Contacts of the helix formed by residues 144 - 156 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81O ALA* 3.1 23.7 + - - +
142O CYS 4.0 0.8 + - - -
143O SER* 1.3 70.0 + - - +
145O ILE* 1.3 64.9 + - - +
146O SER* 3.0 3.2 + - - -
147O ASP* 3.2 25.2 + - - +
148O TYR* 4.1 7.9 + - - -
166O LYS* 3.9 21.3 - - - +
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Residues in contact with ILE 145 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80O TYR 3.6 13.5 - - - +
81O ALA* 3.9 18.2 - - - +
83O PHE* 4.7 12.1 - - + -
86O HIS* 3.7 29.8 - - + +
121O GLY* 4.0 11.2 - - - -
122O THR* 4.3 19.3 - - + +
141O GLU* 3.6 29.4 - - + -
143O SER* 3.7 9.2 + - - -
144O SER* 1.3 79.5 + - - +
146O SER* 1.3 64.2 + - - +
148O TYR* 3.0 32.1 + - + +
149O SER* 3.1 10.2 + - - -
401O SAH 4.3 0.2 - - - +
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Residues in contact with SER 146 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121O GLY 4.6 0.2 - - - -
141O GLU* 4.0 20.2 - - - -
143O SER 2.8 14.9 + - - -
144O SER 3.9 0.3 - - - -
145O ILE* 1.3 84.4 - - - +
147O ASP* 1.3 62.1 + - - -
149O SER* 2.6 28.1 + - - -
150O GLU* 3.0 13.5 + - - +
164O ILE* 4.2 11.4 - - - -
166O LYS* 2.8 39.4 - - - +
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Residues in contact with ASP 147 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144O SER* 3.2 18.9 + - - +
146O SER* 1.3 82.4 + - - +
148O TYR* 1.3 66.1 + - + +
150O GLU* 3.6 13.3 + - - +
151O LYS* 3.5 31.5 + - - +
166O LYS* 3.1 35.0 + - - +
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Residues in contact with TYR 148 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81O ALA 5.4 5.2 - - - -
122O THR* 6.4 0.7 - - + -
144O SER 4.2 13.9 - - - -
145O ILE* 3.0 25.3 + - + +
147O ASP* 1.3 78.4 - - + +
149O SER* 1.3 59.2 + - - +
150O GLU 3.2 1.6 - - - -
151O LYS* 3.3 27.3 + - + +
152O ILE* 2.8 46.3 + - + +
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Residues in contact with SER 149 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120O SER* 4.3 1.0 + - - -
121O GLY 3.2 18.9 + - - -
122O THR* 3.1 29.0 + - - +
123O GLY* 3.9 6.3 - - - -
145O ILE 3.1 6.4 + - - -
146O SER* 2.6 25.7 + - - -
148O TYR* 1.3 74.4 - - - +
150O GLU* 1.3 55.7 + - - +
152O ILE* 3.6 1.4 - - - +
153O ILE* 2.9 40.5 + - - +
164O ILE* 3.7 18.3 - - - +
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Residues in contact with GLU 150 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146O SER 3.0 15.4 + - - +
147O ASP* 3.8 14.5 - - - +
148O TYR 3.2 0.4 - - - -
149O SER* 1.3 74.7 + - - +
151O LYS* 1.3 66.1 + - + +
153O ILE* 3.5 6.7 + - - +
154O LYS* 3.0 24.4 + - - +
159O ASP* 5.7 0.9 - - - +
164O ILE* 3.9 35.7 + - + +
166O LYS* 6.1 2.8 - - - +
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Residues in contact with LYS 151 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147O ASP* 3.5 20.1 + - - +
148O TYR* 3.3 31.6 + - + +
150O GLU* 1.3 77.7 - - + +
152O ILE* 1.3 58.3 + - + +
154O LYS* 3.3 6.8 + - - +
155O ALA* 2.9 30.6 + - - +
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Residues in contact with ILE 152 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122O THR* 3.7 33.4 - - + +
127O MET* 3.9 22.4 - - + -
148O TYR* 2.8 40.5 + - + +
149O SER 3.6 3.6 - - - +
151O LYS* 1.3 73.7 - - + +
153O ILE* 1.3 61.0 + - - +
155O ALA* 3.1 12.3 + - - +
156O ASN* 2.4 39.9 + - - +
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Residues in contact with ILE 153 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123O GLY* 4.8 8.5 - - - +
127O MET* 4.1 25.8 - - + -
149O SER* 2.9 29.5 + - - +
150O GLU* 4.0 4.7 - - - +
152O ILE* 1.3 74.8 - - + +
154O LYS* 1.3 64.5 + - - +
156O ASN* 3.0 13.5 + - - +
157O HIS 3.3 7.4 + - - -
158O LEU* 3.3 39.6 + - + +
159O ASP* 3.5 9.6 - - + +
162O ILE* 3.6 32.3 - - + +
164O ILE* 3.7 23.8 - - + -
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Residues in contact with LYS 154 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150O GLU 3.0 18.5 + - - +
151O LYS* 3.6 7.0 - - - +
153O ILE* 1.3 77.2 - - - +
155O ALA* 1.3 63.0 + - - +
157O HIS* 3.0 20.4 + - - -
159O ASP* 3.8 33.9 - - + +
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Residues in contact with ALA 155 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151O LYS 2.9 14.0 + - - +
152O ILE* 3.4 13.0 - - - +
154O LYS* 1.3 78.2 - - - +
156O ASN* 1.3 61.4 + - - +
157O HIS* 3.4 16.4 + - - -
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Residues in contact with ASN 156 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127O MET* 3.9 18.4 - - - +
131O LYS* 5.4 4.3 + - - -
152O ILE* 2.4 45.9 + - - +
153O ILE 3.0 6.8 + - - +
155O ALA* 1.3 82.0 - - - +
157O HIS* 1.3 75.4 + - - +
158O LEU* 3.4 17.6 + - + +
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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