Contacts of the helix formed by residues 104 - 115 (chain A) in PDB entry 5DO9
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 GLU 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A TYR* 5.6 0.4 - - - -
102A LYS 4.1 2.3 + - - +
103A TYR* 1.3 70.7 - - - +
105A HIS* 1.3 64.0 + - - +
106A ASN 2.9 1.6 + - - -
107A LYS* 3.0 52.1 + - - +
108A ALA* 4.4 0.7 + - - +
293E PRO 5.2 6.5 - - - +
294E GLU* 4.0 26.8 - - - +
296E ASP* 3.2 37.6 - - + +
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Residues in contact with HIS 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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103A TYR* 3.5 31.4 - + + +
104A GLU* 1.3 76.7 - - - +
106A ASN* 1.3 73.3 + - - +
107A LYS 3.3 0.7 + - - -
108A ALA* 3.5 17.0 + - - +
109A HIS* 3.4 41.1 + + + -
134A SER* 2.9 18.9 + - - -
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Residues in contact with ASN 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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101A TYR* 3.8 18.2 - - + -
103A TYR* 3.1 15.2 + - - +
104A GLU 2.9 1.8 + - - -
105A HIS* 1.3 91.8 - - - +
107A LYS* 1.3 59.0 + - - +
109A HIS* 3.4 9.7 + - - +
110A ALA* 2.9 23.2 + - - +
134A SER* 2.6 40.0 + - - +
135A LEU* 3.5 17.8 + - + +
138A ASP* 2.8 32.7 + - - +
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Residues in contact with LYS 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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100A PRO* 6.3 1.1 - - - +
101A TYR* 4.2 34.8 - - + +
104A GLU* 3.0 47.4 + - - +
106A ASN* 1.3 74.5 - - - +
108A ALA* 1.3 60.7 + - - +
110A ALA* 3.1 8.4 + - - +
111A GLN* 2.9 27.7 + - - +
294E GLU* 5.4 6.9 + - - +
296E ASP* 5.4 5.4 - - - +
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Residues in contact with ALA 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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104A GLU 4.4 0.2 + - - -
105A HIS* 3.5 13.3 + - - +
107A LYS* 1.3 78.1 - - - +
109A HIS* 1.3 60.6 + - + +
111A GLN* 3.4 8.6 + - - +
112A LEU* 3.0 28.1 + - - +
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Residues in contact with HIS 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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105A HIS* 3.4 35.4 + + + -
106A ASN* 3.4 25.0 + - - +
107A LYS 3.2 0.4 - - - -
108A ALA* 1.3 80.6 - - + +
110A ALA* 1.3 57.8 + - - +
112A LEU* 3.4 9.0 + - + +
113A VAL* 2.9 33.3 + - - +
127A PRO* 5.6 1.1 - - + -
130A ASP* 4.7 2.3 - - + +
131A ALA* 3.7 29.3 + - + -
134A SER* 3.5 16.3 + - - -
135A LEU* 4.0 13.0 - - + -
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Residues in contact with ALA 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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91A ILE* 3.7 24.8 - - + +
101A TYR* 3.3 29.2 - - + +
106A ASN 2.9 13.6 + - - +
107A LYS* 3.1 9.8 + - - +
109A HIS* 1.3 74.3 - - - +
111A GLN* 1.3 56.0 + - - +
114A ARG* 2.7 42.3 + - - +
135A LEU* 4.1 4.0 - - + +
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Residues in contact with GLN 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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107A LYS 2.9 13.3 + - - +
108A ALA* 3.6 10.8 - - - +
110A ALA* 1.3 74.6 - - - +
112A LEU* 1.3 63.9 + - - +
114A ARG* 3.2 27.1 + - - +
115A GLU* 2.6 61.3 + - - +
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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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108A ALA 3.0 13.6 + - - +
109A HIS* 3.5 11.2 - - + +
111A GLN* 1.3 80.1 - - - +
113A VAL* 1.3 60.8 + - - +
115A GLU* 3.5 17.6 + - - +
116A VAL* 3.7 12.0 - - - +
127A PRO* 4.0 30.1 - - + -
128A TYR* 3.6 37.0 + - + +
131A ALA* 4.1 22.2 - - + -
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Residues in contact with VAL 113 (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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84A PHE* 4.5 8.1 - - + -
87A MET* 4.1 18.4 - - + -
88A GLN* 3.1 24.9 + - + -
91A ILE* 3.7 21.5 - - + -
109A HIS 2.9 22.2 + - - +
112A LEU* 1.3 74.1 - - + +
114A ARG* 1.3 63.5 + - - +
115A GLU 3.3 0.7 + - - -
116A VAL* 3.3 14.8 + - - +
128A TYR* 4.6 9.4 - - + -
131A ALA* 4.0 15.3 - - + -
132A ILE* 3.8 31.0 - - + -
135A LEU* 4.1 5.2 - - + -
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Residues in contact with ARG 114 (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 GLN* 3.3 21.2 + - + +
91A ILE* 3.6 28.7 - - + +
92A ARG* 3.9 29.7 - - - +
95A ASP* 3.4 27.2 + - - -
110A ALA* 2.7 20.8 + - - +
111A GLN* 3.2 47.1 + - - +
113A VAL* 1.3 75.2 - - - +
115A GLU* 1.3 57.8 + - + +
116A VAL 3.2 6.8 + - - +
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Residues in contact with GLU 115 (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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111A GLN* 2.6 52.3 + - - +
112A LEU* 3.8 11.8 - - - +
113A VAL 3.3 0.6 - - - -
114A ARG* 1.3 76.0 - - + +
116A VAL* 1.3 61.7 + - - +
117A ASP* 3.7 1.7 + - - +
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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