Contacts of the helix formed by residues 121 - 134 (chain E) in PDB entry 5U0A
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 VAL 121 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E LYS* 3.3 23.5 + - + +
60E VAL* 3.6 26.0 - - + -
72E ARG* 4.3 19.3 - - - +
120E PRO* 1.3 68.7 - - - +
122E PRO* 1.3 75.3 - - + +
124E ILE* 2.8 31.3 + - + +
125E ASP* 3.2 3.6 + - + +
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Residues in contact with PRO 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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57E ASP* 6.6 0.2 - - + -
58E LYS 4.8 2.5 - - - +
120E PRO* 3.7 10.3 - - + -
121E VAL* 1.3 95.7 - - + +
123E ALA* 1.3 56.7 + - - +
125E ASP* 3.2 9.8 + - + +
126E GLU* 3.0 34.1 + - + +
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Residues in contact with ALA 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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119E LEU* 4.8 6.7 - - + -
120E PRO* 3.3 18.0 + - + +
121E VAL 3.1 1.0 - - - -
122E PRO* 1.3 77.1 - - - +
124E ILE* 1.3 65.5 + - - +
126E GLU* 3.1 6.2 + - - +
127E LEU* 2.9 19.6 + - - +
159E VAL* 3.2 27.8 - - + +
160E LEU* 6.4 0.4 - - + -
162E SER* 3.2 28.9 - - - +
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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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60E VAL* 6.0 4.7 - - + -
62E THR* 5.6 4.5 - - + -
65E ILE* 3.9 27.8 - - + -
68E GLU* 3.5 22.9 - - + -
69E ILE* 3.9 17.0 - - + +
72E ARG* 3.0 39.8 + - - +
119E LEU* 3.8 16.5 - - + +
120E PRO 3.4 3.2 + - - +
121E VAL* 2.8 28.5 + - + +
123E ALA* 1.3 78.2 - - - +
125E ASP* 1.3 63.1 + - - +
127E LEU* 3.1 9.5 + - + +
128E ALA* 3.0 19.4 + - - +
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Residues in contact with ASP 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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72E ARG* 3.8 27.4 - - - +
75E GLU* 4.9 4.1 - - - +
76E ARG* 3.4 22.0 + - - -
121E VAL* 3.2 6.7 + - + +
122E PRO* 3.5 12.8 - - + +
124E ILE* 1.3 83.8 - - - +
126E GLU* 1.3 57.6 + - + +
128E ALA* 3.0 5.0 + - - +
129E ALA 3.0 21.3 + - - -
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Residues in contact with GLU 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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122E PRO* 3.0 22.5 + - + +
123E ALA* 3.1 10.3 + - - +
125E ASP* 1.3 74.6 - - + +
127E LEU* 1.3 66.5 + - - +
129E ALA* 3.0 9.5 + - - +
130E ILE* 2.9 28.2 + - + +
159E VAL* 4.3 19.8 - - + +
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Residues in contact with LEU 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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65E ILE* 4.6 10.3 - - + -
69E ILE* 4.1 26.2 - - + -
90E VAL* 4.4 13.8 - - + +
119E LEU* 5.1 1.3 - - + -
123E ALA 2.9 19.3 + - - +
124E ILE* 3.1 14.6 + - - +
126E GLU* 1.3 75.8 - - - +
128E ALA* 1.3 62.4 + - - +
130E ILE* 3.2 6.9 + - + +
131E ALA* 3.0 23.6 + - - +
156E ILE* 3.7 35.4 - - + +
159E VAL* 3.5 22.0 - - + -
160E LEU* 3.7 22.7 - - + -
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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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69E ILE* 4.2 14.9 - - + +
72E ARG* 3.7 30.7 - - + -
73E LEU* 3.2 25.5 - - + +
76E ARG* 4.1 7.6 - - - +
124E ILE 3.0 11.3 + - - +
125E ASP* 3.0 10.3 + - - +
127E LEU* 1.3 77.8 - - - +
129E ALA* 1.3 56.6 + - - +
131E ALA* 3.3 1.5 + - - +
132E ASP* 2.9 22.9 + - - +
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Residues in contact with ALA 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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76E ARG* 3.6 24.6 - - - +
125E ASP 3.0 9.2 + - - +
126E GLU* 3.0 11.8 + - - +
128E ALA* 1.3 76.9 - - - +
130E ILE* 1.3 58.0 + - + +
132E ASP* 2.9 21.0 + - - +
133E GLU* 3.0 15.8 + - - +
155E ARG* 5.9 0.4 - - - -
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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 GLU* 2.9 15.6 + - + +
127E LEU* 3.2 9.2 + - - +
129E ALA* 1.3 77.6 - - + +
131E ALA* 1.3 63.0 + - - +
132E ASP 3.2 0.3 + - - -
133E GLU* 3.7 4.9 + - - +
134E HIS* 3.3 23.1 - - + -
151E LEU* 4.5 2.8 - - + +
152E PRO* 4.6 21.8 - - + -
155E ARG* 3.9 50.9 - - + +
156E ILE* 4.2 24.0 - - + +
159E VAL* 3.7 29.8 - - + -
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Residues in contact with ALA 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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69E ILE* 5.2 0.2 - - + -
73E LEU* 4.1 17.5 - - + -
78E TRP* 3.2 19.0 - - - -
86E GLY* 4.1 7.4 - - - +
90E VAL* 3.5 30.9 - - + +
127E LEU 3.0 11.4 + - - +
128E ALA* 3.6 5.8 - - - +
130E ILE* 1.3 77.3 - - - +
132E ASP* 1.3 61.3 + - - +
134E HIS* 3.9 9.9 + - - +
138E VAL* 4.4 3.9 - - + +
151E LEU* 4.7 12.1 - - + -
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Residues in contact with ASP 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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73E LEU* 4.2 1.6 - - + -
76E ARG* 3.5 31.5 + - - +
78E TRP* 2.7 33.6 + - - -
128E ALA 2.9 13.1 + - - +
129E ALA* 2.9 14.8 + - - +
131E ALA* 1.3 75.7 - - - +
133E GLU* 1.3 67.4 + - - +
134E HIS 3.1 2.8 + - - -
135E ARG* 3.2 20.3 + - - +
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Residues in contact with GLU 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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129E ALA 3.0 12.6 + - - +
130E ILE* 3.7 6.9 + - - +
131E ALA 3.6 0.2 - - - -
132E ASP* 1.3 77.0 - - - +
134E HIS* 1.3 75.7 + - + +
135E ARG* 3.3 4.9 + - - +
136E ASP* 4.7 3.3 - - - +
155E ARG* 3.8 28.0 + - - -
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Residues in contact with HIS 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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130E ILE* 3.3 24.3 + - + +
131E ALA 4.1 3.8 - - - +
132E ASP 3.1 1.4 - - - -
133E GLU* 1.3 101.1 + - + +
135E ARG* 1.3 61.7 + - - +
136E ASP* 3.4 9.2 - - - -
137E ALA* 3.5 10.8 + - + +
138E VAL* 3.1 23.2 + - - +
150E ILE* 5.9 1.9 - - + +
151E LEU* 3.6 28.9 - - + -
152E PRO* 3.7 25.6 - - + +
155E ARG* 4.3 5.6 + - - -
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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