Contacts of the helix formed by residues 123 - 132 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C SER* 3.0 19.1 + - - -
121C GLY 3.0 3.0 - - - -
122C THR* 1.3 78.3 - - - +
124C ILE* 1.3 63.5 + - - +
125C LEU 3.2 2.9 - - - -
126C SER* 3.2 14.6 + - - -
127C MET* 2.9 29.0 + - - +
149C SER* 4.1 8.1 - - - -
153C ILE* 4.8 8.9 - - - +
164C ILE* 5.3 0.2 - - - -
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Residues in contact with ILE 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C LEU* 3.7 26.0 - - + -
95C ARG* 4.7 2.5 - - - +
96C THR* 4.6 2.9 - - + -
120C SER 4.2 0.4 + - - -
122C THR* 3.3 7.3 + - - +
123C GLY* 1.3 76.8 - - - +
125C LEU* 1.3 70.4 + - + +
127C MET* 3.2 14.1 + - + +
128C PHE* 3.0 47.2 + - + -
401C SAH 3.4 33.9 - - - +
242D VAL 4.1 10.3 - - - +
243D TYR* 4.4 3.8 - - + -
245D PHE* 3.8 28.7 - - + -
247D MET* 4.3 9.6 - - + -
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Residues in contact with LEU 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ARG* 5.6 2.9 - - - +
96C THR* 5.7 1.6 - - + -
99C TYR* 3.8 44.2 - - + -
103C MET* 3.8 3.4 - - + +
117C ASP* 3.3 19.0 + - - +
120C SER 4.9 0.6 + - - -
123C GLY 3.2 0.6 - - - -
124C ILE* 1.3 79.3 - - + +
126C SER* 1.3 65.6 + - - +
128C PHE* 3.2 21.5 + - + +
129C ALA 3.0 18.4 + - - -
183C ILE* 3.6 17.3 - - + +
184C SER* 4.3 4.3 - - - +
185C GLU* 3.9 20.2 - - + +
401C SAH 3.3 35.7 - - - +
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Residues in contact with SER 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ASP* 2.7 35.8 + - - +
120C SER* 4.4 3.1 - - - -
123C GLY* 3.2 11.9 + - - -
125C LEU* 1.3 77.2 - - - +
127C MET* 1.3 57.0 + - - +
129C ALA* 3.3 5.1 + - - +
130C ALA* 3.0 28.1 + - - +
137C VAL* 3.6 23.7 - - - +
139C GLY* 4.4 7.1 - - - -
153C ILE* 5.4 0.2 - - - -
162C ILE* 3.6 21.2 - - - +
164C ILE* 5.3 0.9 - - - -
183C ILE* 4.4 1.8 - - - -
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Residues in contact with MET 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C THR 4.8 0.2 - - - +
123C GLY 2.9 15.8 + - - +
124C ILE* 3.7 21.3 - - - +
125C LEU 3.2 0.2 - - - -
126C SER* 1.3 72.5 - - - +
128C PHE* 1.3 66.5 + - - +
130C ALA* 3.8 1.0 - - - +
131C LYS* 3.1 28.9 + - - +
152C ILE* 3.8 20.6 - - + -
153C ILE* 4.1 15.0 - - + -
156C ASN* 3.9 14.6 - - - -
158C LEU* 3.7 10.4 - - + +
162C ILE* 3.7 20.9 - - + -
245D PHE* 3.6 54.3 - - + -
247D MET* 4.2 8.5 - - + -
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Residues in contact with PHE 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C THR* 3.9 22.0 - - + -
99C TYR 4.4 0.7 - - - -
100C ARG* 3.4 56.8 - - + -
103C MET* 3.7 14.6 - - + -
104C TYR* 3.4 25.1 - - + -
124C ILE* 3.0 41.4 + - + -
125C LEU* 3.2 24.9 + - + +
127C MET* 1.3 74.1 - - - +
129C ALA* 1.3 67.2 + - - +
131C LYS 3.2 1.6 + - - -
132C ALA* 2.9 20.4 + - - +
243D TYR* 4.1 9.9 - + + -
245D PHE* 3.7 21.8 - + - -
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Residues in contact with ALA 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C MET* 3.5 16.5 - - - -
110C PHE* 4.5 5.9 - - + +
115C VAL* 4.2 15.7 - - + -
125C LEU 3.0 13.1 + - - +
126C SER* 3.5 8.7 - - - +
128C PHE* 1.3 76.7 - - - +
130C ALA* 1.3 57.4 + - - +
132C ALA* 2.9 22.0 + - - +
133C GLY 3.3 7.8 + - - -
134C ALA* 3.4 9.6 + - - +
137C VAL* 4.0 13.5 - - + -
183C ILE* 4.1 12.8 - - + -
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Residues in contact with ALA 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C SER 3.0 17.2 + - - +
127C MET 3.8 5.2 - - - +
129C ALA* 1.3 75.5 - - - +
131C LYS* 1.3 58.7 + - - +
133C GLY* 3.0 20.3 + - - -
134C ALA 3.8 6.2 + - - +
137C VAL* 4.0 6.8 - - + +
158C LEU* 4.2 17.5 - - + -
161C ILE* 3.9 30.5 - - + +
162C ILE* 4.0 14.6 - - + -
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Residues in contact with LYS 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C TYR* 3.5 29.8 - - + +
107C LYS* 4.1 12.0 - - - -
127C MET 3.1 18.1 + - - +
128C PHE 3.7 2.5 - - - +
130C ALA* 1.3 78.1 - - - +
132C ALA* 1.3 60.5 + - - +
133C GLY* 3.1 1.4 + - - -
156C ASN 5.3 4.5 + - - -
158C LEU* 4.7 19.3 - - + +
245D PHE* 4.2 18.2 - - + -
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Residues in contact with ALA 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C MET* 3.8 35.0 - - + +
104C TYR* 4.5 2.9 - - + +
107C LYS* 3.4 34.2 - - + +
110C PHE* 3.7 21.4 - - + +
111C LYS* 4.2 1.7 + - - +
128C PHE 2.9 13.0 + - - +
129C ALA 2.9 11.1 + - - +
131C LYS* 1.3 75.6 - - - +
133C GLY* 1.3 57.5 + - - +
134C 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