEU* 3.3 14.1 + - + +
100A ASP* 1.3 74.8 - - - +
102A LEU* 1.3 60.4 + - + +
104A TRP* 3.3 8.2 + - - +
105A ALA* 2.9 28.1 + - + +
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Residues in contact with LEU 102 (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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79A HIS* 5.2 1.2 + - - -
83A ILE* 3.6 29.7 - - + +
86A ALA* 3.5 31.6 - - + -
87A LEU* 4.1 26.9 - - + -
98A LEU 3.0 19.8 + - - +
99A TRP* 3.9 1.3 - - - +
101A LYS* 1.3 75.7 - - + +
103A CYS* 1.3 65.0 + - - +
105A ALA* 3.3 15.9 + - + +
106A GLY* 3.4 5.4 + - - -
119A ILE* 3.6 29.2 - - + +
122A PHE* 3.8 31.9 - - + -
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Residues in contact with CYS 103 (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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99A TRP* 3.0 37.0 + - + +
100A ASP* 3.6 6.3 - - - +
102A LEU* 1.3 76.8 - - - +
104A TRP* 1.3 64.0 + - + +
106A GLY 3.0 6.8 + - - +
107A ALA* 3.0 22.0 + - - -
110A GLY 3.7 22.4 - - - -
111A ARG* 4.0 23.8 - - - -
116A THR* 4.4 5.8 - - - -
119A ILE* 3.4 12.5 - - + +
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Residues in contact with TRP 104 (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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100A ASP* 2.8 41.5 + - + +
101A LYS* 3.7 6.7 - - - +
103A CYS* 1.3 72.4 - - + +
105A ALA* 1.3 62.6 + - - +
106A GLY 2.9 6.8 + - - -
107A ALA* 3.1 33.9 + - + +
111A ARG* 5.2 6.3 - - - -
70B ARG* 4.5 9.7 - - - -
216B GLN* 3.9 36.3 - - + -
243B ASP* 4.2 12.8 - - - -
266B MSE 4.9 3.8 - - + -
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Residues in contact with ALA 105 (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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83A ILE* 4.6 13.9 - - + -
86A ALA* 4.9 11.9 - - + -
101A LYS* 2.9 14.9 + - + +
102A LEU* 3.4 15.7 - - - +
103A CYS 3.2 0.4 - - - -
104A TRP* 1.3 76.6 - - - +
106A GLY* 1.3 57.0 + - - +
107A ALA 3.7 0.4 - - - -
70B ARG* 3.5 11.0 - - - +
71B ALA* 3.1 27.6 + - + +
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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