Contacts of the helix formed by residues 130 - 142 (chain E) in PDB entry 5GAD
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 LYS 130 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320A A 3.3 21.4 + - - +
321A U 3.1 42.5 + - - +
126E VAL* 5.3 0.5 - - - +
128E ALA* 2.5 19.4 + - + +
129E PRO* 1.3 79.5 - - - +
131E THR* 1.3 64.2 + - - +
132E LYS* 4.4 9.9 - - + +
133E LEU* 3.6 28.8 + - + +
134E LEU 3.6 9.2 + - - -
160E ALA* 3.2 17.2 - - - +
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Residues in contact with THR 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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320A A 3.2 71.5 + - + +
321A U 2.8 17.1 + - - -
322A A 4.2 2.8 + - - -
130E LYS* 1.3 69.7 - - - +
132E LYS* 1.3 68.3 + - - +
133E LEU 3.1 0.7 + - - -
134E LEU* 3.1 4.2 + - - +
135E ALA* 3.0 20.9 + - + +
160E ALA* 3.3 22.7 + - - +
163E ASN* 4.4 1.6 - - + +
164E LEU* 3.9 15.5 - - + -
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Residues in contact with LYS 132 (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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319A G 2.7 38.2 + - - -
320A A 3.5 33.7 + - - +
321A U 4.7 0.2 + - - -
130E LYS* 4.4 8.0 - - + +
131E THR* 1.3 81.1 - - - +
133E LEU* 1.3 72.3 + - + +
135E ALA* 3.5 7.6 + - - +
136E GLN* 3.0 28.1 + - + +
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Residues in contact with LEU 133 (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 VAL* 4.3 11.8 - - + +
127E GLU* 4.9 10.3 - - + +
128E ALA* 3.7 33.7 - - + +
130E LYS* 3.6 25.3 + - + +
131E THR 3.1 0.4 - - - -
132E LYS* 1.3 89.8 - - + +
134E LEU* 1.3 60.8 + - - +
136E GLN* 3.1 9.6 + - + +
137E LYS* 2.9 27.9 + - - +
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Residues in contact with LEU 134 (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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124E PHE* 4.0 20.6 - - + -
126E VAL* 3.9 14.9 - - + +
130E LYS 3.6 1.6 + - - -
131E THR 3.1 7.0 + - - +
133E LEU* 1.3 75.2 - - - +
135E ALA* 1.3 67.3 + - - +
137E LYS* 3.3 4.4 + - + +
138E LEU* 2.9 29.7 + - + +
148E ILE* 5.5 2.2 - - + -
157E LEU* 3.9 24.7 - - + -
160E ALA* 3.8 17.3 - - + -
161E ALA* 3.6 42.4 - - + +
164E LEU* 3.7 16.8 - - + -
167E VAL* 4.7 5.2 - - + -
169E VAL* 5.8 0.2 - - + -
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Residues in contact with ALA 135 (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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320A A 4.8 14.1 - - - +
131E THR 3.0 16.6 + - - +
132E LYS* 3.6 8.1 - - - +
134E LEU* 1.3 77.2 - - - +
136E GLN* 1.3 58.6 + - - +
138E LEU* 3.3 7.1 + - - +
139E LYS* 2.9 29.6 + - - +
164E LEU* 4.5 17.0 - - + +
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Residues in contact with GLN 136 (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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132E LYS* 3.0 16.5 + - + +
133E LEU* 3.1 14.1 + - + +
135E ALA* 1.3 74.2 - - - +
137E LYS* 1.3 65.7 + - - +
138E LEU 3.1 0.2 + - - -
139E LYS* 3.2 24.6 + - - +
140E ASP* 3.0 44.9 + - - +
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Residues in contact with LYS 137 (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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123E LYS 4.7 6.5 + - - -
124E PHE* 3.8 40.1 - - + -
125E SER 3.1 34.2 - - - +
126E VAL* 4.6 7.2 - - + -
133E LEU 2.9 12.4 + - - +
134E LEU* 3.7 10.8 - - + +
136E GLN* 1.3 75.4 - - - +
138E LEU* 1.3 60.8 + - + +
140E ASP* 3.7 8.9 + - - +
141E MET* 3.3 54.3 + - + +
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Residues in contact with LEU 138 (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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124E PHE* 3.7 30.5 - - + -
134E LEU* 2.9 26.4 + - + +
135E ALA* 3.5 6.7 - - - +
137E LYS* 1.3 75.6 - - - +
139E LYS* 1.3 65.7 + - - +
140E ASP 3.0 1.8 - - - -
141E MET* 3.0 12.6 + - + -
142E ALA 3.1 10.2 + - - -
143E LEU* 3.3 43.2 + - + +
144E GLU 4.7 3.1 - - - +
146E VAL* 3.5 29.2 - - + -
148E ILE* 5.0 0.4 - - + -
164E LEU* 5.1 2.5 - - + -
167E VAL* 3.9 21.8 - - + -
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Residues in contact with LYS 139 (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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135E ALA 2.9 17.9 + - - +
136E GLN* 3.2 24.4 + - - +
138E LEU* 1.3 76.4 - - - +
140E ASP* 1.3 61.7 + - - +
141E MET 3.6 0.2 + - - -
142E ALA* 3.7 8.8 + - - +
143E LEU 4.4 3.3 + - - -
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Residues in contact with ASP 140 (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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136E GLN* 3.0 38.9 + - - +
137E LYS* 3.7 9.2 - - - +
138E LEU 3.0 0.2 - - - -
139E LYS* 1.3 81.1 - - - +
141E MET* 1.3 62.8 + - + +
142E ALA* 3.3 2.1 + - - +
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Residues in contact with MET 141 (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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6E LYS* 3.2 40.0 + - - +
7E ASP* 4.8 12.8 - - + +
121E VAL* 4.9 14.1 - - + -
123E LYS 6.1 0.2 - - - +
124E PHE* 4.4 18.4 - - + -
137E LYS* 3.3 45.5 + - - +
138E LEU 3.0 3.7 + - - +
140E ASP* 1.3 80.2 - - + +
142E ALA* 1.3 69.9 + - - +
143E LEU* 3.2 24.9 + - + +
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Residues in contact with ALA 142 (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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6E LYS* 5.5 0.4 - - - +
138E LEU 3.1 3.7 + - - -
139E LYS* 3.7 7.2 + - - +
140E ASP 3.3 5.5 - - - +
141E MET* 1.3 80.2 - - - +
143E LEU* 1.3 63.8 + - - +
144E GLU* 4.2 1.4 + - - +
185E LYS* 5.9 1.0 - - - +
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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