Contacts of the helix formed by residues 106 - 120 (chain A) in PDB entry 4OG2
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 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A THR 4.0 1.0 - - - +
104A ALA* 4.9 3.4 - - - +
105A GLY* 1.3 80.6 + - - +
107A GLU* 1.3 64.4 + - - +
108A ALA* 4.0 9.1 - - - +
109A GLY* 2.9 25.6 + - - -
110A THR* 2.9 24.8 + - - -
134A GLN* 3.1 8.4 + - - -
144B ARG* 3.5 39.2 - - + +
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Residues in contact with GLU 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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106A ASP* 1.3 71.6 - - - +
108A ALA* 1.3 67.7 + - - +
110A THR* 3.0 8.2 + - - -
111A ILE* 2.9 28.4 + - - +
133A GLN* 2.9 38.6 + - - +
134A GLN* 4.7 4.7 - - - +
137A SER* 3.6 27.1 - - - +
138A ALA* 5.0 0.3 - - - +
140B PRO* 3.7 26.9 - - + +
141B ILE* 4.4 8.5 - - + +
144B ARG* 2.9 44.1 + - - +
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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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106A ASP* 3.5 10.8 + - - +
107A GLU* 1.3 78.9 + - - +
109A GLY* 1.3 58.2 + - - +
111A ILE* 3.4 5.7 + - - +
112A ASN* 2.9 39.4 + - - +
115B GLN* 3.9 16.1 + - - +
141B ILE* 3.8 23.7 - - + +
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Residues in contact with GLY 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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102A ASP 4.2 1.9 - - - +
103A THR* 3.2 23.4 - - - +
104A ALA* 5.1 2.5 - - - -
106A ASP* 2.9 14.6 + - - -
108A ALA* 1.3 76.8 - - - +
110A THR* 1.3 56.5 + - - +
112A ASN* 3.6 8.9 + - - +
113A ALA* 3.0 28.1 + - - +
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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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103A THR* 3.5 13.5 + - + -
106A ASP 2.9 15.8 + - - -
107A GLU* 3.0 8.4 + - - -
109A GLY* 1.3 76.3 - - - +
111A ILE* 1.3 59.2 + - - +
113A ALA* 3.2 0.9 + - - +
114A PHE* 2.9 40.3 + - + -
129A PRO* 3.6 27.4 - - + -
134A GLN* 3.1 26.5 + - + +
138A ALA* 3.4 22.2 - - + -
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Residues in contact with ILE 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 GLU 2.9 17.6 + - - +
108A ALA* 3.7 5.8 - - - +
110A THR* 1.3 74.7 - - - +
112A ASN* 1.3 62.0 + - - +
114A PHE* 3.7 3.3 - - - +
115A GLN* 2.9 55.3 + - - +
137A SER* 3.4 22.2 - - - +
138A ALA* 4.0 23.6 - - + -
141A ILE* 4.3 7.2 - - + -
111B ILE* 3.6 39.7 - - + -
115B GLN* 6.2 0.4 - - - +
141B ILE* 3.9 21.1 - - + -
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Residues in contact with ASN 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* 2.9 28.5 + - - +
109A GLY* 3.8 8.1 - - - +
111A ILE* 1.3 79.1 - - - +
113A ALA* 1.3 57.7 + - - +
115A GLN* 3.3 13.9 + - - +
116A THR* 2.9 36.4 + - - +
115B GLN* 5.4 8.2 + - - +
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Residues in contact with ALA 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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60A ALA* 4.4 4.3 - - + -
101A GLN* 3.7 24.6 - - + +
102A ASP 3.7 18.4 + - - +
103A THR* 4.0 11.7 - - + -
109A GLY 3.0 18.1 + - - +
110A THR 3.2 4.7 + - - +
112A ASN* 1.3 76.2 - - - +
114A PHE* 1.3 63.5 + - - +
116A THR* 3.4 4.4 + - - -
117A LEU* 2.9 30.3 + - - +
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Residues in contact with PHE 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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60A ALA* 3.6 28.9 - - + -
110A THR* 2.9 34.2 + - + +
111A ILE* 3.7 5.8 - - - +
113A ALA* 1.3 77.3 - - - +
115A GLN* 1.3 56.1 + - - +
117A LEU* 3.3 3.6 + - - +
118A ILE* 2.9 39.9 + - + +
126A ILE* 4.0 29.8 - - + -
128A GLY 4.4 1.6 - - - -
129A PRO* 4.1 18.4 - - + -
138A ALA* 3.6 25.1 - - + -
139A ASN* 3.3 29.6 - - - -
141A ILE* 4.7 6.1 - - + -
142A ALA* 4.3 8.5 - - + -
149A VAL* 4.2 11.4 - - + -
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Residues in contact with GLN 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 ILE* 2.9 40.7 + - - +
112A ASN* 3.9 13.1 - - - +
114A PHE* 1.3 75.5 - - - +
116A THR* 1.3 58.5 + - - +
118A ILE* 4.5 3.1 - - - -
119A ASN* 2.9 49.4 + - - +
141A ILE* 4.0 21.3 - - + +
108B ALA* 3.9 26.3 - - - +
111B ILE* 6.2 0.4 - - - +
112B ASN* 5.5 7.3 + - - +
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Residues in contact with THR 116 (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 GLN* 3.5 34.3 - - - +
112A ASN* 2.9 19.6 + - - +
113A ALA* 3.7 5.2 - - - -
115A GLN* 1.3 77.0 - - - +
117A LEU* 1.3 57.9 + - - +
119A ASN* 5.2 0.2 - - - -
120A LYS* 2.9 49.8 + - + +
121A ASP* 3.0 7.6 + - - +
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Residues in contact with LEU 117 (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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58A GLY* 3.8 21.8 - - - -
59A ILE 4.1 3.1 - - - +
60A ALA* 3.8 28.3 - - + -
99A ILE* 3.5 25.6 - - + +
101A GLN* 3.4 28.0 - - + -
113A ALA 2.9 21.8 + - - +
114A PHE* 3.7 4.5 - - - +
116A THR* 1.3 75.7 - - - +
118A ILE* 1.3 57.5 + - - +
121A ASP* 3.4 12.1 - - - +
122A LYS 3.0 24.1 + - - -
123A VAL* 3.1 24.8 + - + +
126A ILE* 4.3 11.4 - - + -
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Residues in contact with ILE 118 (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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114A PHE* 2.9 27.1 + - + +
115A GLN* 3.9 3.8 - - - +
117A LEU* 1.3 78.7 - - - +
119A ASN* 1.3 75.6 + - - +
122A LYS* 3.6 10.0 + - - +
123A VAL* 4.6 1.1 - - + -
126A ILE* 4.1 20.9 - - + -
141A ILE* 4.5 10.1 - - + -
142A ALA* 4.2 19.3 - - + -
145A ALA* 4.4 14.1 - - + -
147A VAL* 3.9 26.2 - - + -
364A ARG* 3.0 41.6 + - - +
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Residues in contact with ASN 119 (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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115A GLN* 2.9 40.3 + - - +
116A THR* 5.2 0.2 - - - -
118A ILE* 1.3 92.2 - - - +
120A LYS* 1.3 58.5 + - + +
122A LYS* 3.1 30.0 + - - +
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Residues in contact with LYS 120 (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 GLN* 4.0 8.3 - - - +
116A THR* 2.9 36.7 + - + +
119A ASN* 1.3 75.3 - - - +
121A ASP* 1.3 90.0 + - - +
122A LYS* 3.3 10.9 + - - +
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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