Contacts of the helix formed by residues 105 - 115 (chain E) in PDB entry 3GHG
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 105 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101E ASN* 3.2 45.4 + - - +
104E VAL* 1.3 80.3 - - + +
106E ALA* 1.3 58.1 + - - +
107E VAL 3.3 1.8 - - - -
108E SER* 3.7 6.3 - - - -
109E GLN* 3.3 35.1 + - - +
43F LEU* 5.9 4.1 - - + +
46F ILE* 6.4 1.8 - - + -
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Residues in contact with ALA 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E ASN 3.9 18.9 + - - +
103E ASN* 5.6 0.2 - - - -
105E GLU* 1.3 77.0 - - - +
107E VAL* 1.3 61.4 + - + +
109E GLN* 4.2 14.3 - - - +
110E THR* 3.1 25.5 + - - +
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Residues in contact with VAL 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D LEU* 5.2 2.0 - - + -
76D TYR* 3.6 31.6 - - + -
77D GLN* 4.8 17.7 - - + +
80D ASN* 5.6 6.3 - - - +
103E ASN* 3.5 24.9 - - - +
104E VAL* 4.0 4.5 - - - -
106E ALA* 1.3 79.7 - - + +
108E SER* 1.3 55.7 + - - +
110E THR* 3.1 15.9 - - + +
111E SER* 2.6 30.8 + - - -
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Residues in contact with SER 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E VAL* 2.5 33.1 + - - +
105E GLU* 3.5 10.0 + - - -
107E VAL* 1.3 76.0 - - - +
109E GLN* 1.3 59.3 + - - +
110E THR 3.4 0.2 - - - -
111E SER* 3.5 7.7 - - - -
112E SER* 2.9 33.6 + - - -
46F ILE* 4.3 16.4 - - - +
50F VAL* 5.7 2.4 - - - +
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Residues in contact with GLN 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E GLU* 3.3 18.9 + - - +
106E ALA* 4.2 11.3 - - - +
107E VAL 3.4 0.2 - - - -
108E SER* 1.3 77.6 - - - +
110E THR* 1.3 52.3 + - + +
112E SER* 4.6 1.7 - - - -
113E SER* 2.5 41.3 + - - -
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Residues in contact with THR 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E ALA 3.1 17.6 + - - +
107E VAL* 3.0 31.4 + - + +
109E GLN* 1.3 75.0 - - + +
111E SER* 1.3 55.3 + - - +
113E SER* 3.4 7.6 - - - +
114E SER* 2.6 44.4 + - - -
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Residues in contact with SER 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D TYR* 3.8 11.4 - - - -
107E VAL 2.6 24.5 + - - -
108E SER* 3.5 12.5 + - - -
110E THR* 1.3 73.9 + - - +
112E SER* 1.3 58.9 + - - +
114E SER* 2.9 1.3 + - - -
115E PHE* 2.6 65.7 + - - -
50F VAL* 4.5 15.9 - - - +
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Residues in contact with SER 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E SER* 2.9 16.4 + - - -
109E GLN* 4.6 2.0 - - - -
111E SER* 1.3 82.1 + - - +
113E SER* 1.3 56.8 + - - +
115E PHE* 4.1 6.8 - - - +
116E GLN* 2.9 31.0 + - - +
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Residues in contact with SER 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E GLN 2.5 25.8 + - - -
110E THR* 3.4 8.8 - - - +
112E SER* 1.3 76.5 - - - +
114E SER* 1.3 59.4 + - - +
116E GLN* 4.0 13.6 + - - -
117E TYR* 3.1 47.3 + - - -
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Residues in contact with SER 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D SER* 5.7 0.3 + - - -
84D HIS* 5.7 4.5 - - - -
87D THR* 5.4 4.2 + - - +
110E THR* 2.6 27.8 + - - -
111E SER* 3.8 1.8 - - - -
113E SER* 1.3 71.9 - - - +
115E PHE* 1.3 64.6 + - - +
116E GLN 3.2 1.7 + - - -
117E TYR* 4.5 11.7 + - - +
118E MET* 5.3 6.4 + - - +
57F VAL* 5.0 3.6 - - - +
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Residues in contact with PHE 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D TYR* 3.2 25.4 - + - -
111E SER* 2.6 55.5 + - - +
112E SER* 4.0 5.4 - - - +
114E SER* 1.3 74.5 - - - +
116E GLN* 1.3 59.4 + - - +
117E TYR 3.7 0.2 - - - -
118E MET* 3.9 15.9 - - - +
119E TYR* 6.1 0.3 - - - -
50F VAL* 5.2 6.1 - - + -
53F LYS* 3.7 14.4 - - + +
54F THR* 3.6 42.6 - - - -
57F VAL* 3.3 34.7 - - + +
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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