Contacts of the helix formed by residues 144 - 156 (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 SER 144 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81J ALA* 3.3 23.3 + - - +
142J CYS 4.0 0.4 + - - -
143J SER* 1.3 69.8 + - - +
145J ILE* 1.3 64.2 + - - +
146J SER* 3.0 3.4 - - - -
147J ASP* 2.9 28.3 + - - +
148J TYR* 4.1 6.8 + - - -
166J LYS* 3.8 22.6 - - - +
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Residues in contact with ILE 145 (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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250I ILE* 4.8 4.7 - - + -
80J TYR 3.7 13.0 - - - +
81J ALA* 3.9 19.3 - - - +
83J PHE* 4.7 11.9 - - + -
86J HIS* 3.7 27.4 - - + +
121J GLY* 3.9 11.7 - - - +
122J THR* 4.1 21.1 - - + +
141J GLU* 3.6 25.8 - - + -
143J SER* 3.0 12.3 + - - -
144J SER* 1.3 79.6 + - - +
146J SER* 1.3 64.4 + - - +
148J TYR* 2.9 33.0 + - + +
149J SER* 3.0 9.7 + - - -
401J SAH 4.4 0.4 - - - +
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Residues in contact with SER 146 (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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141J GLU* 4.0 19.7 - - - -
143J SER 2.7 21.3 + - - -
144J SER 3.7 0.2 - - - -
145J ILE* 1.3 83.0 - - - +
147J ASP* 1.3 56.5 + - - -
149J SER* 2.8 35.6 + - - -
150J GLU* 2.9 12.7 + - - +
164J ILE* 4.2 12.3 - - - -
166J LYS* 2.9 35.5 - - - +
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Residues in contact with ASP 147 (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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144J SER* 2.9 21.7 + - - +
146J SER* 1.3 79.0 + - - +
148J TYR* 1.3 68.7 + - + +
150J GLU* 3.5 13.7 + - - +
151J LYS* 3.4 32.7 + - - +
166J LYS* 3.2 31.7 + - - +
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Residues in contact with TYR 148 (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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249I CYS* 3.9 25.4 - - + -
250I ILE* 4.1 26.9 - - + -
253I VAL* 3.3 39.2 - - + +
81J ALA 5.4 5.4 - - - -
144J SER 4.3 9.4 - - - -
145J ILE* 2.9 24.4 + - + +
147J ASP* 1.3 78.1 - - + +
149J SER* 1.3 60.1 + - - +
150J GLU 3.1 1.8 - - - -
151J LYS* 3.1 23.5 + - + +
152J ILE* 2.8 36.2 + - + +
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Residues in contact with SER 149 (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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120J SER* 4.0 0.9 + - - -
121J GLY 3.2 24.6 + - - -
122J THR* 3.3 22.7 + - - +
123J GLY* 3.9 6.5 - - - -
145J ILE 3.0 5.2 + - - -
146J SER* 2.8 28.6 + - - -
148J TYR* 1.3 72.0 - - - +
150J GLU* 1.3 54.9 + - - -
152J ILE* 3.7 1.0 - - - +
153J ILE* 2.9 39.5 + - - +
164J ILE* 3.6 20.8 - - - +
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Residues in contact with GLU 150 (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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146J SER* 2.9 14.2 + - - +
147J ASP* 3.6 15.7 - - - +
148J TYR 3.1 0.2 - - - -
149J SER* 1.3 77.2 + - - +
151J LYS* 1.3 63.0 + - + +
153J ILE* 3.4 6.7 + - - +
154J LYS* 3.1 23.9 + - - +
159J ASP* 5.7 0.5 - - - +
164J ILE* 4.0 34.9 + - + +
166J LYS* 6.1 3.1 - - - +
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Residues in contact with LYS 151 (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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249I CYS* 4.0 27.6 - - + -
147J ASP* 3.4 20.0 + - - +
148J TYR* 3.1 27.4 + - + +
150J GLU* 1.3 77.2 - - + +
152J ILE* 1.3 58.2 + - - +
154J LYS* 3.4 6.0 + - - +
155J ALA* 2.9 29.9 + - - +
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Residues in contact with ILE 152 (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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246I ASP 3.6 8.3 - - - +
247I MET* 4.0 25.1 - - + +
249I CYS* 3.8 17.0 - - - -
250I ILE* 3.8 28.7 - - + -
122J THR* 3.7 20.6 - - + +
127J MET* 3.8 22.2 - - + -
148J TYR* 2.8 27.6 + - + +
149J SER* 3.7 4.7 - - - +
151J LYS* 1.3 72.3 - - - +
153J ILE* 1.3 60.9 + - + +
155J ALA* 2.9 15.2 + - - +
156J ASN* 2.5 37.0 + - - +
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Residues in contact with ILE 153 (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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123J GLY* 4.8 8.1 - - - +
126J SER* 5.3 0.2 - - - -
127J MET* 4.1 18.2 - - + -
149J SER* 2.9 26.0 + - - +
150J GLU* 3.8 4.3 - - - +
152J ILE* 1.3 75.1 - - + +
154J LYS* 1.3 64.5 + - - +
156J ASN* 2.9 13.2 + - - +
157J HIS 3.2 9.2 + - - -
158J LEU* 3.2 42.0 + - + +
159J ASP* 3.5 9.9 - - + +
162J ILE* 3.6 40.2 - - + +
164J ILE* 3.8 23.3 - - + -
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Residues in contact with LYS 154 (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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150J GLU 3.1 17.1 + - - +
151J LYS* 3.7 7.0 - - - +
153J ILE* 1.3 78.7 - - - +
155J ALA* 1.3 62.1 + - - +
157J HIS* 3.0 20.1 + - - -
159J ASP* 3.4 35.3 - - + +
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Residues in contact with ALA 155 (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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246I ASP* 4.0 25.8 - - + +
249I CYS* 6.5 0.7 - - + -
151J LYS 2.9 15.3 + - - +
152J ILE* 2.9 14.1 + - - +
154J LYS* 1.3 77.2 - - - +
156J ASN* 1.3 58.8 + - - +
157J HIS* 3.6 16.7 + - - -
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Residues in contact with ASN 156 (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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244I GLY 4.6 0.7 - - - +
245I PHE* 3.3 26.2 - - + +
246I ASP* 2.7 46.9 + - - +
127J MET* 3.8 8.2 - - - -
131J LYS* 5.4 4.0 + - - -
152J ILE* 2.5 36.0 + - - +
153J ILE 2.9 6.8 + - - +
155J ALA* 1.3 75.6 - - - +
157J HIS* 1.3 74.2 + - - +
158J LEU* 3.3 14.1 + - + +
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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