Contacts of the helix formed by residues 130 - 139 (chain B) in PDB entry 1ADO
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 LEU 130 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B VAL* 4.0 22.9 - - + -
126B GLY 3.5 14.6 - - - +
127B LEU* 3.1 25.2 + - + +
128B ASP 3.1 1.0 - - - -
129B GLY* 1.3 74.9 - - - +
131B SER* 1.3 60.5 + - - +
133B ARG* 3.2 18.2 + - + +
134B CYS* 2.8 44.9 + - - -
147B TRP* 4.4 3.6 - - + -
173B TYR* 4.1 29.4 - - + +
176B ILE* 3.9 33.2 - - + -
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Residues in contact with SER 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A VAL* 5.5 6.6 - - - +
129B GLY* 5.0 0.3 - - - -
130B LEU* 1.3 76.4 + - - +
132B GLU* 1.3 79.3 + - - +
134B CYS* 3.2 1.6 + - - +
135B ALA* 2.9 25.7 + - - +
176B ILE* 3.4 24.0 - - - +
180B ASN* 3.4 21.5 - - - +
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Residues in contact with GLU 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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113A VAL* 6.2 0.2 - - - +
125A GLN* 5.6 1.4 + - - -
129B GLY* 3.3 24.9 - - - +
130B LEU 3.3 0.2 - - - -
131B SER* 1.3 92.7 + - - +
133B ARG* 1.3 63.2 + - + +
135B ALA* 3.4 8.2 + - - +
136B GLN* 3.1 23.0 + - - +
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Residues in contact with ARG 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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108B VAL* 2.6 38.0 + - - +
110B LYS* 4.3 26.6 - - - +
126B GLY 2.9 24.0 + - - -
128B ASP 3.2 19.1 + - - -
129B GLY 3.1 16.0 + - - +
130B LEU* 3.2 24.3 + - + +
132B GLU* 1.3 76.3 - - + +
134B CYS* 1.3 57.8 + - - +
136B GLN* 3.2 6.7 + - - +
137B TYR* 2.8 59.2 + - + +
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Residues in contact with CYS 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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108B VAL* 5.1 7.2 - - - -
130B LEU* 2.8 42.3 + - - +
131B SER 3.2 5.4 + - - +
133B ARG* 1.3 75.1 - - - +
135B ALA* 1.3 54.7 + - - +
137B TYR* 3.2 3.3 + - - -
138B LYS* 2.8 36.6 + - - +
176B ILE* 4.5 3.8 - - - -
177B CYS* 4.1 29.8 - - - -
180B ASN* 3.7 21.1 - - + +
182B ILE* 3.5 16.8 - - + +
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Residues in contact with ALA 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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131B SER 2.9 15.5 + - - +
132B GLU* 3.5 9.9 - - - +
134B CYS* 1.3 75.0 - - - +
136B GLN* 1.3 62.3 + - - +
138B LYS* 3.8 5.9 - - - +
139B LYS* 3.2 22.9 + - - +
180B ASN* 3.7 15.2 + - - +
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Residues in contact with GLN 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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84B TYR* 4.2 8.1 - - - +
132B GLU 3.1 13.6 + - - +
133B ARG* 3.5 10.5 - - - +
134B CYS 3.2 0.2 - - - -
135B ALA* 1.3 76.0 - - - +
137B TYR* 1.3 61.0 - - + +
139B LYS* 3.1 37.1 + - - +
140B ASP* 2.8 47.0 + - - +
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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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80B HIS* 2.6 44.8 + + - +
83B LEU* 3.5 22.8 - - + +
84B TYR* 3.7 10.5 - - - -
106B ILE* 3.9 31.6 - - + +
107B LYS 5.0 2.7 + - - -
108B VAL* 4.0 17.9 - - + -
133B ARG* 2.8 54.9 + - + +
134B CYS* 3.7 6.5 - - - +
136B GLN* 1.3 76.2 - - + +
138B LYS* 1.3 62.4 + - - +
140B ASP* 3.1 11.4 + - - +
141B GLY 3.2 0.9 + - - -
142B ALA* 2.9 35.0 + - + +
182B ILE* 4.5 3.6 - - + -
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Residues in contact with LYS 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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14B GLU* 2.7 32.0 + - - -
18B ILE* 3.9 3.0 - - - +
134B CYS 2.8 20.4 + - - +
135B ALA* 3.8 6.5 - - - +
137B TYR* 1.3 71.5 - - - +
139B LYS* 1.3 64.1 + - - +
141B GLY* 3.1 14.6 + - - -
142B ALA 3.3 20.4 + - - +
143B ASP* 2.9 23.3 + - - +
180B ASN 3.7 17.3 - - - +
181B GLY* 2.9 30.3 + - - +
182B ILE* 4.2 4.9 - - + +
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Residues in contact with LYS 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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135B ALA 3.2 10.8 + - - +
136B GLN* 3.1 36.1 + - - +
138B LYS* 1.3 81.2 - - - +
140B ASP* 1.3 79.0 + - - +
141B GLY 3.2 3.3 + - - -
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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