Contacts of the helix formed by residues 124 - 135 (chain F) in PDB entry 6DV9
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 SER 124 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123F LEU* 1.3 76.4 - - - +
125F ALA* 1.3 61.4 + - - +
126F GLU* 3.9 11.1 + - - -
127F HIS* 2.3 43.6 + - - +
128F ARG* 2.8 27.0 + - - +
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Residues in contact with ALA 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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123F LEU 3.7 1.2 + - - -
124F SER* 1.3 73.9 - - - +
126F GLU* 1.3 71.8 + - - +
128F ARG* 3.9 24.8 + - - +
129F ALA* 3.2 25.6 + - - +
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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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124F SER* 3.0 11.7 - - - +
125F ALA* 1.3 90.6 + - - +
127F HIS* 1.3 69.2 + - + +
129F ALA* 3.4 3.5 + - - +
130F VAL* 3.1 29.2 + - - +
148F LEU* 5.2 0.4 - - - +
158F ARG* 3.4 39.0 - - - +
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Residues in contact with HIS 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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123F LEU* 4.2 13.0 - - + -
124F SER* 2.3 33.6 + - - +
126F GLU* 1.3 78.8 - - + +
128F ARG* 1.3 66.3 - - - +
130F VAL* 3.1 14.9 + - - +
131F ILE* 3.1 20.9 + - - +
158F ARG* 3.5 40.3 + - + +
161F TYR* 3.2 42.5 - + - +
162F ALA* 3.6 13.6 - - + +
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Residues in contact with ARG 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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120F LEU* 3.4 41.7 + - + +
121F ALA* 4.0 11.4 + - - +
123F LEU* 2.9 34.1 + - + +
124F SER 2.8 14.8 + - - +
125F ALA* 3.9 23.5 + - - +
127F HIS* 1.3 73.1 - - - +
129F ALA* 1.3 56.3 + - - +
130F VAL 3.1 2.8 + - - -
131F ILE* 3.4 8.7 - - - +
132F GLN* 3.3 37.7 + - - +
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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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125F ALA 3.2 19.6 + - - +
126F GLU* 3.4 3.3 + - - +
127F HIS 3.2 0.6 - - - -
128F ARG* 1.3 77.5 - - - +
130F VAL* 1.3 61.0 + - + +
132F GLN* 3.9 12.8 - - - +
133F ARG* 3.0 44.4 + - - +
148F LEU* 4.2 7.6 - - + +
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Residues in contact with VAL 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 3.1 18.6 - - - +
127F HIS* 3.1 7.7 + - - +
129F ALA* 1.3 76.7 - - - +
131F ILE* 1.3 65.3 + - - +
132F GLN 3.3 1.1 - - - -
133F ARG* 3.3 6.4 + - - +
134F SER* 3.2 22.2 + - - -
144F ILE* 4.0 5.5 - - + +
148F LEU* 3.6 26.5 - - + -
150F ILE* 5.2 1.3 - - + -
155F VAL* 4.0 18.2 - - + -
158F ARG* 4.0 27.8 - - + -
159F LEU* 3.5 27.8 - - + +
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Residues in contact with ILE 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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820C LEU* 4.6 17.2 - - + +
120F LEU* 3.6 42.6 - - + -
123F LEU* 4.3 7.2 - - + -
127F HIS 3.1 16.7 + - - +
128F ARG* 3.4 13.2 - - - +
130F VAL* 1.3 76.5 - - - +
132F GLN* 1.3 72.5 + - - +
133F ARG 3.2 0.2 - - - -
135F TYR* 3.0 43.6 + - + +
136F TYR* 3.7 1.8 + - + -
159F LEU* 3.7 22.0 - - + -
162F ALA* 3.7 29.2 - - + -
163F VAL* 4.8 2.9 - - + +
166F LEU* 4.9 2.5 - - + -
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Residues in contact with GLN 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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120F LEU* 5.4 3.1 - - + +
128F ARG* 3.3 29.7 + - - +
129F ALA* 3.9 12.5 - - - +
131F ILE* 1.3 84.6 - - + +
133F ARG* 1.3 74.8 + - - +
136F TYR* 3.2 41.7 - - + +
137F ARG* 3.2 40.2 + - - +
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Residues in contact with ARG 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 41.0 + - - +
130F VAL 3.3 7.9 + - - +
131F ILE 3.2 0.8 - - - -
132F GLN* 1.3 96.2 - - - +
134F SER* 1.3 57.3 + - - +
137F ARG* 3.8 30.6 - - - +
139F TRP* 3.3 43.7 + - + +
144F ILE* 3.5 27.9 - - + +
147F ASP* 3.0 28.9 + - - -
148F LEU* 3.9 14.9 - - - +
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Residues in contact with SER 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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819C ARG* 5.6 1.6 + - - -
67D ARG* 5.4 3.6 + - - -
130F VAL 3.2 11.5 + - - -
131F ILE 3.4 0.4 + - - -
133F ARG* 1.3 79.7 - - - +
135F TYR* 1.3 74.2 + - - +
138F GLY* 3.3 20.6 - - - -
139F TRP 4.1 8.5 + - - +
140F SER 6.0 0.3 - - - -
144F ILE* 3.6 18.2 - - - -
159F LEU* 3.9 25.5 - - - +
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Residues in contact with TYR 135 (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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816C PRO* 3.4 31.4 - - - +
819C ARG* 3.8 51.6 + - + +
820C LEU* 3.8 35.0 - - + -
823C ALA* 3.4 22.3 - - + +
131F ILE* 3.0 20.0 + - + +
134F SER* 1.3 91.2 - - - +
136F TYR* 1.3 65.7 + - + +
137F ARG 3.5 0.4 - - - -
138F GLY* 4.1 4.3 + - - -
159F LEU* 4.1 22.0 - - + +
163F VAL* 4.2 11.2 - - + +
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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