Contacts of the helix formed by residues 135 - 150 (chain B) in PDB entry 2IOY
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 ALA 135 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B VAL 5.1 0.2 - - - -
90B ARG* 3.5 42.4 - - + +
132B ILE* 2.9 17.6 + - + +
133B PRO 3.1 0.2 - - - -
134B GLY* 1.3 78.2 - - - +
136B SER* 1.3 65.2 + - - +
137B ALA* 4.9 0.2 - - + -
138B ALA* 3.1 14.3 + - - +
139B ARG* 3.2 16.7 + - - +
165B PHE* 3.9 14.4 - - + -
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Residues in contact with SER 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B SER* 3.9 5.2 + - - -
89B ASP 4.5 0.7 + - - -
90B ARG* 3.3 9.8 - - - +
91B SER* 2.9 43.8 + - - -
100B HIS* 5.3 0.7 + - - -
105B ASN* 5.7 0.3 + - - -
135B ALA* 1.3 69.3 - - - +
137B ALA* 1.3 58.6 + - - +
138B ALA 3.3 0.2 + - - -
139B ARG* 3.3 27.0 + - - +
140B ASP* 2.9 45.5 + - - +
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Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ASP 4.1 8.1 - - - +
90B ARG* 4.4 2.6 - - + +
105B ASN* 3.5 29.1 - - - +
135B ALA* 3.1 1.2 - - + +
136B SER* 1.3 82.0 + - - +
138B ALA* 1.3 56.3 + - - +
141B ARG* 3.1 51.4 + - - +
165B PHE* 4.7 0.4 - - + -
402B RIP 3.4 28.0 - - - +
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Residues in contact with ALA 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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130B GLU* 5.9 0.2 - - + -
131B GLY* 3.8 8.5 - - - +
132B ILE 3.2 27.4 - - - +
133B PRO* 4.9 1.6 - - + -
135B ALA 3.1 2.5 + - - +
137B ALA* 1.3 77.3 - - - +
139B ARG* 1.3 65.9 + - - +
141B ARG* 3.3 2.5 + - - +
142B GLY* 3.0 18.7 + - - -
165B PHE* 3.6 21.4 - - + -
190B GLN* 3.2 28.0 + - - +
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Residues in contact with ARG 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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68B SER* 3.0 35.5 + - - -
91B SER* 5.1 0.6 + - - -
93B ASN* 4.5 11.6 + - - +
133B PRO* 3.0 38.1 + - + +
134B GLY* 3.4 11.9 - - - -
135B ALA 3.2 4.7 + - - +
136B SER* 3.5 24.3 - - - +
138B ALA* 1.3 75.9 - - - +
140B ASP* 1.3 60.1 + - - +
142B GLY* 3.3 1.7 + - - -
143B LYS* 3.0 52.2 + - - +
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Residues in contact with ASP 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ASN* 3.6 23.9 + - + +
106B VAL* 3.4 35.3 + - + +
136B SER* 2.9 31.9 + - - +
137B ALA* 4.8 0.2 - - - -
139B ARG* 1.3 76.0 + - - +
141B ARG* 1.3 65.1 + - - +
143B LYS* 3.3 14.8 + - - +
144B GLY 3.0 19.6 + - - -
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Residues in contact with ARG 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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105B ASN* 2.8 46.3 + - + +
109B GLY* 3.5 8.6 - - - +
128B GLU* 4.6 0.2 - - - -
137B ALA* 3.1 26.7 + - - +
138B ALA* 3.3 4.7 + - - +
140B ASP* 1.3 75.5 - - - +
142B GLY* 1.3 58.2 + - - +
144B GLY 3.5 0.2 + - - -
145B PHE* 2.9 30.9 + - - +
165B PHE* 3.7 14.1 - - - -
188B PHE* 4.4 2.8 - - + -
190B GLN* 2.9 49.3 + - + -
215B PHE* 3.3 32.1 - - + -
236B GLN* 3.1 13.5 + - - +
402B RIP 2.8 43.0 + - - -
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Residues in contact with GLY 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B GLU* 3.5 11.9 - - - +
130B GLU* 5.5 3.1 - - - -
138B ALA 3.0 12.0 + - - -
139B ARG* 3.8 3.1 - - - -
141B ARG* 1.3 77.0 - - - +
143B LYS* 1.3 57.5 + - - +
145B PHE* 3.4 1.0 + - - +
146B ASP* 2.9 35.3 + - - +
