Contacts of the helix formed by residues 100 - 110 (chain E) in PDB entry 2GER
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 THR 100 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98E GLY 3.1 9.1 + - - -
99E VAL* 1.3 85.5 - - - +
101E ILE* 1.3 70.6 + - + +
102E SER* 3.3 16.4 + - - +
103E SER* 3.1 31.9 + - - +
104E ILE* 3.5 6.6 + - - +
119E ARG* 3.5 12.1 + - - +
164E GLU* 3.2 13.9 - - - +
269E GLN* 4.1 16.1 + - - -
273E ASP* 4.7 3.1 + - - -
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Residues in contact with ILE 101 (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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99E VAL 3.4 1.9 + - - -
100E THR* 1.3 71.5 - - + +
102E SER* 1.3 81.9 + - - +
104E ILE* 3.2 11.5 + - - +
105E GLU* 2.9 34.0 + - + +
117E VAL* 3.5 26.4 - - + +
119E ARG* 4.0 11.9 - - + +
136E ALA* 3.9 9.6 - - + +
137E THR 3.8 5.8 - - - +
138E GLY* 2.9 42.2 - - - +
139E THR* 4.2 2.9 - - - +
164E GLU* 3.0 36.6 + - - +
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Residues in contact with SER 102 (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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100E THR* 3.1 8.7 - - - +
101E ILE* 1.3 89.3 - - - +
103E SER* 1.3 68.4 + - - +
104E ILE 2.6 3.6 + - - -
105E GLU* 2.8 23.1 + - - +
106E LYS* 3.0 23.6 + - - +
139E THR* 5.3 1.7 + - - -
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Residues in contact with SER 103 (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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79E LEU* 4.7 1.1 - - - +
98E GLY 5.3 0.5 + - - -
99E VAL* 4.9 4.0 - - - -
100E THR* 3.1 35.3 + - - -
102E SER* 1.3 77.9 - - - +
104E ILE* 1.3 62.8 + - - +
106E LYS* 4.0 7.4 - - - +
107E LYS* 3.7 21.5 + - - +
273E ASP* 3.6 19.6 + - - -
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Residues in contact with ILE 104 (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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68E LEU* 4.4 6.7 - - + -
75E ILE* 3.3 28.0 - - + -
79E LEU* 3.4 27.8 - - + -
92E VAL* 5.7 1.6 - - + -
94E SER* 4.3 13.5 - - - +
99E VAL* 3.4 21.3 - - + -
100E THR 3.5 3.3 + - - +
101E ILE* 3.2 12.0 + - - +
102E SER 2.6 1.6 + - - -
103E SER* 1.3 80.2 - - - +
105E GLU* 1.3 65.3 + - - +
106E LYS 3.1 2.5 + - - -
107E LYS* 3.6 1.7 + - - +
108E LEU* 3.3 32.1 + - + +
117E VAL* 3.8 28.7 - - + -
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Residues in contact with GLU 105 (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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101E ILE* 2.9 28.7 + - + +
102E SER* 2.8 18.9 + - - +
104E ILE* 1.3 74.1 - - - +
106E LYS* 1.3 56.6 + - + +
108E LEU* 4.1 4.8 - - - +
109E SER* 2.5 42.2 + - - +
115E PRO* 4.1 16.4 - - + +
117E VAL* 4.4 17.5 + - + +
138E GLY* 4.1 3.1 - - - -
139E THR* 2.9 50.8 + - - +
140E HIS* 3.8 11.8 + - + +
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Residues in contact with LYS 106 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102E SER* 3.0 23.4 + - - +
103E SER* 4.0 6.7 - - - +
105E GLU* 1.3 73.8 - - + +
107E LYS* 1.3 57.6 + - + +
108E LEU 2.7 15.3 + - - -
109E SER* 2.9 16.0 + - - -
110E ALA* 3.2 11.5 + - - +
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Residues in contact with LYS 107 (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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76E PRO* 3.0 32.2 + - - +
77E PHE* 4.3 0.8 - - - +
79E LEU* 3.4 38.9 - - + +
80E ASP* 2.4 43.9 + - - +
103E SER 3.7 9.4 + - - +
104E ILE 3.6 1.9 + - - +
106E LYS* 1.3 79.3 - - + +
108E LEU* 1.3 58.5 + - - +
110E ALA* 3.6 6.0 - - - +
111E PHE* 3.1 26.0 - - - -
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Residues in contact with LEU 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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79E LEU* 4.0 29.8 - - + +
82E ILE* 6.0 0.7 - - + -
83E GLY* 3.8 13.0 - - - +
86E ILE* 3.2 34.9 - - + +
92E VAL* 4.7 13.0 - - + -
104E ILE* 3.3 30.2 + - + +
105E GLU* 4.1 2.0 - - - +
106E LYS 2.7 5.1 + - - -
107E LYS* 1.3 76.8 - - - +
109E SER* 1.3 56.1 + - - +
110E ALA 2.9 6.3 - - - -
111E PHE* 3.0 26.7 + - - +
112E ARG* 3.4 7.8 + - - +
115E PRO* 4.1 20.0 - - + +
117E VAL* 4.6 10.1 - - + -
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Residues in contact with SER 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* 2.5 27.7 + - - +
106E LYS* 2.9 6.9 + - - -
108E LEU* 1.3 71.9 - - - +
110E ALA* 1.3 56.1 + - - +
111E PHE 2.9 20.0 + - - +
112E ARG 3.6 10.6 - - - +
113E PRO* 3.7 16.6 + - - +
115E PRO* 3.8 9.2 - - - +
140E HIS* 4.1 9.9 + - - -
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Residues in contact with ALA 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 LYS 3.2 9.2 + - - +
107E LYS* 3.6 19.1 - - - +
108E LEU 2.9 0.2 - - - -
109E SER* 1.3 76.1 - - - +
111E PHE* 1.3 68.8 + - + +
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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