Contacts of the helix formed by residues 114 - 131 (chain E) in PDB entry 1GUL
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 PRO 114 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112E LEU 3.3 8.1 - - - +
113E LYS* 1.3 93.0 - - + -
115E ASP* 1.3 63.7 + - - +
116E ASP 3.3 0.2 - - - -
117E GLN* 3.3 32.4 + - + +
118E GLN* 3.9 5.2 + - - +
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Residues in contact with ASP 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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113E LYS* 2.6 9.8 + - + +
114E PRO* 1.3 79.1 - - - +
116E ASP* 1.3 74.6 + - - +
117E GLN 3.2 1.0 + - - -
118E GLN* 3.5 11.3 + - - +
119E LYS* 4.0 6.4 + - - +
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Residues in contact with ASP 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 LEU* 4.1 9.2 - - + -
113E LYS* 2.3 58.9 + - - +
115E ASP* 1.3 82.2 - - - +
117E GLN* 1.3 64.1 + - - -
118E GLN 3.1 2.5 - - - -
119E LYS* 3.4 8.6 + - + +
120E GLU* 2.8 31.4 + - + +
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Residues in contact with GLN 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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109E HIS* 2.8 59.7 + - + +
110E PRO* 3.6 20.2 + - - +
112E LEU* 3.3 25.9 + - + -
114E PRO* 3.4 30.4 - - + +
115E ASP 3.1 0.8 - - - -
116E ASP* 1.3 79.2 - - - +
118E GLN* 1.3 65.4 + - - +
120E GLU* 3.1 8.3 - - - +
121E VAL* 3.2 5.9 + - - +
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Residues in contact with GLN 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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109E HIS* 5.7 0.5 - - - -
114E PRO 3.9 3.7 + - - +
115E ASP 3.5 9.0 + - - +
116E ASP 3.1 0.8 - - - -
117E GLN* 1.3 79.5 - - - +
119E LYS* 1.3 66.8 + - - +
120E GLU 3.0 2.1 + - - -
121E VAL* 3.1 36.0 + - - +
122E VAL* 3.3 17.7 + - + +
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Residues in contact with LYS 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 ASP 4.0 4.0 + - - +
116E ASP* 3.4 14.7 + - + +
118E GLN* 1.3 77.8 - - - +
120E GLU* 1.3 67.3 + - + +
122E VAL* 3.1 17.9 + - + +
123E ASN* 2.8 67.4 + - - +
126E GLN* 4.3 7.2 + - - -
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Residues in contact with GLU 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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105E LEU* 5.0 11.4 - - - +
108E MET* 5.4 6.5 - - - +
109E HIS* 3.9 8.5 - - + -
112E LEU* 3.4 25.1 - - + +
116E ASP* 2.8 22.4 - - + +
117E GLN 3.1 6.7 - - - +
119E LYS* 1.3 87.8 - - + +
121E VAL* 1.3 61.7 + - - +
123E ASN* 3.1 17.6 + - - +
124E MET* 2.9 35.0 + - + +
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Residues in contact with VAL 121 (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 HIS* 3.7 17.9 - - + +
117E GLN 3.2 14.3 + - - +
118E GLN* 3.1 30.0 + - - +
120E GLU* 1.3 75.2 - - - +
122E VAL* 1.3 69.4 + - + +
124E MET* 3.1 10.6 + - + +
125E ALA* 2.9 21.9 + - + +
170E LYS* 4.4 21.5 - - + +
171E ILE* 3.8 26.1 - - + +
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Residues in contact with VAL 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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118E GLN* 3.3 16.8 + - + +
119E LYS* 3.1 18.1 + - + +
121E VAL* 1.3 83.0 - - + +
123E ASN* 1.3 64.6 + - - +
125E ALA* 3.0 9.6 + - + +
126E GLN* 2.9 41.0 + - + +
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Residues in contact with ASN 123 (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 LEU* 4.1 14.3 - - - +
119E LYS* 2.8 32.5 + - - +
