Contacts of the helix formed by residues 144 - 156 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81L ALA* 3.3 22.2 - - - +
142L CYS 3.9 0.4 + - - -
143L SER* 1.3 69.9 + - - +
145L ILE* 1.3 63.8 + - - +
146L SER* 3.0 3.6 + - - -
147L ASP* 3.2 25.8 + - - +
148L TYR* 4.1 8.1 - - - -
166L LYS* 3.9 22.4 - - - +
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Residues in contact with ILE 145 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250K ILE* 4.7 14.1 - - + -
80L TYR 3.7 13.0 - - - +
81L ALA* 3.9 20.0 - - - +
83L PHE* 4.8 8.3 - - - -
86L HIS* 3.6 28.0 - - + +
121L GLY* 3.9 11.0 - - - +
122L THR* 4.1 13.2 - - + +
141L GLU* 3.6 29.4 - - + -
143L SER* 3.0 10.8 + - - -
144L SER* 1.3 78.6 + - - +
146L SER* 1.3 65.1 + - - +
148L TYR* 3.0 32.8 + - + +
149L SER* 3.0 10.2 + - - -
401L SAH 4.4 0.2 - - - +
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Residues in contact with SER 146 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141L GLU* 4.0 20.0 - - - -
143L SER 2.7 22.2 + - - -
145L ILE* 1.3 79.5 - - - +
147L ASP* 1.3 65.0 + - - +
149L SER* 2.8 26.0 + - - -
150L GLU* 3.0 17.6 + - - +
164L ILE* 4.2 9.4 - - - -
166L LYS* 2.9 35.7 - - - +
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Residues in contact with ASP 147 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144L SER* 3.5 19.7 - - - +
145L ILE 3.2 0.6 - - - -
146L SER* 1.3 76.3 + - - +
148L TYR* 1.3 67.4 + - + +
150L GLU* 3.6 10.2 + - - +
151L LYS* 3.4 31.7 + - - +
166L LYS* 3.1 33.2 + - - +
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Residues in contact with TYR 148 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249K CYS* 4.1 23.1 - - + -
250K ILE* 4.3 23.3 - - + -
253K VAL* 3.2 39.2 - - + +
81L ALA 5.4 4.9 - - - -
122L THR* 6.4 0.2 - - - -
144L SER 4.1 14.8 - - - -
145L ILE* 3.0 21.4 + - + +
147L ASP* 1.3 79.8 - - + +
149L SER* 1.3 59.6 + - - +
150L GLU 3.1 0.4 - - - -
151L LYS* 3.1 23.4 + - + +
152L ILE* 2.8 36.9 + - + +
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Residues in contact with SER 149 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120L SER* 4.2 1.4 + - - -
121L GLY 3.2 24.9 + - - -
122L THR* 3.2 22.8 - - - +
123L GLY* 3.9 5.6 - - - -
145L ILE 3.0 7.2 + - - -
146L SER* 2.8 25.7 + - - -
148L TYR* 1.3 76.0 - - - +
150L GLU* 1.3 56.7 + - - +
152L ILE* 3.5 2.3 - - - +
153L ILE* 2.8 39.8 + - - +
164L ILE* 3.8 17.1 - - - +
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Residues in contact with GLU 150 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146L SER 3.0 16.0 + - - +
147L ASP* 3.8 11.8 - - - +
148L TYR 3.1 0.2 - - - -
149L SER* 1.3 73.4 + - - +
151L LYS* 1.3 66.0 + - + +
153L ILE* 3.8 6.7 - - - +
154L LYS* 3.0 24.3 + - - +
159L ASP* 5.7 0.5 - - - +
164L ILE* 3.8 37.0 + - + +
166L LYS* 6.2 0.8 - - - +
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Residues in contact with LYS 151 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249K CYS* 4.2 24.9 - - + -
147L ASP* 3.4 18.5 + - - +
148L TYR* 3.1 27.2 + - + +
150L GLU* 1.3 78.7 - - + +
152L ILE* 1.3 62.2 + - - +
154L LYS* 3.4 6.2 + - - +
155L ALA* 3.0 23.3 + - - +
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Residues in contact with ILE 152 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246K ASP 3.6 8.5 - - - +
247K MET* 4.1 22.0 - - + -
249K CYS* 3.5 17.9 - - - -
250K ILE* 3.7 29.4 - - + -
122L THR* 3.7 19.3 - - + +
127L MET* 3.9 21.5 - - + -
148L TYR* 2.8 23.8 + - + +
149L SER* 3.5 4.7 - - - +
151L LYS* 1.3 76.3 - - - +
153L ILE* 1.3 60.1 + - + +
155L ALA* 3.0 14.0 + - - +
156L ASN* 2.6 38.7 + - - +
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Residues in contact with ILE 153 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123L GLY* 4.8 8.5 - - - +
127L MET* 4.1 27.1 - - + -
149L SER* 2.8 27.9 + - - +
150L GLU* 3.8 5.6 - - - +
152L ILE* 1.3 73.2 - - + +
154L LYS* 1.3 66.0 + - - +
156L ASN* 3.1 11.3 + - - +
157L HIS 3.3 0.2 + - - -
158L LEU* 3.3 45.7 + - + +
159L ASP* 3.5 9.4 - - + +
162L ILE* 3.6 33.0 - - + +
164L ILE* 3.7 24.0 - - + -
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Residues in contact with LYS 154 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150L GLU 3.0 17.3 + - - +
151L LYS* 3.6 6.7 - - - +
153L ILE* 1.3 78.4 - - - +
155L ALA* 1.3 64.0 + - - +
157L HIS* 3.0 20.6 + - - -
159L ASP* 3.4 34.3 - - + +
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Residues in contact with ALA 155 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246K ASP* 4.3 21.8 - - - +
249K CYS* 6.4 1.6 - - + -
151L LYS 3.0 14.7 + - - +
152L ILE* 3.0 13.6 + - - +
154L LYS* 1.3 76.4 - - - +
156L ASN* 1.3 62.2 + - - +
157L HIS* 3.4 17.3 + - - -
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Residues in contact with ASN 156 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244K GLY 4.9 0.5 - - - +
245K PHE* 3.6 23.6 - - + +
246K ASP* 2.8 48.6 + - - +
127L MET* 3.8 9.7 - - - -
131L LYS* 5.4 4.3 + - - -
152L ILE* 2.6 35.2 + - - +
153L ILE 3.1 5.6 + - - +
154L LYS 3.1 1.2 - - - -
155L ALA* 1.3 76.2 - - - +
157L HIS* 1.3 76.3 + - - +
158L LEU* 3.4 13.1 - - + +
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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