Contacts of the helix formed by residues 152 - 164 (chain Q) in PDB entry 5I2D
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 ASP 152 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141Q VAL* 5.3 1.6 - - - -
150Q THR* 3.0 23.4 + - - +
151Q LEU* 1.3 75.4 - - - +
153Q PRO* 1.3 73.1 - - + +
154Q LYS* 3.1 34.4 - - - +
155Q THR* 2.8 38.6 + - - -
156Q VAL* 3.0 15.4 + - - +
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Residues in contact with PRO 153 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141Q VAL* 4.3 26.6 - - + -
152Q ASP* 1.3 86.7 - - + +
154Q LYS* 1.3 56.4 + - - +
156Q VAL* 3.2 15.1 - - + +
157Q GLU* 2.9 36.5 + - + +
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Residues in contact with LYS 154 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152Q ASP* 3.0 14.3 + - - +
153Q PRO* 1.3 79.5 - - - +
155Q THR* 1.3 59.0 + - - +
157Q GLU* 3.2 8.1 + - - +
158Q GLU* 2.9 47.4 + - + +
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Residues in contact with THR 155 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126Q LEU* 4.8 9.6 - - + -
149Q GLU* 4.4 17.7 - - + +
150Q THR 3.6 13.7 + - - +
151Q LEU* 5.0 3.6 - - + -
152Q ASP* 2.8 33.2 + - - -
154Q LYS* 1.3 71.1 - - - +
156Q VAL* 1.3 62.3 + - - +
158Q GLU* 3.1 15.8 + - - +
159Q ILE* 2.9 45.9 + - + +
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Residues in contact with VAL 156 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130Q VAL* 3.7 26.0 - - + +
133Q ALA* 4.6 20.0 - - + -
134Q LYS* 5.1 7.4 - - + -
141Q VAL* 5.1 8.3 - - + -
151Q LEU* 4.1 28.3 - - + -
152Q ASP 3.0 14.7 + - - +
153Q PRO* 3.2 21.5 - - + +
155Q THR* 1.3 76.2 - - - +
157Q GLU* 1.3 68.6 + - - +
160Q ASP* 2.9 31.2 + - - +
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Residues in contact with GLU 157 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134Q LYS* 3.2 34.7 + - - -
153Q PRO* 2.9 24.1 + - + +
154Q LYS* 3.3 8.3 - - - +
155Q THR 3.1 0.2 - - - -
156Q VAL* 1.3 78.9 - - - +
158Q GLU* 1.3 59.2 + - + +
160Q ASP* 3.4 3.4 + - - +
161Q GLN* 2.9 51.8 + - + +
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Residues in contact with GLU 158 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154Q LYS* 2.9 35.2 + - + +
155Q THR* 3.3 17.6 - - + +
157Q GLU* 1.3 77.4 - - - +
159Q ILE* 1.3 63.8 + - + +
161Q GLN* 3.4 5.3 + - - +
162Q LYS* 2.9 37.6 + - - +
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Residues in contact with ILE 159 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122Q LEU* 4.0 26.5 - - + -
126Q LEU* 3.9 27.4 - - + -
127Q ILE* 5.0 6.3 - - + -
130Q VAL* 3.7 32.8 - - + -
149Q GLU* 5.6 1.6 - - - +
155Q THR* 2.9 29.9 + - + +
158Q GLU* 1.3 78.2 - - + +
160Q ASP* 1.3 61.4 + - - +
162Q LYS* 3.1 17.2 + - - +
163Q LEU* 2.9 40.0 + - + +
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Residues in contact with ASP 160 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130Q VAL* 4.1 10.9 - - + +
131Q VAL* 6.1 0.3 - - - -
134Q LYS* 3.3 30.4 + - - +
156Q VAL 2.9 20.6 + - - +
157Q GLU* 3.9 6.7 - - - +
159Q ILE* 1.3 76.9 - - - +
161Q GLN* 1.3 60.5 + - + +
163Q LEU* 3.5 5.6 + - - +
164Q LYS* 3.1 57.5 + - - +
174Q LEU* 4.7 8.7 - - - +
178Q ARG* 2.8 26.4 + - - -
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Residues in contact with GLN 161 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157Q GLU* 2.9 35.3 + - + +
158Q GLU* 3.7 5.2 - - - +
160Q ASP* 1.3 77.7 + - + +
162Q LYS* 1.3 62.2 + - - +
164Q LYS* 3.5 21.6 + - - +
165Q SER* 2.8 28.8 + - - -
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Residues in contact with LYS 162 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120Q THR* 4.6 17.3 - - + +
122Q LEU* 4.3 25.1 - - + +
158Q GLU* 2.9 23.6 + - - +
159Q ILE* 3.1 22.1 + - + +
161Q GLN* 1.3 76.3 - - - +
163Q LEU* 1.3 63.4 + - + +
165Q SER* 3.4 17.8 + - - -
166Q LEU* 4.0 10.0 + - - +
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Residues in contact with LEU 163 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116Q LEU* 4.2 27.8 - - + -
120Q THR* 4.3 21.5 - - + +
122Q LEU* 6.0 2.0 - - + -
127Q ILE* 4.2 26.9 - - + -
130Q VAL* 5.0 4.3 - - + -
131Q VAL* 4.8 5.2 - - + -
159Q ILE* 2.9 33.0 + - + +
160Q ASP* 3.8 9.2 - - - +
162Q LYS* 1.3 77.3 - - + +
164Q LYS* 1.3 59.6 + - - +
165Q SER 3.1 2.2 - - - -
166Q LEU* 3.3 25.6 - - + +
171Q LYS* 4.3 8.3 - - - +
174Q LEU* 3.7 34.8 - - + +
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Residues in contact with LYS 164 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408O GLU* 3.7 23.1 + - - +
409O VAL* 4.5 3.8 - - - +
410O SER* 4.5 9.0 - - - -
413O ASP* 3.1 27.9 + - - -
134Q LYS* 5.3 1.8 - - - +
160Q ASP* 3.1 43.2 + - - +
161Q GLN* 3.5 24.3 + - - +
162Q LYS 3.3 0.2 - - - -
163Q LEU* 1.3 72.1 - - - +
165Q SER* 1.3 58.1 + - - +
166Q LEU 3.2 8.7 + - - +
171Q LYS* 3.4 33.1 + - - +
174Q LEU* 4.0 12.3 - - + -
178Q ARG* 4.4 4.5 - - - +
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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