Contacts of the helix formed by residues 123 - 132 (chain F) in PDB entry 5DST
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 GLY 123 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120F SER* 2.8 19.8 + - - -
121F GLY 2.9 3.0 + - - -
122F THR* 1.3 78.2 - - - +
124F ILE* 1.3 66.5 + - - +
125F LEU 3.1 2.9 - - - -
126F SER* 2.9 23.8 + - - -
127F MET* 3.0 18.2 + - - +
149F SER* 4.2 7.2 - - - -
153F ILE* 4.9 8.7 - - - -
164F ILE* 5.3 0.4 - - - -
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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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242E VAL* 4.1 15.7 - - + +
243E TYR* 4.4 1.6 - - + -
245E PHE* 3.8 28.0 - - + -
247E MET* 4.1 15.9 - - + -
90F LEU* 3.8 23.1 - - + -
95F ARG* 4.7 2.2 - - - +
96F THR* 4.5 2.9 - - + -
120F SER 4.1 0.2 + - - -
122F THR* 3.4 8.1 + - - +
123F GLY* 1.3 75.8 - - - +
125F LEU* 1.3 69.7 + - + +
127F MET* 3.2 10.2 + - + +
128F PHE* 3.1 46.6 + - + -
401F SAH 3.4 35.0 - - - +
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Residues in contact with LEU 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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95F ARG* 5.6 2.7 - - - +
96F THR* 5.7 1.6 - - + -
99F TYR* 3.8 43.3 - - + -
103F MET* 3.9 3.7 - - + +
117F ASP* 3.3 19.2 + - - +
120F SER 4.8 0.4 + - - -
123F GLY 3.1 1.2 - - - -
124F ILE* 1.3 77.7 - - + +
126F SER* 1.3 65.0 + - - +
128F PHE* 3.4 20.7 + - + +
129F ALA 3.1 16.6 + - - -
183F ILE* 3.4 18.6 - - + +
184F SER* 4.3 4.9 - - - +
185F GLU* 3.9 21.5 - - + +
401F SAH 3.4 35.9 - - - +
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Residues in contact with SER 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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117F ASP* 2.8 32.3 + - - +
120F SER* 4.5 3.5 - - - -
123F GLY* 2.9 12.2 + - - -
125F LEU* 1.3 77.0 - - - +
127F MET* 1.3 57.5 + - - +
129F ALA* 3.3 3.3 + - - +
130F ALA* 3.0 23.6 + - - +
137F VAL* 3.6 23.6 - - - +
139F GLY* 4.3 7.1 - - - -
153F ILE* 5.3 0.2 - - - -
162F ILE* 3.6 25.4 - - - +
164F ILE* 5.2 1.1 - - - -
183F ILE* 4.4 2.5 - - - -
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Residues in contact with MET 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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245E PHE* 3.6 54.5 - - + -
247E MET* 4.3 5.8 - - + -
123F GLY 3.0 12.9 + - - +
124F ILE* 3.2 27.1 + - + +
126F SER* 1.3 73.7 - - - +
128F PHE* 1.3 64.1 + - - +
130F ALA* 3.3 2.1 + - - +
131F LYS* 2.9 27.7 + - - +
152F ILE* 3.9 21.5 - - + -
153F ILE* 4.1 13.0 - - + -
156F ASN* 3.8 15.7 - - - -
158F LEU* 3.8 11.5 - - + +
162F ILE* 3.8 20.4 - - + -
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Residues in contact with PHE 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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243E TYR* 4.0 10.3 - + + -
245E PHE* 3.7 20.4 - + - -
96F THR* 3.8 27.4 - - + -
99F TYR 4.4 1.1 - - - -
100F ARG* 3.4 55.2 - - + -
103F MET* 3.9 13.7 - - + -
104F TYR* 3.4 25.8 - - + -
124F ILE* 3.1 38.2 + - + -
125F LEU* 3.6 25.1 - - + +
127F MET* 1.3 75.9 - - - +
129F ALA* 1.3 63.9 + - - +
131F LYS 3.0 2.4 + - - -
132F ALA* 3.0 20.1 + - - +
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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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103F MET* 3.6 16.0 - - - -
110F PHE* 4.5 4.3 - - + +
115F VAL* 4.2 15.7 - - + -
125F LEU 3.1 10.8 + - - +
126F SER* 3.5 8.5 - - - +
128F PHE* 1.3 80.3 - - - +
130F ALA* 1.3 62.9 + - - +
132F ALA* 3.1 16.5 + - - +
133F GLY 3.4 7.4 + - - -
134F ALA* 3.4 10.7 + - - +
137F VAL* 4.0 13.9 - - + -
183F ILE* 4.1 12.1 - - + -
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Residues in contact with ALA 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 SER 3.0 16.7 + - - +
127F MET 3.6 4.3 - - - +
129F ALA* 1.3 75.3 - - - +
131F LYS* 1.3 59.2 + - - +
133F GLY* 3.1 18.9 + - - -
134F ALA* 3.8 6.5 + - - +
137F VAL* 4.0 6.9 - - + +
158F LEU* 4.2 16.7 - - + +
161F ILE* 3.9 30.7 - - + +
162F ILE* 4.0 15.3 - - + -
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Residues in contact with LYS 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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245E PHE* 3.9 20.6 - - + -
104F TYR* 3.4 32.8 - - + +
107F LYS* 4.1 11.4 - - - -
127F MET 2.9 17.5 + - - +
128F PHE 3.0 2.2 + - - +
130F ALA* 1.3 76.1 - - - +
132F ALA* 1.3 58.3 + - - +
133F GLY* 3.1 2.2 + - - -
156F ASN 5.4 3.6 + - - -
158F LEU* 4.6 20.4 - - + +
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Residues in contact with ALA 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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103F MET* 3.8 34.3 - - + +
104F TYR* 4.5 2.7 - - + +
107F LYS* 3.4 34.6 - - + +
110F PHE* 3.6 23.0 - - + +
111F LYS* 4.1 1.7 + - - +
128F PHE 3.0 11.4 + - - +
129F ALA 3.1 10.9 + - - +
131F LYS* 1.3 76.6 - - - +
133F GLY* 1.3 56.9 + - - +
134F ALA 3.7 0.2 - - - -
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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