Contacts of the helix formed by residues 108 - 122 (chain E) in PDB entry 3Q2K
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 ARG 108 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A LYS* 5.7 7.5 - - - +
350A ASP 6.1 1.3 - - - -
106E ALA* 3.4 4.5 - - - +
107E THR* 1.3 93.7 + - - +
109E TRP* 1.3 67.2 + - - +
110E GLU* 3.2 7.2 - - + +
111E ASP* 3.1 33.6 + - - +
112E GLY 3.0 18.2 + - - -
178E TRP* 4.9 4.2 + - - +
179E GLU* 3.3 53.6 + - - +
329E LEU* 3.9 4.6 - - - +
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Residues in contact with TRP 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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108E ARG* 1.3 72.5 - - - +
110E GLU* 1.3 80.3 + - - +
112E GLY* 3.2 2.6 + - - -
113E LYS* 3.1 53.7 + - + +
326E LEU* 3.6 31.9 - - + -
329E LEU* 3.8 17.3 - - + -
330E ALA* 3.3 39.7 - - + -
333E THR* 3.8 26.8 + - + +
337E ARG* 4.1 10.8 - - - +
349E LEU* 3.9 27.9 - - + +
350E ASP 2.7 29.0 + - - -
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Residues in contact with GLU 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ASP* 5.8 3.3 - - - +
108E ARG* 3.2 6.0 - - + -
109E TRP* 1.3 96.1 + - - +
111E ASP* 1.3 65.4 + - - +
113E LYS* 3.3 19.2 + - - +
114E ARG* 3.0 38.4 + - - +
337E ARG* 3.8 13.7 + - - -
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Residues in contact with ASP 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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83E GLY 5.2 1.0 - - - +
86E PRO* 3.7 28.7 - - + +
87E TRP* 3.2 39.2 + - + -
106E ALA* 4.3 1.6 - - + -
107E THR* 5.2 1.6 + - - -
108E ARG* 3.1 39.6 + - + +
110E GLU* 1.3 82.2 - - - +
112E GLY* 1.3 61.8 + - - +
114E ARG* 3.5 10.6 + - - +
115E MET* 3.0 23.4 + - - +
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Residues in contact with GLY 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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105E MET* 4.8 1.1 - - - -
106E ALA* 3.7 9.4 - - - +
108E ARG 3.0 12.3 + - - -
109E TRP 3.2 3.8 + - - -
111E ASP* 1.3 76.1 - - - +
113E LYS* 1.3 61.3 + - - +
115E MET* 3.2 11.8 - - - +
116E VAL* 3.2 25.1 + - - +
326E LEU* 3.8 8.9 - - - +
329E LEU* 3.8 18.8 - - - -
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Residues in contact with LYS 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E TRP* 3.1 54.5 + - + +
110E GLU* 3.9 18.7 + - - +
112E GLY* 1.3 74.7 - - - +
114E ARG* 1.3 58.7 + - - +
116E VAL* 3.3 7.1 + - - +
117E LYS* 2.9 27.5 + - - +
326E LEU* 4.0 14.3 - - + +
350E ASP* 3.0 36.0 + - - +
108H ARG* 5.9 4.7 - - - +
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Residues in contact with ARG 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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117A LYS* 4.8 7.9 - - - +
87E TRP* 3.5 29.2 - - - -
90E ILE* 3.0 30.5 - - + -
110E GLU* 3.0 26.0 + - - +
111E ASP* 4.0 10.1 + - - +
113E LYS* 1.3 74.5 - - - +
115E MET* 1.3 64.4 + - - +
117E LYS* 3.0 34.1 + - - +
118E ALA* 2.9 22.4 + - + +
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Residues in contact with MET 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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85E HIS 4.2 0.9 - - - +
86E PRO* 3.5 33.4 - - + +
89E ALA* 3.8 26.0 - - + -
90E ILE* 4.0 12.2 - - + +
101E SER* 4.1 18.6 - - - +
105E MET* 3.3 53.6 - - + +
111E ASP 3.0 11.5 + - - +
112E GLY* 3.2 16.8 - - - +
114E ARG* 1.3 75.1 - - - +
116E VAL* 1.3 65.3 + - - +
118E ALA* 3.4 1.4 + - - +
119E CYS* 3.0 28.1 + - - -
126E LEU* 4.4 11.4 - - + -
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Residues in contact with VAL 116 (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 MET* 3.7 23.3 - - + -
112E GLY 3.2 15.6 + - - +
113E LYS 3.5 8.1 - - - +
115E MET* 1.3 75.5 - - - +
117E LYS* 1.3 64.2 + - - +
119E CYS* 3.4 2.6 + - - +
120E ASP* 3.1 22.8 + - - +
126E LEU* 4.0 14.1 - - + -
322E GLY* 4.1 7.9 - - - -
323E ARG* 3.6 40.2 - - + +
326E LEU* 4.0 19.7 - - + -
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Residues in contact with LYS 117 (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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113E LYS 2.9 15.4 + - - +
114E ARG* 3.3 41.5 - - - +
116E VAL* 1.3 75.8 - - - +
118E ALA* 1.3 57.7 + - - +
120E ASP* 2.8 33.6 + - - +
121E GLU* 3.0 34.5 + - + +
87H TRP* 6.3 4.5 - - + -
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Residues in contact with ALA 118 (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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90E ILE* 4.1 33.7 - - + +
93E ALA* 3.9 7.3 - - + +
94E GLN* 5.8 4.0 - - + +
114E ARG* 2.9 15.4 + - + +
115E MET 3.8 3.4 - - - +
117E LYS* 1.3 77.7 - - - +
119E CYS* 1.3 61.9 + - - +
120E ASP 3.0 4.7 - - - -
121E GLU* 3.6 11.7 + - - +
122E ALA* 3.2 25.1 + - - +
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Residues in contact with CYS 119 (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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89E ALA* 4.4 6.7 - - - -
93E ALA* 4.1 15.5 - - - -
99E VAL* 4.1 24.5 - - - -
115E MET 3.0 20.8 + - - +
116E VAL 4.0 4.3 - - - +
118E ALA* 1.3 77.0 - - - +
120E ASP* 1.3 61.7 + - - +
122E ALA* 4.0 0.9 - - - -
123E GLY* 3.2 1.9 + - - -
124E VAL* 3.1 43.5 + - - +
125E ARG 4.6 1.8 - - - -
126E LEU* 3.8 33.7 - - + -
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Residues in contact with ASP 120 (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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116E VAL* 3.1 17.3 + - - +
117E LYS* 2.8 19.3 + - + +
119E CYS* 1.3 77.3 - - - +
121E GLU* 1.3 62.1 + - + +
123E GLY* 3.2 13.2 + - - -
323E ARG* 3.0 41.0 + - - -
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Residues in contact with GLU 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E LYS* 3.0 45.3 + - + +
118E ALA* 4.3 7.6 - - - +
120E ASP* 1.3 75.7 - - + +
122E ALA* 1.3 59.5 + - - +
123E GLY* 3.1 1.1 + - - -
87H TRP* 6.1 1.0 - - - -
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Residues in contact with ALA 122 (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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93E ALA* 3.1 34.1 - - + +
94E GLN* 5.3 0.7 - - - -
96E GLY* 5.4 3.0 - - - -
118E ALA 3.2 19.3 + - - +
119E CYS 4.3 2.0 - - - +
121E GLU* 1.3 76.3 - - - +
123E GLY* 1.3 64.3 + - - +
124E VAL* 3.4 11.7 + - + +
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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