Contacts of the helix formed by residues 105 - 119 (chain E) in PDB entry 1GN2
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 SER 105 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99E ILE* 4.7 0.2 - - - -
100E ALA* 3.6 15.5 + - - +
103E PHE 2.9 4.4 + - - +
104E GLY* 1.3 81.0 - - - +
106E PHE* 1.3 64.1 + - - +
107E ASP* 3.2 8.4 + - - +
108E LYS* 2.8 38.3 + - - +
109E PHE* 3.0 13.3 + - - +
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Residues in contact with PHE 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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89E ASP 4.4 7.2 - - - -
90E LYS* 3.9 36.8 - - + -
91E PRO* 3.1 40.8 - - + -
96E ALA 6.1 0.2 - - - +
99E ILE* 4.1 17.9 - - + +
100E ALA* 4.5 5.0 - - + +
105E SER* 1.3 72.3 - - - +
107E ASP* 1.3 66.1 + - - +
109E PHE* 3.6 14.3 - + - +
110E ARG* 3.1 58.7 + - - +
182E TRP* 4.6 2.9 - + - -
187E TRP* 3.5 24.9 - + - -
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Residues in contact with ASP 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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90E LYS* 4.4 12.7 + - - -
105E SER* 3.0 7.6 + - - +
106E PHE* 1.3 87.2 - - - +
108E LYS* 1.3 58.7 + - + +
110E ARG* 3.5 27.6 + - - +
111E ALA* 3.1 24.8 + - - +
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Residues in contact with LYS 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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103E PHE 3.3 22.0 - - - +
104E GLY* 4.8 4.9 - - - -
105E SER* 2.8 23.7 + - - +
107E ASP* 1.3 75.4 - - + +
109E PHE* 1.3 64.9 + - - +
111E ALA* 3.2 8.5 + - + +
112E GLN* 3.2 21.3 + - - +
51G ARG* 3.8 39.5 + - + +
52G ALA* 4.0 17.8 + - - +
54G GLU* 5.2 9.2 - - + -
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Residues in contact with PHE 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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99E ILE* 4.0 13.9 - - + -
103E PHE* 3.6 46.6 - + + +
105E SER 3.0 8.6 + - - +
106E PHE* 3.6 28.0 - + - +
108E LYS* 1.3 76.4 - - - +
110E ARG* 1.3 73.8 + - + +
112E GLN* 3.1 5.2 + - - +
113E PHE* 2.9 46.2 + + - +
128E LEU* 3.8 29.6 - - + -
139E ILE* 3.8 12.2 - - + +
157E LEU* 4.4 12.1 - - + -
182E TRP* 3.6 29.2 - + - -
187E TRP* 4.3 5.8 - + - -
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Residues in contact with ARG 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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90E LYS* 5.4 7.5 - - - +
106E PHE* 3.1 39.6 + - - +
107E ASP* 3.7 22.3 + - - +
109E PHE* 1.3 95.4 - - + +
111E ALA* 1.3 58.8 + - - +
113E PHE* 4.0 1.4 - - - +
114E HIS* 3.3 22.4 + - + +
179E LYS 5.3 0.4 + - - -
182E TRP* 3.3 65.8 - - + +
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Residues in contact with ALA 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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107E ASP 3.1 13.8 + - - +
108E LYS* 3.6 11.4 - - + +
109E PHE 3.1 0.6 - - - -
110E ARG* 1.3 75.7 - - - +
112E GLN* 1.3 66.0 + - - +
114E HIS* 3.5 6.5 + - - +
115E ALA* 3.1 22.3 + - - +
56G HIS* 3.9 12.7 - - + +
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Residues in contact with GLN 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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103E PHE* 3.8 5.3 - - - -
108E LYS 3.2 7.2 + - - +
109E PHE 3.1 7.5 + - - +
111E ALA* 1.3 79.5 - - - +
113E PHE* 1.3 65.8 + - - +
115E ALA* 2.9 5.5 + - - +
116E ALA* 2.9 20.8 + - - +
139E ILE* 3.5 25.6 + - + +
