Contacts of the helix formed by residues 144 - 156 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81M ALA* 3.3 23.0 + - - +
142M CYS 4.0 0.4 + - - -
143M SER* 1.3 70.6 + - - +
145M ILE* 1.3 61.4 + - - +
146M SER* 2.9 10.3 - - - -
147M ASP* 2.9 28.9 + - - +
148M TYR* 4.1 7.1 + - - -
166M LYS* 3.9 19.2 - - - +
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Residues in contact with ILE 145 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80M TYR 3.7 13.2 - - - +
81M ALA* 3.7 19.3 - - - +
83M PHE* 4.7 11.0 - - + -
86M HIS* 3.7 28.3 - - + +
121M GLY* 4.1 10.1 - - - -
122M THR* 4.1 14.6 - - + +
141M GLU* 3.6 29.2 - - + -
143M SER* 3.7 9.7 + - - -
144M SER* 1.3 79.2 + - - +
146M SER* 1.3 64.1 + - - +
148M TYR* 3.0 33.1 + - + +
149M SER* 3.1 10.9 + - - -
250N ILE* 4.8 11.0 - - + -
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Residues in contact with SER 146 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141M GLU* 4.0 19.7 - - - -
143M SER 2.8 17.7 + - - -
144M SER 3.7 0.7 - - - -
145M ILE* 1.3 82.5 - - - +
147M ASP* 1.3 67.6 + - - +
149M SER* 2.8 27.8 + - - -
150M GLU* 3.0 12.4 + - - +
164M ILE* 4.3 11.2 - - - -
166M LYS* 2.9 35.9 - - - +
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Residues in contact with ASP 147 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144M SER* 2.9 21.2 + - - +
146M SER* 1.3 82.1 + - - +
148M TYR* 1.3 68.6 + - + +
150M GLU* 3.5 11.3 + - - +
151M LYS* 3.4 31.1 + - - +
166M LYS* 3.1 33.0 + - - +
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Residues in contact with TYR 148 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81M ALA 5.3 5.2 - - - -
144M SER 4.2 13.5 - - - -
145M ILE* 3.0 22.2 + - + +
147M ASP* 1.3 79.3 - - + +
149M SER* 1.3 54.6 + - - +
151M LYS* 3.0 24.2 + - + +
152M ILE* 2.7 42.9 + - + +
249N CYS* 3.9 24.9 - - + -
250N ILE* 4.3 22.2 - - + -
253N VAL* 3.2 39.9 - - + +
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Residues in contact with SER 149 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120M SER* 4.2 1.0 + - - -
121M GLY 3.2 26.3 + - - -
122M THR* 3.2 21.9 + - - +
123M GLY* 3.9 6.3 - - - -
145M ILE 3.1 6.2 + - - -
146M SER* 2.8 23.5 + - - -
148M TYR* 1.3 73.5 - - - +
150M GLU* 1.3 57.2 + - - +
152M ILE* 3.6 1.6 - - - +
153M ILE* 2.9 40.0 + - - +
164M ILE* 3.6 20.4 - - - +
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Residues in contact with GLU 150 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146M SER 3.0 14.5 + - - +
147M ASP* 3.7 12.1 - - - +
148M TYR 3.1 0.2 - - - -
149M SER* 1.3 74.8 + - - +
151M LYS* 1.3 65.6 + - + +
153M ILE* 3.8 6.8 - - - +
154M LYS* 3.1 24.4 + - - +
159M ASP* 5.7 0.5 - - - +
163M THR* 6.1 0.2 - - - +
164M ILE* 3.8 38.1 + - + +
166M LYS* 6.1 1.6 - - - +
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Residues in contact with LYS 151 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147M ASP* 3.4 18.6 + - - +
148M TYR* 3.0 27.1 + - + +
150M GLU* 1.3 78.5 - - + +
152M ILE* 1.3 64.2 + - - +
154M LYS* 3.3 5.9 + - - +
155M ALA* 3.0 24.1 + - - +
249N CYS* 4.1 25.8 - - + -
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Residues in contact with ILE 152 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122M THR* 3.6 20.0 - - + +
127M MET* 3.8 22.7 - - + -
148M TYR* 2.7 27.8 + - + +
149M SER* 3.6 4.0 - - - +
151M LYS* 1.3 72.5 - - - +
153M ILE* 1.3 61.8 + - + +
155M ALA* 3.0 13.1 + - - +
156M ASN* 2.5 38.0 + - - +
246N ASP 3.7 7.6 - - - +
247N MET* 4.1 23.6 - - + -
249N CYS* 3.6 17.0 - - - -
250N ILE* 3.7 29.4 - - + -
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Residues in contact with ILE 153 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123M GLY* 4.8 7.6 - - - +
126M SER* 5.4 0.2 - - - -
127M MET* 4.2 27.6 - - + -
149M SER* 2.9 26.6 + - - +
150M GLU* 3.8 5.4 - - - +
152M ILE* 1.3 76.2 - - + +
154M LYS* 1.3 64.7 + - - +
156M ASN* 3.2 10.7 + - - +
157M HIS 3.3 0.2 + - - -
158M LEU* 3.2 28.2 + - + +
159M ASP* 3.5 28.7 - - + +
162M ILE* 3.6 33.2 - - + +
164M ILE* 3.8 23.3 - - + -
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Residues in contact with LYS 154 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150M GLU 3.1 18.3 + - - +
151M LYS* 3.7 6.1 - - - +
153M ILE* 1.3 76.5 - - - +
155M ALA* 1.3 63.6 + - - +
157M HIS* 3.0 19.8 + - - -
159M ASP* 3.5 35.6 - - + +
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Residues in contact with ALA 155 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151M LYS 3.0 13.6 + - - +
152M ILE* 3.2 12.8 - - - +
154M LYS* 1.3 77.0 - - - +
156M ASN* 1.3 61.6 + - - +
157M HIS* 3.4 19.6 + - - -
246N ASP* 4.3 20.5 - - + +
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Residues in contact with ASN 156 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127M MET* 4.0 4.5 - - - -
131M LYS* 5.4 4.0 + - - -
152M ILE* 2.5 37.1 + - - +
153M ILE 3.2 4.0 + - - +
154M LYS 3.2 0.4 - - - -
155M ALA* 1.3 76.8 - - - +
157M HIS* 1.3 76.3 + - - +
158M LEU* 3.4 16.8 + - + +
244N GLY 4.6 1.4 - - - +
245N PHE* 3.3 27.6 - - + +
246N ASP* 2.8 47.6 + - - +
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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