Contacts of the helix formed by residues 123 - 132 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120D SER* 3.0 15.8 + - - -
121D GLY 3.0 5.6 - - - -
122D THR* 1.3 77.7 - - - +
124D ILE* 1.3 64.5 + - - +
125D LEU 3.2 2.7 - - - -
126D SER* 3.1 13.6 + - - -
127D MET* 2.9 29.6 + - - +
149D SER* 4.1 8.7 - - - -
153D ILE* 4.8 8.7 - - - -
164D ILE* 5.4 0.2 - - - -
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Residues in contact with ILE 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C VAL* 4.2 10.1 - - + +
243C TYR* 4.4 3.6 - - + -
245C PHE* 3.8 20.6 - - + -
247C MET* 4.3 14.1 - - + -
90D LEU* 3.9 26.5 - - + -
95D ARG* 4.8 2.2 - - - +
96D THR* 4.5 2.7 - - + -
122D THR* 3.4 6.6 + - - +
123D GLY* 1.3 77.3 - - - +
125D LEU* 1.3 65.6 + - + +
127D MET* 3.3 8.9 + - - +
128D PHE* 3.0 64.6 + - + -
401D SAH 3.4 35.2 - - - +
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Residues in contact with LEU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D ARG* 5.6 1.6 - - - +
96D THR* 5.6 3.1 - - + -
99D TYR* 3.8 44.6 - - + -
103D MET* 3.9 2.9 - - + +
117D ASP* 3.2 19.4 + - - +
120D SER 4.8 0.4 + - - -
123D GLY 3.2 0.8 - - - -
124D ILE* 1.3 79.6 - - + +
126D SER* 1.3 66.6 + - - +
128D PHE* 3.2 20.7 + - + +
129D ALA 3.0 18.9 + - - -
183D ILE* 3.5 17.0 - - + +
184D SER* 4.3 4.0 - - - +
185D GLU* 3.9 20.9 - - + +
401D SAH 3.3 34.3 - - - +
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Residues in contact with SER 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D ASP* 2.8 32.7 + - - +
120D SER* 4.5 2.6 - - - -
123D GLY* 3.4 12.1 - - - -
125D LEU* 1.3 77.0 - - - +
127D MET* 1.3 56.9 + - - +
129D ALA* 3.3 2.8 + - - +
130D ALA* 3.0 28.8 + - - +
137D VAL* 3.6 23.9 - - - +
139D GLY* 4.3 7.6 - - - -
162D ILE* 3.6 20.7 - - - +
164D ILE* 5.2 0.7 - - - -
183D ILE* 4.4 3.6 - - - -
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Residues in contact with MET 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C PHE* 3.6 56.1 - - + -
247C MET* 4.2 8.5 - - + -
123D GLY 2.9 15.8 + - - +
124D ILE* 3.7 20.0 - - - +
125D LEU 3.2 0.2 - - - -
126D SER* 1.3 72.5 - - - +
128D PHE* 1.3 66.2 + - - +
130D ALA* 3.8 1.4 - - - +
131D LYS* 3.1 29.3 + - - +
152D ILE* 3.8 21.5 - - + -
153D ILE* 4.1 13.9 - - + -
156D ASN* 3.9 14.8 - - - -
158D LEU* 3.8 10.7 - - + +
162D ILE* 3.8 20.2 - - + -
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Residues in contact with PHE 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243C TYR* 4.1 9.4 - + + -
245C PHE* 3.7 21.1 - + - -
96D THR* 3.8 28.5 - - + -
99D TYR 4.4 1.6 - - - -
100D ARG* 3.5 54.3 - - + -
103D MET* 3.7 13.5 - - + -
104D TYR* 3.5 23.4 - - + -
124D ILE* 3.0 38.0 + - + -
125D LEU* 3.4 23.6 - - + +
127D MET* 1.3 74.0 - - - +
129D ALA* 1.3 66.7 + - - +
131D LYS* 3.0 4.0 + - - -
132D ALA* 2.9 19.4 + - - +
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Residues in contact with ALA 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D MET* 3.5 15.8 - - - -
110D PHE* 4.5 5.8 - - + +
115D VAL* 4.2 16.6 - - + -
125D LEU 3.0 13.1 + - - +
126D SER* 3.3 8.3 + - - +
128D PHE* 1.3 76.7 - - - +
130D ALA* 1.3 61.4 + - - +
132D ALA* 2.9 17.4 + - - +
133D GLY 3.3 7.8 + - - -
134D ALA* 3.4 10.0 + - - +
137D VAL* 4.1 13.0 - - + -
183D ILE* 4.1 12.3 - - + -
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Residues in contact with ALA 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D SER 3.0 16.3 + - - +
127D MET 3.8 4.7 - - - +
129D ALA* 1.3 74.2 - - - +
131D LYS* 1.3 59.7 + - - +
133D GLY* 3.0 19.9 + - - -
134D ALA 3.8 4.9 + - - +
137D VAL* 4.0 7.3 - - + +
158D LEU* 4.2 17.3 - - + -
161D ILE* 3.8 32.4 - - + +
162D ILE* 4.0 14.8 - - + -
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Residues in contact with LYS 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C PHE* 4.1 19.7 - - + -
104D TYR* 3.4 31.1 - - + +
107D LYS* 4.1 11.8 - - - -
127D MET 3.1 18.5 + - - +
128D PHE 3.0 3.6 + - - +
130D ALA* 1.3 77.2 - - - +
132D ALA* 1.3 57.9 + - - +
133D GLY* 3.1 1.8 + - - -
156D ASN 5.4 3.4 + - - -
158D LEU* 4.7 20.6 - - + +
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Residues in contact with ALA 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D MET* 3.8 35.4 - - + +
104D TYR* 4.4 2.4 - - + +
107D LYS* 3.3 39.9 - - + +
110D PHE* 3.8 15.5 - - + +
111D LYS* 4.2 2.1 + - - +
128D PHE 2.9 11.7 + - - +
129D ALA 2.9 10.0 + - - +
131D LYS* 1.3 75.6 - - - +
133D GLY* 1.3 58.1 + - - +
134D ALA 3.8 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