47G LEU* 3.9 20.4 - - - +
51G ARG* 2.9 37.7 + - + +
56G HIS* 3.4 21.3 + - + +
59G ILE* 3.8 16.3 - - + +
63G GLU* 3.2 22.2 + - - +
66G LEU* 6.1 0.2 - - - +
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Residues in contact with PHE 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 PHE* 2.9 33.1 + + + +
110E ARG* 4.1 4.3 - - - +
112E GLN* 1.3 77.4 - - - +
114E HIS* 1.3 63.6 + - - +
116E ALA* 3.4 7.1 + - - +
117E ALA* 3.0 20.4 + - - +
126E ALA* 3.6 25.2 - - + +
127E ALA 4.0 3.8 - - - -
128E LEU* 3.9 26.9 - - + -
139E ILE* 3.9 19.9 - - + +
157E LEU* 4.2 22.4 - - + -
159E LEU* 3.8 33.9 - - + -
181E PHE* 4.2 8.5 - + - -
182E TRP* 3.7 23.8 - + + -
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Residues in contact with HIS 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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110E ARG 3.3 17.0 + - - +
111E ALA* 3.7 7.4 + - - +
112E GLN 3.1 0.4 - - - -
113E PHE* 1.3 81.7 - - - +
115E ALA* 1.3 58.9 + - - +
117E ALA* 3.4 2.9 + - - +
118E THR* 2.7 51.3 + - + +
159E LEU* 6.1 1.1 - - - -
175E VAL* 3.8 27.2 + - + +
178E ALA* 3.7 31.0 - - + -
179E LYS* 4.0 29.9 + - + -
182E TRP* 5.0 8.7 - - - +
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Residues in contact with ALA 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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111E ALA 3.1 13.6 + - - +
112E GLN 2.9 10.5 + - - +
114E HIS* 1.3 80.2 + - - +
116E ALA* 1.3 61.5 - - - +
118E THR* 3.4 5.2 + - - -
119E THR* 3.1 33.1 + - + +
56G HIS* 3.8 29.2 - - + +
59G ILE* 4.1 12.1 - - + -
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Residues in contact with ALA 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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112E GLN 2.9 11.3 + - - +
113E PHE 3.6 7.6 - - - +
115E ALA* 1.3 77.4 - - - +
117E ALA* 1.3 60.3 + - - +
120E VAL* 3.6 3.1 - - - +
126E ALA* 4.3 8.1 - - + +
139E ILE* 4.1 22.4 - - + -
140E PHE 4.8 0.7 - - - +
141E GLN* 3.0 46.5 + - + +
59G ILE* 4.0 9.3 - - + +
63G GLU* 4.3 9.6 - - - +
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Residues in contact with ALA 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 PHE 3.0 13.3 + - - +
114E HIS* 3.4 4.2 + - - +
116E ALA* 1.3 78.1 - - - +
118E THR* 1.3 64.5 + - + +
119E THR 3.6 0.7 + - - -
120E VAL* 3.7 10.5 + - - +
126E ALA* 3.4 24.2 - - + +
159E LEU* 4.1 13.5 - - + -
161E MET* 3.2 45.0 - - + +
174E LYS* 4.9 1.4 - - - -
178E ALA* 5.1 1.1 - - + -
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Residues in contact with THR 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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114E HIS* 2.7 37.8 + - - +
115E ALA* 3.4 7.8 + - - -
117E ALA* 1.3 78.2 - - - +
119E THR* 1.3 60.8 + - - +
120E VAL 3.6 0.9 - - - -
161E MET* 4.8 1.3 - - + -
174E LYS* 3.0 32.6 + - + +
175E VAL* 4.1 26.8 - - + +
178E ALA* 3.8 28.3 - - + -
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Residues in contact with THR 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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115E ALA* 3.1 19.2 + - + +
117E ALA 3.4 0.6 - - - -
118E THR* 1.3 83.7 - - - +
120E VAL* 1.3 67.8 + - - +
121E GLN* 3.3 6.6 + - - +
141E GLN* 2.7 25.6 + - - -
174E LYS* 5.1 0.4 - - - +
56G HIS 5.7 0.2 - - - +
59G ILE* 3.6 22.5 - - + +
60G LEU* 3.6 19.0 + - - +
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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