190B GLN* 3.4 18.1 - - - +
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Residues in contact with LYS 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B VAL* 4.9 9.2 - - + -
139B ARG* 3.0 41.3 + - - +
140B ASP* 3.6 18.6 + - - +
142B GLY* 1.3 76.5 - - - +
144B GLY* 1.3 56.3 + - - +
146B ASP* 3.7 5.4 - - - +
147B GLU* 2.9 31.2 + - - +
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Residues in contact with GLY 144 (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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106B VAL* 3.4 31.7 - - - +
110B GLU* 3.4 23.1 - - - +
140B ASP 3.0 11.1 + - - -
141B ARG 3.9 0.7 - - - -
143B LYS* 1.3 72.1 - - - +
145B PHE* 1.3 65.9 + - - +
147B GLU* 3.3 3.6 + - - +
148B ALA* 3.1 21.0 + - - +
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Residues in contact with PHE 145 (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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109B GLY 3.3 15.5 - - - +
113B ALA* 3.5 31.9 - - + +
116B ILE* 4.0 8.1 - - + -
126B VAL* 3.8 22.2 - - + -
128B GLU* 3.6 28.0 - - + +
141B ARG 2.9 19.9 + - - +
142B GLY 3.7 3.4 - - - +
144B GLY* 1.3 77.3 - - - +
146B ASP* 1.3 63.4 + - - +
149B ILE* 3.0 46.7 + - + +
157B ILE* 3.9 19.1 - - + -
188B PHE* 3.3 42.8 - + + -
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Residues in contact with ASP 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B GLU* 4.8 4.9 - - - +
142B GLY 2.9 19.7 + - - +
143B LYS* 3.7 5.4 - - - +
145B PHE* 1.3 75.8 - - - +
147B GLU* 1.3 64.3 + - - +
149B ILE* 4.0 2.6 - - - +
150B ALA* 2.9 28.3 + - - +
157B ILE* 3.4 25.6 - - - +
160B LYS* 5.0 10.5 - - - +
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Residues in contact with GLU 147 (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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106B VAL* 4.3 11.8 - - - +
110B GLU* 3.5 27.2 - - - +
143B LYS 2.9 16.7 + - - +
144B GLY* 3.3 4.1 + - - +
146B ASP* 1.3 78.7 - - - +
148B ALA* 1.3 61.9 + - - +
150B ALA* 3.7 13.6 - - - +
151B LYS* 3.8 22.3 + - - +
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Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B GLU* 4.0 19.3 - - + +
113B ALA* 3.6 22.0 - - + -
114B GLU* 3.7 16.8 - - + +
144B GLY 3.1 10.2 + - - +
147B GLU* 1.3 80.1 - - - +
149B ILE* 1.3 63.5 + - - +
150B ALA 3.2 0.2 - - - -
151B LYS* 3.3 31.4 + - - +
152B TYR* 3.5 12.6 - - - -
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Residues in contact with ILE 149 (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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113B ALA* 3.7 32.1 - - + +
116B ILE* 4.7 6.3 - - + -
117B ALA* 4.7 2.0 - - + -
126B VAL* 5.2 0.7 - - + -
145B PHE* 3.0 45.4 + - + +
146B ASP* 4.0 4.3 - - - +
148B ALA* 1.3 73.6 - - - +
150B ALA* 1.3 61.1 + - - +
152B TYR* 2.9 31.4 + - - +
155B ILE* 3.7 47.1 - - + +
157B ILE* 4.2 19.5 - - + -
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Residues in contact with ALA 150 (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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146B ASP 2.9 19.3 + - - +
147B GLU* 3.7 10.1 - - - +
148B ALA 3.2 0.2 - - - -
149B ILE* 1.3 78.6 - - - +
151B LYS* 1.3 59.0 + - - +
152B TYR 3.1 5.4 + - - -
153B PRO* 4.3 5.9 - - - +
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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
------------------------------------------------------------
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