Contacts of the helix formed by residues 118 - 130 (chain E) in PDB entry 5IFM
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 118 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62E PHE* 3.0 45.2 + - + +
63E ARG* 3.9 24.0 - - + -
67E GLU* 3.4 11.9 - - - +
69E THR* 4.5 4.0 - - + -
74E SER* 3.3 14.5 - - - -
116E LEU 4.4 0.9 - - - -
117E GLU* 1.3 87.2 - - + +
119E ARG* 1.3 63.2 + - - +
121E LEU* 3.4 25.1 + - - +
122E ALA* 3.2 17.7 + - - +
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Residues in contact with ARG 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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64E LYS* 5.3 8.5 - - + -
67E GLU* 2.9 21.4 + - - +
73E ARG* 3.0 83.3 + - + +
74E SER* 3.8 7.4 - - - -
118E THR* 1.3 70.0 - - - +
120E THR* 1.3 58.6 + - - +
122E ALA* 3.4 3.2 + - - +
123E GLU* 2.9 54.0 + - - +
143E PHE* 3.5 36.9 - - - +
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Residues in contact with THR 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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59E LEU* 5.2 6.1 - - + -
61E ASN 5.8 0.2 - - - +
62E PHE* 3.2 36.2 + - + +
64E LYS* 5.2 9.0 - - - +
67E GLU* 5.1 1.9 + - - -
118E THR* 3.3 1.2 + - - -
119E ARG* 1.3 77.6 - - - +
121E LEU* 1.3 56.5 + - - +
123E GLU* 3.2 15.0 + - + +
124E ILE* 3.0 47.0 + - + +
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Residues in contact with LEU 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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59E LEU* 4.4 23.3 - - + -
62E PHE* 3.6 39.0 - - + -
97E TYR* 3.8 37.1 - - + +
98E GLY* 5.2 3.4 - - - -
116E LEU* 3.9 8.8 - - + +
117E GLU* 4.0 19.7 - - + +
118E THR* 3.4 19.0 + - - +
120E THR* 1.3 74.3 - - - +
122E ALA* 1.3 56.2 + - - +
124E ILE* 3.4 12.5 + - + +
125E ALA* 3.1 28.2 + - - +
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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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74E SER* 3.7 23.6 - - - +
76E LEU* 3.6 10.4 - - + +
116E LEU* 3.7 13.3 - - + +
118E THR 3.2 13.9 + - - +
119E ARG 3.5 6.3 - - - +
121E LEU* 1.3 73.1 - - - +
123E GLU* 1.4 54.2 + - - +
125E ALA 3.4 0.5 + - - -
126E LYS* 2.9 35.3 + - - +
143E PHE* 3.5 26.0 - - + -
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Residues in contact with GLU 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119E ARG* 2.9 44.7 + - - +
120E THR* 3.2 18.3 + - + +
122E ALA* 1.4 72.4 - - - +
124E ILE* 1.3 62.9 + - + +
126E LYS* 3.6 3.9 + - + +
127E VAL* 3.2 32.4 + - + +
143E PHE* 3.6 21.7 - - + -
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Residues in contact with ILE 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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59E LEU* 4.4 23.8 - - + -
97E TYR* 3.9 20.9 - - + -
120E THR* 3.0 35.8 + - + +
121E LEU* 3.7 14.1 - - + +
122E ALA 3.3 0.2 - - - -
123E GLU* 1.3 73.7 - - + +
125E ALA* 1.3 63.6 + - - +
127E VAL* 3.4 5.4 + - - +
128E GLU* 3.0 36.4 + - + +
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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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76E LEU* 4.0 7.2 - - + -
94E PHE* 4.1 7.6 - - + -
97E TYR* 3.7 34.7 - - + -
116E LEU* 3.7 18.4 - - + -
121E LEU 3.1 16.5 + - - +
122E ALA 3.8 2.2 - - - +
124E ILE* 1.3 75.8 - - - +
126E LYS* 1.3 54.5 + - - +
129E LEU* 2.8 38.7 + - - +
141E VAL* 4.7 1.1 - - - +
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Residues in contact with LYS 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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76E LEU* 4.1 10.9 - - + +
122E ALA 2.9 18.8 + - - +
123E GLU* 3.8 6.3 - - - +
124E ILE 3.3 0.2 - - - -
125E ALA* 1.3 75.3 - - - +
127E VAL* 1.3 64.5 + - + +
130E ASP* 2.8 60.1 + - - +
141E VAL* 3.4 35.9 - - + +
142E ARG* 4.3 9.2 - - - +
143E PHE* 3.9 26.7 - - + +
234E GLU* 3.3 31.0 + - - -
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Residues in contact with VAL 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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123E GLU* 3.2 19.8 + - + +
124E ILE* 3.9 4.9 - - - +
126E LYS* 1.3 87.8 - - + +
128E GLU* 1.3 64.7 + - + +
130E ASP* 4.2 9.7 + - - +
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Residues in contact with GLU 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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97E TYR* 3.2 36.2 + - + +
124E ILE* 3.0 26.4 + - + +
125E ALA 3.8 1.8 - - - +
127E VAL* 1.3 81.6 - - + +
129E LEU* 1.3 63.9 + - + +
130E ASP 4.5 2.6 - - - +
132E MET* 4.6 6.8 - - - +
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Residues in contact with LEU 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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93E LEU* 3.4 34.1 - - + +
94E PHE* 3.6 34.5 - - + -
96E LYS* 4.3 8.7 - - - +
97E TYR* 3.8 22.4 - - + +
125E ALA 2.8 19.5 + - - +
128E GLU* 1.3 73.8 - - - +
130E ASP* 1.4 65.3 + - - +
131E ASN 3.4 0.7 + - - -
132E MET* 3.2 44.5 + - - +
139E LEU* 4.0 8.6 - - + +
141E VAL* 3.6 19.3 - - + +
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Residues in contact with ASP 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 LYS* 2.8 40.7 + - - +
127E VAL* 4.2 9.7 + - - +
128E GLU 3.6 3.2 - - - +
129E LEU* 1.4 71.1 - - - +
131E ASN* 1.4 85.3 + - - +
132E MET* 3.2 1.6 + - - -
139E LEU 3.7 0.2 - - - +
140E ARG* 3.6 4.9 - - - -
141E VAL* 3.0 38.6 + - - +
142E ARG* 3.1 26.5 + - - -
234E GLU* 4.6 2.3 - - - +
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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