Contacts of the helix formed by residues 131 - 143 (chain B) in PDB entry 3IO6
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 GLU 131 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126B PRO* 3.6 18.4 - - + +
127B LYS* 2.8 28.9 + - - +
128B THR* 3.1 29.9 + - - +
130B GLU* 1.3 75.5 - - - +
132B ILE* 1.3 59.0 + - - +
133B PRO 3.4 1.6 - - - -
134B ALA* 3.5 11.5 + - + +
135B LEU* 3.0 28.0 + - + +
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Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B LEU* 6.2 0.2 - - + -
126B PRO* 4.1 15.7 - - + -
128B THR 3.9 9.4 - - - +
129B TRP* 3.1 46.4 + - + +
131B GLU* 1.3 76.4 - - - +
133B PRO* 1.4 63.6 - - + +
135B LEU* 3.8 4.6 - - - +
136B ASP* 3.0 28.1 + - + +
146B ALA* 4.2 18.2 - - + -
147B LEU* 4.2 24.9 - - + -
198B LEU* 5.1 11.7 - - + -
203B HIS* 5.3 1.7 - - + -
224B MET* 4.3 10.1 - - + -
248B PRO* 4.3 13.0 - - + -
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Residues in contact with PRO 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B TRP 3.5 9.4 - - - +
130B GLU* 3.2 19.7 - - - +
132B ILE* 1.4 90.0 - - + +
134B ALA* 1.3 63.8 + - - +
136B ASP* 3.0 13.9 + - - +
137B LYS* 3.3 27.2 + - - +
194B PHE* 4.3 9.2 - - + -
198B LEU* 3.9 19.7 - - + -
201B ASN* 5.8 0.2 - - - +
203B HIS* 3.7 25.3 + - + +
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Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLU 4.8 0.9 + - - +
131B GLU* 3.5 15.1 + - + +
133B PRO* 1.3 80.1 - - - +
135B LEU* 1.3 60.0 + - - +
136B ASP 3.7 0.2 + - - -
137B LYS* 3.7 22.5 - - - +
138B GLU* 3.9 15.1 + - - +
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B LEU* 3.7 33.0 - - + -
124B ASN 5.6 0.2 - - - +
126B PRO* 3.8 39.5 - - + -
131B GLU* 3.0 17.2 + - + +
132B ILE* 3.9 6.3 - - - +
133B PRO 3.1 0.2 - - - -
134B ALA* 1.3 75.2 - - - +
136B ASP* 1.3 63.5 + - - +
138B GLU* 3.4 20.9 - - - +
139B LEU* 3.3 35.5 + - + +
146B ALA* 4.2 3.4 - - + -
224B MET* 4.3 6.5 - - + -
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Residues in contact with ASP 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ILE* 3.0 19.1 + - + +
133B PRO 3.0 5.3 + - - +
135B LEU* 1.3 77.2 - - - +
137B LYS* 1.3 52.4 + - - +
139B LEU* 3.1 4.5 + - - +
140B LYS* 2.8 63.0 + - - +
145B SER* 3.6 8.3 - - - -
146B ALA* 2.6 40.4 + - + +
147B LEU 4.3 0.9 + - - -
203B HIS* 3.2 39.7 - - + +
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Residues in contact with LYS 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B PRO* 3.3 30.5 + - - +
134B ALA* 3.7 14.8 - - - +
136B ASP* 1.3 71.6 - - - +
138B GLU* 1.3 63.6 + - - +
140B LYS* 3.9 12.0 - - + +
141B ALA* 3.5 18.9 + - - +
203B HIS* 4.3 5.1 - - + +
450B ZN 2.8 31.2 - - - -
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Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ALA 3.9 12.9 + - - +
135B LEU* 3.4 28.4 + - + +
136B ASP 3.1 0.4 - - - -
137B LYS* 1.3 79.5 - - - +
139B LEU* 1.3 62.3 + - + +
141B ALA* 3.3 20.6 - - - +
142B LYS* 3.8 5.9 + - - +
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B LEU* 4.0 33.9 - - + +
122B LEU* 5.0 1.8 - - + -
135B LEU* 3.3 32.5 + - + +
136B ASP 3.1 6.1 + - - +
138B GLU* 1.3 76.1 - - + +
140B LYS* 1.3 61.8 + - - +
141B ALA 3.1 2.2 - - - -
142B LYS* 3.1 12.3 + - + +
143B GLY 3.1 6.1 + - - -
144B LYS* 2.8 47.3 + - + +
145B SER 3.8 4.7 - - - +
146B ALA* 3.5 28.0 - - + -
223B ALA* 3.9 12.3 - - + -
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Residues in contact with LYS 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ASP* 2.8 50.0 + - - +
137B LYS* 3.9 11.2 - - + +
138B GLU 3.3 0.2 - - - -
139B LEU* 1.3 77.0 - - - +
141B ALA* 1.3 60.1 + - - +
143B GLY* 3.4 10.4 + - - -
144B LYS 3.1 12.5 + - - +
145B SER* 3.8 26.9 - - - -
202B LYS 3.5 20.0 + - - -
203B HIS* 4.0 6.4 + - + -
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Residues in contact with ALA 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B LYS 3.5 11.1 + - - +
138B GLU* 3.3 15.4 + - - +
139B LEU 3.1 0.4 - - - -
140B LYS* 1.3 79.9 - - - +
142B LYS* 1.3 59.1 + - + +
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Residues in contact with LYS 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B LEU* 6.1 4.0 - - + -
138B GLU 3.8 4.4 + - - +
139B LEU* 3.1 17.2 + - + +
141B ALA* 1.3 79.5 + - + +
143B GLY* 1.3 58.6 + - - +
144B LYS* 4.5 16.8 - - + +
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Residues in contact with GLY 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B LEU 3.1 1.6 + - - -
140B LYS* 3.4 9.7 + - - -
141B ALA 3.4 3.6 + - - -
142B LYS* 1.3 79.3 - - - +
144B LYS* 1.3 73.7 + - - +
221B GLU* 4.7 1.4 - - - +
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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