Contacts of the helix formed by residues 121 - 134 (chain F) in PDB entry 5U07
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58F LYS* 3.2 30.9 + - + +
60F VAL* 3.6 25.4 - - + -
72F ARG* 3.1 47.5 + - - +
120F PRO* 1.3 71.2 - - - +
122F PRO* 1.3 71.1 - - + +
124F ILE* 2.9 17.0 + - - +
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Residues in contact with PRO 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F ASP* 5.1 5.8 - - - +
58F LYS 4.5 3.1 - - - +
120F PRO* 3.5 14.1 - - + -
121F VAL* 1.3 95.5 - - + +
123F ALA* 1.3 52.9 + - - +
125F ASP* 3.0 12.2 + - + +
126F GLU* 2.6 47.5 + - - +
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Residues in contact with ALA 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119F LEU* 3.9 15.3 - - + -
120F PRO* 3.0 17.5 + - + +
122F PRO* 1.3 77.5 - - - +
124F ILE* 1.3 66.5 + - - +
126F GLU* 3.0 11.6 + - - -
127F LEU* 2.9 21.9 + - - +
159F VAL* 3.4 21.4 - - + +
160F LEU* 5.5 0.7 - - + -
162F SER* 3.4 26.2 - - - +
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Residues in contact with ILE 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F VAL* 5.7 8.5 - - + -
62F THR* 5.9 0.2 - - - +
65F ILE* 4.5 22.9 - - + +
68F GLU* 3.0 34.1 - - + +
69F ILE* 3.9 23.0 - - + +
72F ARG* 3.2 21.3 - - - +
119F LEU* 3.4 28.7 - - + -
120F PRO 3.4 2.2 + - - +
121F VAL* 2.9 9.5 + - - +
123F ALA* 1.3 77.5 - - - +
125F ASP* 1.3 63.4 + - - +
127F LEU* 3.1 10.8 + - + +
128F ALA* 3.0 20.4 + - - +
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Residues in contact with ASP 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F ARG* 2.9 25.2 - - - +
76F ARG* 4.1 16.6 + - - -
122F PRO* 3.0 16.6 + - + +
124F ILE* 1.3 76.6 - - - +
126F GLU* 1.3 63.5 + - + +
128F ALA* 3.2 9.1 + - - +
129F ALA* 3.0 19.7 + - - +
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Residues in contact with GLU 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F PRO* 2.6 41.1 + - - +
123F ALA* 3.0 16.9 + - - +
125F ASP* 1.3 74.1 - - + +
127F LEU* 1.3 67.1 + - - +
129F ALA* 3.1 8.7 + - + +
130F ILE* 2.9 29.4 + - + +
159F VAL* 3.9 23.3 - - + +
162F SER* 5.3 2.8 + - - -
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Residues in contact with LEU 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F ILE* 5.7 3.6 - - + -
69F ILE* 4.0 26.7 - - + -
90F VAL* 4.3 17.0 - - + +
119F LEU* 5.1 2.0 - - + -
123F ALA 2.9 19.1 + - - +
124F ILE* 3.1 17.5 + - + +
126F GLU* 1.3 75.8 - - - +
128F ALA* 1.3 63.9 + - - +
130F ILE* 3.3 4.6 + - - +
131F ALA* 3.0 23.7 + - - +
156F ILE* 3.8 36.2 - - + +
159F VAL* 3.8 17.0 - - + -
160F LEU* 3.8 25.4 - - + -
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Residues in contact with ALA 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F ILE* 4.4 12.2 - - + +
72F ARG* 4.4 20.2 - - + -
73F LEU* 3.5 27.8 - - + +
76F ARG* 5.0 6.7 - - + +
124F ILE 3.0 12.4 + - - +
125F ASP* 3.4 14.4 - - - +
127F LEU* 1.3 76.6 - - - +
129F ALA* 1.3 56.8 + - - +
131F ALA* 3.3 2.6 + - - -
132F ASP* 2.9 27.4 + - - +
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Residues in contact with ALA 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F ARG* 4.7 14.3 - - - +
125F ASP* 3.0 14.8 + - - +
126F GLU* 3.1 11.6 + - + +
128F ALA* 1.3 76.2 - - - +
130F ILE* 1.3 58.7 + - + +
132F ASP* 2.8 23.4 + - - +
133F GLU* 3.0 15.6 + - - +
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Residues in contact with ILE 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F GLU* 2.9 19.1 + - + +
127F LEU* 3.3 4.7 + - - +
129F ALA* 1.3 76.8 - - + +
131F ALA* 1.3 61.7 + - - +
132F ASP 3.2 0.7 + - - -
133F GLU* 3.4 17.4 - - - +
134F HIS* 3.4 11.8 - - - -
151F LEU* 3.2 19.8 - - + +
152F PRO* 4.4 15.3 - - + -
155F ARG* 4.0 24.7 - - + +
156F ILE* 3.6 40.4 - - + +
159F VAL* 3.7 28.3 - - + -
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Residues in contact with ALA 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F ILE* 5.5 0.2 - - + -
73F LEU* 4.4 15.5 - - + -
78F TRP* 3.8 15.8 - - - -
86F GLY* 4.3 9.8 - - - +
90F VAL* 3.6 30.7 - - + +
127F LEU 3.0 12.4 + - - +
128F ALA* 3.6 5.2 - - - +
130F ILE* 1.3 77.8 - - - +
132F ASP* 1.3 60.7 + - - +
134F HIS* 3.9 9.2 + - - -
138F VAL* 4.4 6.9 - - + +
151F LEU* 3.6 13.8 - - + +
156F ILE* 5.9 0.2 - - - +
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Residues in contact with ASP 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F LEU* 4.6 5.8 - - + -
76F ARG* 3.1 30.5 + - - +
78F TRP* 3.0 33.3 + - + -
128F ALA 2.9 13.5 + - - +
129F ALA* 2.8 14.2 + - - +
131F ALA* 1.3 74.9 - - - +
133F GLU* 1.3 65.8 + - - +
134F HIS 3.1 3.8 + - - -
135F ARG* 3.4 18.7 + - - +
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Residues in contact with GLU 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F ALA 3.0 9.3 + - - +
130F ILE* 3.4 13.1 - - - +
132F ASP* 1.3 76.8 - - - +
134F HIS* 1.3 88.4 + - + +
135F ARG* 3.4 3.8 + - - +
136F ASP* 5.1 1.2 - - - +
155F ARG* 2.3 42.2 + - - -
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Residues in contact with HIS 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F ILE 3.4 12.6 - - - -
131F ALA 3.9 5.0 + - - +
132F ASP 3.1 1.6 + - - -
133F GLU* 1.3 105.4 + - + +
135F ARG* 1.3 62.6 + - - +
136F ASP* 3.4 9.1 + - - -
137F ALA* 3.4 13.0 + - + +
138F VAL* 3.1 23.9 + - + +
150F ILE* 5.3 8.4 - - + +
151F LEU* 3.3 36.8 - - + -
152F PRO* 3.6 21.9 - - + +
155F ARG* 4.5 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