120E GLU* 3.5 21.1 + - - +
121E VAL 3.1 0.4 - - - -
122E VAL* 1.3 77.8 - - - +
124E MET* 1.3 63.5 + - - +
126E GLN* 3.0 11.7 + - - +
127E LYS* 2.8 54.3 + - - +
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Residues in contact with MET 124 (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 LEU* 4.4 3.0 - - + +
105E LEU* 3.8 43.9 - - + +
106E LEU* 3.8 29.8 - - + -
109E HIS* 3.6 34.1 - - + +
120E GLU* 2.9 19.3 + - + +
121E VAL* 3.5 14.1 - - - +
123E ASN* 1.3 72.8 - - - +
125E ALA* 1.3 65.4 + - - +
127E LYS* 3.7 1.5 - - - +
128E ALA* 2.8 27.4 + - - +
167E LEU* 3.9 21.5 - - + -
170E LYS* 4.5 11.9 - - + -
171E ILE* 4.5 3.1 - - + -
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Residues in contact with ALA 125 (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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121E VAL* 2.9 10.1 + - + +
122E VAL* 3.2 12.8 - - + +
124E MET* 1.3 82.3 - - - +
126E GLN* 1.3 65.2 + - + +
128E ALA* 3.2 0.3 + - - +
129E ILE* 2.9 33.8 + - + +
171E ILE* 3.7 24.4 - - + +
174E ILE* 4.1 9.6 - - + -
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Residues in contact with GLN 126 (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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119E LYS* 4.3 11.8 + - - -
122E VAL* 2.9 36.4 + - + +
123E ASN* 3.0 12.9 + - - +
125E ALA* 1.3 80.2 - - + +
127E LYS* 1.3 59.9 + - - +
129E ILE* 4.5 4.3 - - - -
130E ILE* 2.8 54.4 + - + +
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Residues in contact with LYS 127 (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 LEU* 4.2 13.7 - - + -
105E LEU* 4.2 8.7 - - + -
123E ASN* 2.8 50.4 + - - +
124E MET* 3.7 3.6 - - - +
126E GLN* 1.3 77.5 - - - +
128E ALA* 1.3 60.0 + - - +
130E ILE* 4.8 4.0 - - - +
131E ARG* 2.6 69.0 + - - +
132E TYR* 3.2 14.4 + - + -
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Residues in contact with ALA 128 (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 LEU* 4.2 14.3 - - + +
124E MET 2.8 17.8 + - - +
125E ALA 3.5 3.6 - - - +
127E LYS* 1.3 80.8 - - - +
129E ILE* 1.3 61.4 + - - +
132E TYR* 3.3 1.9 + - - -
133E PHE* 2.8 51.4 + - + +
167E LEU* 4.3 9.2 - - + -
174E ILE* 3.9 19.7 - - + -
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Residues in contact with ILE 129 (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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125E ALA* 2.9 25.2 + - + +
126E GLN* 3.7 5.4 - - - +
128E ALA* 1.3 82.5 - - + +
130E ILE* 1.3 67.6 + - + +
133E PHE* 4.4 1.1 - - + -
134E PRO* 2.9 22.3 - - - +
174E ILE* 3.8 36.3 - - + +
177E ALA* 6.2 1.1 - - + -
178E PHE* 3.7 23.0 - - + -
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Residues in contact with ILE 130 (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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126E GLN* 2.8 38.3 + - + +
127E LYS* 4.8 4.5 - - - +
129E ILE* 1.3 91.6 - - + +
131E ARG* 1.3 75.3 + - + +
132E TYR 3.7 0.2 - - - -
134E PRO* 3.7 11.8 - - - +
53F GLN* 5.4 5.1 - - + +
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Residues in contact with ARG 131 (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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127E LYS* 2.6 49.8 + - + +
130E ILE* 1.3 86.0 - - + +
132E TYR* 1.3 85.4 + - + +
134E PRO* 4.5 0.8 - - - +
135E VAL* 3.6 18.5 - - - +
45F GLN* 4.7 2.8 - - - +
52F PHE* 3.3 29.4 + - - +
53F GLN* 3.7 27.5 - - - +
54F GLN* 4.2 13.0 - - - +
301F IBG 2.9 36.4 + - - -
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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