Contacts of the helix formed by residues 96 - 104 (chain D) in PDB entry 1O9I
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 SER 96 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94D ASP* 2.7 27.3 + - - -
95D PRO* 1.3 79.5 - - - +
97D LEU* 1.3 63.6 + - - +
98D ALA* 3.0 2.8 + - - +
99D THR* 3.3 20.1 + - - -
100D THR* 4.4 1.2 + - - -
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Residues in contact with LEU 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D PRO* 4.1 35.9 - - + -
90D ASP* 3.6 24.9 - - + +
91D LEU* 4.2 7.9 - - + -
93D ARG* 5.5 1.6 - - + -
94D ASP* 2.9 34.6 + - + +
96D SER* 1.3 78.4 + - - +
98D ALA* 1.3 62.9 + - - +
99D THR 3.1 0.7 - - - -
100D THR* 3.2 17.4 + - + +
101D MET* 2.9 23.6 + - - +
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Residues in contact with ALA 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A THR* 3.8 16.9 - - + +
91D LEU* 3.7 19.0 - - + +
95D PRO 3.1 14.0 + - - +
96D SER 3.0 1.6 + - - -
97D LEU* 1.3 78.7 - - - +
99D THR* 1.3 57.1 + - - +
101D MET* 3.7 6.6 - - - +
102D ALA* 2.9 29.5 + - - +
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Residues in contact with THR 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A THR* 4.2 17.6 + - + +
98C ALA* 4.1 37.0 - - + +
99C THR* 4.4 10.3 + - - +
102C ALA* 3.8 10.4 - - + +
96D SER 3.3 11.7 + - - -
97D LEU 3.1 0.4 - - - -
98D ALA* 1.3 73.6 - - - +
100D THR* 1.3 67.0 + - - +
102D ALA* 3.3 5.6 + - - +
103D GLY* 3.2 16.3 + - - -
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Residues in contact with THR 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D PRO* 3.6 33.7 - - + -
20D ILE* 3.5 16.3 - - + +
85D PRO* 3.9 17.3 - - + -
96D SER 5.1 0.5 + - - -
97D LEU* 3.2 23.8 + - + +
99D THR* 1.3 80.1 - - - +
101D MET* 1.3 63.0 + - - +
103D GLY 3.1 10.6 + - - -
104D MET* 3.2 16.8 + - + +
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Residues in contact with MET 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ILE* 6.0 0.9 - - + -
24A ARG* 3.6 27.6 - - - +
85D PRO* 3.4 35.4 - - + +
86D PHE* 3.7 24.0 - - - -
87D GLY* 3.8 4.7 - - - +
90D ASP* 5.0 0.2 - - - -
91D LEU* 3.5 42.8 - - + -
97D LEU 2.9 15.8 + - - +
98D ALA* 3.7 5.4 - - - +
100D THR* 1.3 75.8 - - - +
102D ALA* 1.3 64.1 + - - +
104D MET* 3.1 27.2 + - - +
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Residues in contact with ALA 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ILE* 6.1 0.7 - - + -
23A ARG* 4.7 5.0 + - - -
99A THR* 3.7 26.5 - - + +
102A ALA* 3.7 14.2 - - + +
103A GLY* 3.7 29.0 - - - +
102C ALA* 3.8 5.8 - - + +
23D ARG* 5.1 1.4 + - - -
98D ALA 2.9 17.9 + - - +
99D THR* 3.5 7.4 - - - +
100D THR 3.2 0.4 - - - -
101D MET* 1.3 78.5 - - - +
103D GLY* 1.3 59.0 + - - +
104D MET 3.7 4.2 + - - +
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Residues in contact with GLY 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C ALA* 3.6 25.0 - - - +
20D ILE* 3.5 22.0 - - - +
23D ARG* 2.9 29.0 + - - -
99D THR 3.2 6.6 + - - -
100D THR 3.1 7.0 + - - -
102D ALA* 1.3 74.1 - - - +
104D MET* 1.3 62.4 + - - +
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Residues in contact with MET 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ARG* 4.8 3.8 + - - -
19D PRO* 3.8 32.3 - - + +
20D ILE* 4.2 4.5 - - + -
23D ARG* 4.0 8.5 + - - +
81D LEU* 4.8 4.0 - - + -
84D ALA* 3.7 19.3 - - + -
85D PRO* 3.4 38.6 - - - +
86D PHE* 5.5 0.2 - - + -
100D THR 3.2 15.5 + - - +
101D MET* 3.1 19.6 + - - +
102D ALA 4.2 3.8 - - - +
103D GLY* 1.3 82.4 - - - +
105D ASP* 1.3 71.3 + - - +
106D PRO* 3.4 11.1 - - + +
108D HIS* 5.1 3.6 - - + +
109D SER* 5.4 4.9 - - - +
114D LEU* 4.4 13.0 - - + -
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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