Contacts of the helix formed by residues 105 - 111 (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 ASP 105 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A ASN* 2.8 29.7 + - - -
23D ARG* 3.8 20.4 - - + +
26D GLN* 5.5 1.7 - - - +
104D MET* 1.3 78.3 - - - +
106D PRO* 1.3 67.2 - - - +
107D GLU* 2.8 19.6 + - - +
108D HIS* 3.0 50.3 + - + +
109D SER* 4.3 1.4 + - - -
117D SER* 4.9 7.4 + - - -
119D ASN* 5.3 1.6 + - - -
120D ASN 4.7 4.0 - - - +
121D PRO 4.4 8.7 - - - +
123D GLY* 4.6 7.6 + - - -
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Residues in contact with PRO 106 (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* 3.5 46.2 - - + +
24A ARG* 5.1 16.2 - - + +
121A PRO* 4.0 19.3 - - + -
122A ASN* 4.0 4.0 - - - +
23D ARG* 6.4 0.2 - - - -
104D MET* 3.4 10.3 - - + +
105D ASP* 1.3 89.1 - - - +
107D GLU* 1.3 59.9 + - - +
109D SER* 3.2 9.9 + - - +
110D LEU* 3.2 24.9 + - + +
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Residues in contact with GLU 107 (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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27A GLU* 2.4 37.3 - - - +
120A ASN* 3.2 27.6 + - - -
121A PRO* 4.3 9.0 - - + -
122A ASN* 3.2 24.2 + - - +
105D ASP* 2.8 11.8 + - - +
106D PRO* 1.3 76.4 - - - +
108D HIS* 1.3 66.2 + - - +
109D SER 3.2 1.1 - - - -
110D LEU* 4.5 1.1 - - + -
111D VAL* 3.0 35.1 + - + +
112D HIS* 3.1 16.4 + - + -
119D ASN* 4.0 17.9 + - - +
123D GLY* 4.7 1.2 - - - +
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Residues in contact with HIS 108 (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 4.9 1.6 + - - -
22D ALA* 4.2 3.6 - - + -
23D ARG* 4.0 22.3 + - - +
26D GLN* 2.8 41.5 + - + +
77D ILE* 4.2 0.6 - - + +
81D LEU* 3.8 34.0 - - + +
104D MET* 5.1 4.3 - - + +
105D ASP* 3.0 37.8 + - + +
107D GLU* 1.3 79.2 - - - +
109D SER* 1.3 52.3 + - - +
112D HIS* 3.5 6.2 - + - +
113D GLY 3.2 7.1 + - - -
114D LEU* 2.8 32.3 + - + -
115D ASN 3.4 20.8 + - - -
117D SER* 4.3 8.1 - - - -
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Residues in contact with SER 109 (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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24A ARG* 5.9 0.2 + - - -
157A ARG* 3.7 7.6 + - - -
161A MET* 3.5 16.5 - - - +
86D PHE* 3.7 30.8 - - - +
104D MET* 5.4 3.8 - - - +
105D ASP 4.3 0.9 + - - -
106D PRO* 3.2 12.0 + - - +
108D HIS* 1.3 80.1 - - - +
110D LEU* 1.3 72.6 + - - +
113D GLY* 3.0 21.0 + - - -
114D LEU* 3.8 21.5 - - - +
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Residues in contact with LEU 110 (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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24A ARG* 3.6 22.0 - - + +
27A GLU* 3.6 38.6 - - + +
121A PRO* 4.9 3.4 - - + -
154A GLN* 3.6 39.7 - - + +
157A ARG* 3.0 32.6 + - + +
158A LEU* 3.8 21.8 - - + -
161A MET* 4.0 14.1 - - + -
106D PRO 3.2 16.1 + - - +
107D GLU* 4.5 1.3 - - - -
109D SER* 1.3 81.7 + - - +
111D VAL* 1.3 59.6 + - - +
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Residues in contact with VAL 111 (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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27A GLU* 3.3 38.6 - - + +
32A GLN* 4.5 15.3 - - - +
33A TRP* 6.0 0.9 - - + -
150A GLU* 5.6 1.6 - - - +
153A LEU* 5.3 2.3 - - - +
154A GLN* 4.0 17.4 + - - +
157A ARG* 3.2 12.8 + - - -
107D GLU* 3.0 25.9 + - + +
110D LEU* 1.3 79.7 - - + +
112D HIS* 1.3 87.7 + - + +
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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