Contacts of the helix formed by residues 123 - 132 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120J SER* 3.0 17.6 + - - -
121J GLY 3.0 1.6 - - - -
122J THR* 1.3 78.3 - - - +
124J ILE* 1.3 66.2 + - - +
125J LEU 3.3 3.4 - - - -
126J SER* 3.2 13.0 + - - -
127J MET* 2.9 29.8 + - - +
149J SER* 4.1 9.4 - - - -
153J ILE* 4.8 7.9 - - - -
164J ILE* 5.4 0.4 - - - -
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Residues in contact with ILE 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242I VAL* 4.2 13.2 - - + +
243I TYR* 4.5 2.0 - - + -
245I PHE* 4.1 19.3 - - + -
247I MET* 4.2 17.3 - - + -
90J LEU* 3.8 24.7 - - + -
95J ARG* 4.7 2.9 - - - +
96J THR* 4.5 2.5 - - + -
120J SER 4.2 0.2 + - - -
122J THR* 3.4 7.1 - - - +
123J GLY* 1.3 77.5 - - - +
125J LEU* 1.3 70.8 + - + +
127J MET* 3.2 9.4 + - + +
128J PHE* 3.1 53.6 + - + -
401J SAH 3.5 34.8 - - - +
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Residues in contact with LEU 125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95J ARG* 5.5 3.4 - - - +
96J THR* 5.6 1.1 - - + -
99J TYR* 3.7 45.1 - - + -
103J MET* 3.9 3.2 - - + +
117J ASP* 3.3 19.2 + - - +
120J SER 4.8 0.6 + - - -
123J GLY 3.3 0.6 - - - -
124J ILE* 1.3 82.9 - - + +
126J SER* 1.3 58.6 + - - +
128J PHE* 3.1 20.3 + - + +
129J ALA 2.9 23.9 + - - -
183J ILE* 3.7 15.6 - - + +
184J SER* 4.3 4.9 - - - +
185J GLU* 3.8 22.2 - - + +
401J SAH 3.5 36.1 - - - +
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Residues in contact with SER 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117J ASP* 2.9 32.3 + - - +
120J SER* 4.4 2.9 - - - -
123J GLY* 3.2 11.9 + - - -
125J LEU* 1.3 75.0 - - - +
127J MET* 1.3 58.0 + - - +
129J ALA* 3.4 4.2 + - - +
130J ALA* 2.9 28.8 + - - +
137J VAL* 3.6 22.6 - - - +
139J GLY* 4.3 8.1 - - - -
153J ILE* 5.3 0.2 - - - -
162J ILE* 3.5 22.8 - - - +
164J ILE* 5.2 0.9 - - - -
183J ILE* 4.5 1.8 - - - -
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Residues in contact with MET 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245I PHE* 3.7 45.0 - - + -
247I MET* 4.0 14.4 - - + -
123J GLY 2.9 22.5 + - - +
124J ILE* 3.6 9.9 - - + +
125J LEU 3.2 0.2 - - - -
126J SER* 1.3 75.2 - - - +
128J PHE* 1.3 63.0 + - - +
130J ALA* 3.6 1.6 + - - +
131J LYS* 3.1 28.8 + - - +
152J ILE* 3.8 23.3 - - + -
153J ILE* 4.1 15.3 - - + -
156J ASN* 3.8 21.8 - - - -
158J LEU* 3.8 12.6 - - + +
162J ILE* 3.8 14.4 - - + -
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Residues in contact with PHE 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243I TYR* 4.0 9.9 - + + -
245I PHE* 3.9 12.8 - + - -
96J THR* 3.7 28.7 - - + -
99J TYR 4.4 1.3 - - - -
100J ARG* 3.4 54.1 - - + -
103J MET* 3.7 14.4 - - + -
104J TYR* 3.5 25.3 - - + -
124J ILE* 3.1 44.5 + - + -
125J LEU* 3.4 24.0 - - + +
127J MET* 1.3 74.7 - - - +
129J ALA* 1.3 66.8 + - - +
131J LYS 3.0 2.1 + - - -
132J ALA* 2.8 20.6 + - - +
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Residues in contact with ALA 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103J MET* 3.5 11.4 - - - -
110J PHE* 4.6 5.4 - - + +
115J VAL* 4.2 15.7 - - + -
125J LEU 2.9 13.1 + - - +
126J SER* 3.6 8.1 - - - +
128J PHE* 1.3 76.8 - - - +
130J ALA* 1.3 62.7 + - - +
132J ALA* 2.9 17.1 + - - +
133J GLY 3.3 7.8 + - - -
134J ALA* 3.4 10.8 + - - +
137J VAL* 4.0 13.2 - - + -
183J ILE* 4.0 17.5 - - + -
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Residues in contact with ALA 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126J SER 2.9 17.7 + - - +
127J MET 3.9 4.9 - - - +
128J PHE 3.2 0.2 - - - -
129J ALA* 1.3 75.0 - - - +
131J LYS* 1.3 62.1 + - - +
133J GLY* 3.1 14.6 + - - -
134J ALA 3.8 5.1 + - - +
137J VAL* 4.0 7.5 - - + +
158J LEU* 4.2 16.9 - - + +
161J ILE* 3.8 32.0 - - + +
162J ILE* 3.9 14.6 - - + -
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Residues in contact with LYS 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245I PHE* 4.0 19.1 - - + -
104J TYR* 3.4 31.2 - - + +
107J LYS* 4.2 10.8 - - - -
127J MET 3.1 18.0 + - - +
128J PHE 3.0 3.6 + - - +
130J ALA* 1.3 73.0 - - - +
132J ALA* 1.3 57.6 + - - +
133J GLY* 3.0 9.3 + - - -
156J ASN 5.4 3.4 + - - -
158J LEU* 4.6 20.1 - - + +
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Residues in contact with ALA 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103J MET* 3.6 35.0 - - + +
104J TYR* 4.5 2.7 - - + +
107J LYS* 3.5 32.3 - - + +
110J PHE* 3.5 25.7 - - + +
111J LYS* 4.1 1.2 + - - +
128J PHE 2.8 13.4 + - - +
129J ALA 2.9 11.8 + - - +
131J LYS* 1.3 76.2 - - - +
133J GLY* 1.3 55.7 + - - +
134J ALA 3.6 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