Contacts of the helix formed by residues 102 - 112 (chain A) in PDB entry 1DMO
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 ALA 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A ILE 3.7 0.4 + - - -
101A SER* 1.3 71.3 + - - +
103A ALA* 1.3 66.9 + - - +
105A LEU* 3.3 8.2 - - - +
106A ARG* 3.0 20.8 + - - +
125A ILE* 4.1 19.4 - - + +
130A ILE* 5.2 5.2 - - + -
134A GLY* 2.7 29.9 + - - +
136A VAL* 3.5 20.6 - - + -
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Residues in contact with ALA 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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101A SER* 3.3 4.3 + - - +
102A ALA* 1.3 76.3 - - - +
104A GLU* 1.3 86.1 + - - +
106A ARG* 2.9 22.4 + - - +
107A HIS* 3.3 4.0 + - - +
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Residues in contact with GLU 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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92A PHE* 3.8 37.4 - - + -
100A ILE* 6.0 0.7 - - + -
101A SER* 2.6 38.7 + - - +
102A ALA 3.5 0.2 - - - -
103A ALA* 1.3 86.1 - - - +
105A LEU* 1.3 57.6 + - - +
107A HIS* 2.5 39.8 + - - +
108A VAL* 3.1 6.3 + - - +
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Residues in contact with LEU 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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89A PHE* 4.0 6.1 - - + -
100A ILE* 3.9 19.9 - - + +
101A SER 3.0 22.1 + - - +
102A ALA* 3.3 7.9 - - - +
104A GLU* 1.3 76.9 - - - +
106A ARG* 1.3 62.1 + - - +
108A VAL* 2.6 41.0 + - - +
109A MET* 3.2 6.0 + - + +
125A ILE* 2.9 46.7 - - + -
136A VAL* 3.7 23.6 - - + -
141A PHE* 3.4 37.2 - - + -
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Residues in contact with ARG 106 (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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102A ALA 3.0 8.9 + - - +
103A ALA* 2.9 13.6 + - - +
105A LEU* 1.3 81.8 - - - +
107A HIS* 1.3 59.0 + - - +
109A MET* 3.2 16.6 + - - +
110A THR* 2.9 14.5 + - - -
118A ASP* 2.9 57.2 + - - +
121A VAL* 3.8 16.8 - - + +
122A ASP* 4.9 3.3 - - - +
125A ILE* 3.7 19.7 - - + -
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Residues in contact with HIS 107 (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 PHE* 5.1 10.7 - + + -
103A ALA 3.3 2.9 + - - +
104A GLU* 2.5 27.4 + - - +
106A ARG* 1.3 72.4 - - - +
108A VAL* 1.3 58.1 + - - +
110A THR* 2.6 39.8 + - + +
111A ASN* 3.2 26.0 + - - +
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Residues in contact with VAL 108 (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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88A ALA* 3.4 35.4 - - + +
89A PHE* 3.5 31.0 - - + -
92A PHE* 3.6 30.7 - - + -
100A ILE* 5.2 0.4 - - + -
104A GLU 3.1 5.5 + - - +
105A LEU* 2.6 22.4 + - - +
107A HIS* 1.3 72.9 - - - +
109A MET* 1.3 60.1 + - + +
111A ASN* 3.1 19.5 + - + +
112A LEU* 3.2 24.1 + - + +
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Residues in contact with MET 109 (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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85A ILE* 5.4 0.4 - - + -
89A PHE* 3.9 24.5 - - + -
105A LEU 3.2 6.2 + - - +
106A ARG* 3.4 13.0 - - - +
107A HIS 3.1 0.4 - - - -
108A VAL* 1.3 81.8 - - + +
110A THR* 1.3 57.6 + - - +
112A LEU* 3.3 32.9 - - + +
113A GLY* 3.0 26.9 + - - -
114A GLU* 4.7 7.5 + - - -
116A LEU* 5.4 2.5 - - - -
121A VAL* 3.9 34.3 - - + -
141A PHE* 4.3 6.1 - - + -
145A MET* 2.9 42.0 - - + -
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Residues in contact with THR 110 (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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106A ARG* 2.9 13.3 + - - -
107A HIS* 2.6 30.3 + - + +
109A MET* 1.3 77.0 - - - +
111A ASN* 1.3 62.3 + - - +
113A GLY* 4.0 6.7 + - - -
118A ASP* 5.8 3.6 - - - +
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Residues in contact with ASN 111 (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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88A ALA* 6.0 2.5 - - + -
92A PHE* 5.6 4.5 - - - -
107A HIS* 3.2 31.9 + - - +
108A VAL* 3.1 11.7 + - + +
110A THR* 1.3 80.4 - - - +
112A LEU* 1.3 71.2 + - + +
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Residues in contact with LEU 112 (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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81A SER* 6.0 0.4 - - - +
84A GLU* 4.3 10.1 - - + +
85A ILE* 4.0 42.4 - - + -
88A ALA* 4.3 9.4 - - + -
108A VAL* 3.2 19.5 + - + +
109A MET* 3.3 38.4 - - + +
111A ASN* 1.3 82.7 - - + +
113A GLY* 1.3 68.3 + - - +
114A GLU* 3.6 16.0 - - + +
145A MET* 6.3 0.4 - - + -
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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