Contacts of the helix formed by residues 123 - 132 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120N SER* 3.0 18.7 + - - -
121N GLY 3.1 2.3 - - - -
122N THR* 1.3 78.5 - - - +
124N ILE* 1.3 65.5 + - - +
125N LEU 3.2 2.6 + - - -
126N SER* 3.3 11.9 + - - -
127N MET* 2.9 31.5 + - - +
149N SER* 4.2 7.6 - - - -
153N ILE* 4.8 8.9 - - - +
164N ILE* 5.4 0.4 - - - -
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Residues in contact with ILE 124 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242M VAL* 4.1 15.9 - - + +
243M TYR* 4.4 1.3 - - + -
245M PHE* 3.8 19.1 - - + -
247M MET* 4.2 14.6 - - + -
90N LEU* 3.8 29.4 - - + -
95N ARG* 4.7 2.9 - - - +
96N THR* 4.4 3.1 - - + -
120N SER 4.2 0.2 + - - -
122N THR* 3.4 8.2 - - - +
123N GLY* 1.3 77.1 - - - +
125N LEU* 1.3 66.3 + - + +
127N MET* 3.2 9.3 + - + +
128N PHE* 3.0 63.3 + - + -
401N SAH 3.8 27.6 - - - +
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Residues in contact with LEU 125 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95N ARG* 5.6 2.9 - - - +
96N THR* 5.7 1.1 - - + -
99N TYR* 3.7 45.5 - - + -
103N MET* 3.9 3.5 - - + +
117N ASP* 3.4 19.2 + - - +
120N SER 4.9 0.8 + - - -
123N GLY 3.2 0.6 - - - -
124N ILE* 1.3 84.2 - - + +
126N SER* 1.3 61.7 + - - +
128N PHE* 3.2 19.5 + - + +
129N ALA 3.0 23.0 + - - -
183N ILE* 3.6 17.1 - - + +
184N SER* 4.3 4.9 - - - +
185N GLU* 3.9 22.2 - - + +
401N SAH 3.5 33.2 - - - +
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Residues in contact with SER 126 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117N ASP* 2.7 39.2 + - - +
120N SER* 4.5 1.9 - - - -
123N GLY* 3.8 11.0 - - - -
125N LEU* 1.3 76.5 - - - +
127N MET* 1.3 57.1 + - - +
129N ALA* 3.5 3.7 + - - +
130N ALA* 3.0 21.7 + - - +
137N VAL* 3.6 22.4 - - - +
139N GLY* 4.3 6.4 - - - -
162N ILE* 3.4 28.2 - - - +
164N ILE* 5.3 1.6 - - - -
183N ILE* 4.4 1.6 - - - -
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Residues in contact with MET 127 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245M PHE* 3.6 54.5 - - + -
247M MET* 4.2 8.1 - - + -
123N GLY 2.9 24.2 + - - +
124N ILE* 3.6 13.2 - - - +
126N SER* 1.3 74.7 - - - +
128N PHE* 1.3 64.9 + - - +
130N ALA* 3.5 1.4 + - - +
131N LYS* 3.1 27.9 + - - +
152N ILE* 3.9 22.0 - - + -
153N ILE* 4.2 12.3 - - + -
156N ASN* 3.9 15.0 - - - -
158N LEU* 3.7 18.1 - - + +
162N ILE* 3.7 14.4 - - + -
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Residues in contact with PHE 128 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243M TYR* 3.9 12.1 - + + -
245M PHE* 3.7 25.6 - + - -
96N THR* 3.8 27.8 - - + -
99N TYR 4.4 1.6 - - - -
100N ARG* 3.5 52.5 - - + -
103N MET* 3.8 13.9 - - + -
104N TYR* 3.4 19.7 - - + -
124N ILE* 3.0 39.9 + - + -
125N LEU* 3.2 23.8 + - + +
127N MET* 1.3 75.5 - - - +
129N ALA* 1.3 64.9 + - - +
131N LYS 3.0 3.5 + - - -
132N ALA* 2.9 19.5 + - - +
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Residues in contact with ALA 129 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103N MET* 3.5 17.2 - - - -
110N PHE* 4.4 7.2 - - + +
115N VAL* 4.2 13.0 - - + -
125N LEU 3.0 16.6 + - - +
126N SER* 3.7 6.3 - - - +
128N PHE* 1.3 75.8 - - - +
130N ALA* 1.3 64.5 + - - +
132N ALA* 2.9 18.1 + - - +
133N GLY 3.3 5.5 + - - -
134N ALA* 3.4 10.2 + - - +
137N VAL* 4.1 12.8 - - + -
183N ILE* 4.0 12.1 - - + -
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Residues in contact with ALA 130 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126N SER 3.0 18.4 + - - +
127N MET 3.8 4.7 - - - +
128N PHE 3.3 0.2 - - - -
129N ALA* 1.3 75.7 - - - +
131N LYS* 1.3 58.9 + - - +
133N GLY* 2.9 21.1 + - - -
134N ALA 3.6 6.5 + - - +
137N VAL* 4.0 6.4 - - + +
158N LEU* 4.3 16.2 - - + -
161N ILE* 3.7 31.4 - - + +
162N ILE* 3.9 13.7 - - + -
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Residues in contact with LYS 131 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245M PHE* 3.9 20.0 - - + -
104N TYR* 3.3 31.0 - - + +
107N LYS* 4.3 10.9 - - - -
127N MET 3.1 14.6 + - - +
128N PHE 3.0 6.5 + - - +
130N ALA* 1.3 76.7 - - - +
132N ALA* 1.3 57.0 + - - +
133N GLY* 3.0 3.9 + - - -
156N ASN 5.4 3.9 + - - -
158N LEU* 4.6 20.4 - - + +
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Residues in contact with ALA 132 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103N MET* 3.6 34.5 - - + +
104N TYR* 4.4 2.8 - - + +
107N LYS* 3.5 32.7 - - + +
110N PHE* 3.5 27.8 - - + +
111N LYS* 4.1 1.4 + - - +
128N PHE 2.9 11.4 + - - +
129N ALA 2.9 11.3 + - - +
131N LYS* 1.3 75.3 - - - +
133N GLY* 1.3 55.7 + - - +
134N 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