Contacts of the helix formed by residues 133 - 142 (chain B) in PDB entry 1ADI
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 ILE 133 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B GLY* 4.5 2.9 - - - -
36B GLY* 3.6 29.4 - - - +
37B HIS* 3.6 14.8 - - + +
38B ASN* 3.9 20.2 - - - +
73B VAL* 3.8 22.7 - - + +
106B ILE* 4.6 3.8 - - - +
114B ASP* 4.2 1.5 + - - +
130B GLY* 3.2 38.4 - - - +
131B ARG 3.2 2.9 + - - +
132B GLY* 1.3 79.0 - - - +
134B GLY* 1.3 63.0 + - - +
136B ALA* 3.0 16.5 + - - +
137B TYR* 3.5 12.6 + - + -
239B THR* 6.1 0.4 - - - +
240B SER* 4.0 12.8 - - - +
241B SER* 5.8 0.9 - - - +
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Residues in contact with GLY 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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141A VAL* 5.3 1.3 - - - -
143A ARG* 5.3 3.4 - - - -
114B ASP* 4.6 2.0 + - - -
132B GLY 3.3 1.0 - - - -
133B ILE* 1.3 79.5 - - - +
135B PRO* 1.3 60.6 - - - +
137B TYR* 2.7 27.1 + - - +
138B GLU* 3.0 18.6 + - - +
240B SER* 3.8 23.6 + - - -
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Residues in contact with PRO 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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110B HIS* 3.2 43.5 + - + +
113B LEU* 3.7 29.6 - - + -
114B ASP* 3.7 24.9 - - + +
117B ARG* 4.1 12.3 - - - +
132B GLY* 3.4 12.3 - - - +
134B GLY* 1.3 84.5 - - - +
136B ALA* 1.3 57.9 + - - -
138B GLU* 3.8 14.7 - - + +
139B ASP* 3.3 18.7 + - - +
168B HIS* 5.2 0.5 + - - -
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Residues in contact with ALA 136 (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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73B VAL* 3.9 18.8 - - + -
104B PRO* 4.6 6.6 - - + +
105B LEU 4.3 12.1 - - - +
106B ILE* 4.1 15.5 - - + -
110B HIS* 3.8 13.0 - - + +
132B GLY 3.2 9.0 + - - +
133B ILE 3.0 12.5 + - - +
134B GLY 2.8 2.8 + - - -
135B PRO* 1.3 74.2 - - - +
137B TYR* 1.3 63.5 + - - +
139B ASP* 3.5 2.1 + - - +
140B LYS* 2.9 28.4 + - - +
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Residues in contact with TYR 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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141A VAL* 3.3 24.7 - - + -
34B GLN* 4.4 0.5 - - - -
35B GLY 3.4 18.2 + - - -
71B GLY* 2.6 28.0 + - - -
73B VAL* 3.7 28.9 - - + -
104B PRO* 5.5 2.0 - - + -
133B ILE* 3.5 17.0 + - + -
134B GLY 2.7 10.6 + - - +
136B ALA* 1.3 71.3 - - - +
138B GLU* 1.3 68.9 - - - +
140B LYS* 2.9 30.9 + - + +
141B VAL* 3.0 18.7 + - + +
240B SER* 3.5 28.7 - - - -
241B SER* 3.7 25.0 - - - -
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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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138A GLU* 3.7 25.0 - - + +
141A VAL* 3.6 18.1 - - + +
142A ALA* 3.1 25.6 - - + +
144A ARG* 3.6 12.0 + - - -
113B LEU* 5.7 1.0 - - - +
117B ARG* 2.6 43.9 + - - -
134B GLY* 3.0 15.1 + - - +
135B PRO* 3.8 12.5 - - + +
137B TYR* 1.3 79.9 - - - +
139B ASP* 1.3 62.8 + - - +
141B VAL* 2.8 14.0 + - - +
142B ALA* 2.9 16.6 + - - +
144B ARG* 5.1 1.1 + - - +
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Residues in contact with ASP 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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109B TYR* 4.0 1.2 + - - -
110B HIS* 2.8 21.6 + - + +
135B PRO 3.3 17.7 + - - +
136B ALA* 3.8 4.7 - - - +
137B TYR 3.3 0.6 - - - -
138B GLU* 1.3 77.8 - - - +
140B LYS* 1.3 56.8 + - - +
142B ALA 3.8 0.3 + - - -
143B ARG 3.4 1.7 + - - -
144B ARG* 2.5 55.5 + - - +
145B GLY* 2.9 33.2 + - - -
164B VAL* 3.9 5.8 - - - +
168B HIS* 2.7 32.3 + - - -
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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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230A ILE* 3.7 30.7 - - + +
231A ASP* 3.0 38.5 + - - +
235A TYR* 6.1 2.2 - - + -
242A ASN* 4.8 3.8 + - - -
102B ALA 5.5 0.4 - - - +
104B PRO* 3.7 31.0 - - + -
136B ALA 2.9 13.5 + - - +
137B TYR* 2.9 24.5 + - + +
139B ASP* 1.3 76.2 - - - +
141B VAL* 1.3 78.0 + - - +
143B ARG* 3.5 10.7 + - - +
145B GLY* 4.8 5.4 - - - +
147B ARG* 6.4 2.7 - - + -
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Residues in contact with VAL 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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134A GLY* 4.4 11.8 - - - +
137A TYR* 3.9 16.9 - - + +
138A GLU* 3.7 33.9 - - - +
141A VAL* 4.3 16.8 - - + -
230A ILE* 3.9 15.6 - - + +
240A SER* 4.4 6.8 - - - +
137B TYR* 3.2 18.6 - - + +
138B GLU* 2.8 8.6 + - - +
140B LYS* 1.3 87.1 - - - +
142B ALA* 1.3 62.5 + - - +
143B ARG* 3.0 15.4 + - - +
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Residues in contact with ALA 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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117A ARG* 4.0 8.9 + - - +
134A GLY* 4.9 8.1 - - - +
138A GLU* 2.9 32.3 - - + +
138B GLU 2.9 11.9 + - - +
139B ASP 4.4 1.1 - - - +
141B VAL* 1.3 76.1 - - - +
143B ARG* 1.3 66.6 + - - +
144B ARG* 3.1 26.9 + - - +
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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
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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