Contacts of the helix formed by residues 134 - 142 (chain B) in PDB entry 1A7A
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 134 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B CYS* 4.5 4.7 - - - -
79B CYS* 3.9 7.3 - - + +
110B TYR* 2.7 36.2 + - + +
114B ILE* 4.3 13.5 - - + +
130B ASP* 3.5 2.2 + - - +
131B ASP 5.8 0.2 - - - +
132B GLY 3.3 1.2 - - - -
133B GLY* 1.3 75.9 - - - +
135B LEU* 1.3 58.9 + - - +
137B ASN* 3.7 4.8 - - - +
138B LEU* 2.8 32.1 + - - +
301B HIS* 4.3 2.9 + - - -
302B PHE* 3.6 34.7 - - - -
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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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51B ALA* 2.9 42.0 - - + +
52B GLY 4.5 0.4 - - - -
53B CYS* 3.8 23.1 - - + +
114B ILE* 4.3 16.4 - - + -
117B THR* 5.3 2.7 - - - +
118B LEU* 4.2 12.3 - - + -
125B LEU* 4.5 0.9 - - + -
128B ILE* 3.5 17.3 - - + -
129B LEU 4.5 0.4 - - - +
130B ASP* 2.9 14.4 + - - +
134B ASP* 1.3 79.0 - - - +
136B THR* 1.3 65.5 + - - +
138B LEU* 3.0 6.6 + - + +
139B ILE* 3.0 49.8 + - + +
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Residues in contact with THR 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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128B ILE* 3.3 33.0 - - + -
130B ASP* 2.7 21.5 + - + +
133B GLY* 3.1 16.3 + - - -
135B LEU* 1.3 71.4 - - - +
137B ASN* 1.3 63.0 + - - +
139B ILE* 4.1 0.4 - - - +
140B HIS* 3.0 32.0 + - - +
153B ILE* 3.2 46.4 - - + -
155B GLU* 5.5 1.0 - - + +
164B LEU* 4.6 10.0 - - - +
167B MSE 5.0 7.2 - - - +
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Residues in contact with ASN 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 GLY 2.7 26.0 + - - +
134B ASP* 3.7 5.6 - - - +
136B THR* 1.3 72.2 + - - +
138B LEU* 1.3 66.1 + - - +
140B HIS* 3.4 2.2 + - - -
141B THR* 2.9 42.7 + - - +
163B ASN* 4.5 11.1 - - - +
167B MSE 3.4 29.7 - - + +
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Residues in contact with LEU 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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111B LEU* 4.0 28.5 - - + -
114B ILE* 3.5 33.0 - - + -
115B GLU* 4.4 11.9 - - + +
118B LEU* 4.9 4.9 - - + -
134B ASP 2.8 21.4 + - - +
135B LEU* 3.4 4.5 - - + +
137B ASN* 1.3 73.4 + - - +
139B ILE* 1.3 56.7 + - + +
141B THR* 3.1 4.3 + - - +
142B LYS* 2.6 63.6 + - + +
143B TYR* 4.0 15.5 - - + -
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Residues in contact with ILE 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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118B LEU* 4.3 13.2 - - + -
125B LEU* 3.3 37.0 - - + -
128B ILE* 3.6 5.8 - - + -
135B LEU* 3.0 31.5 + - + +
136B THR 4.1 3.6 - - - +
138B LEU* 1.3 75.9 - - + +
140B HIS* 1.3 62.3 + - - +
143B TYR* 2.8 59.1 + - + +
146B LEU* 4.8 2.2 - - + -
147B LEU* 3.4 27.8 - - + +
150B ILE* 3.5 16.8 - - + -
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Residues in contact with HIS 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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128B ILE* 6.0 0.9 - - + -
136B THR* 3.0 26.5 + - - +
137B ASN* 3.9 4.7 - - - +
139B ILE* 1.3 81.3 - - - +
141B THR* 1.3 63.8 + - + +
144B PRO* 4.0 14.0 - - - +
147B LEU* 3.5 37.3 - - + +
153B ILE* 4.2 11.2 - - + -
167B MSE 4.9 10.5 - - + -
172B ILE* 3.1 37.2 - - + +
173B LEU* 3.8 8.3 - - + +
174B LYS* 3.0 25.5 + - + +
175B VAL* 3.8 18.8 - - + -
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Residues in contact with THR 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 ASN* 2.9 34.4 + - - +
138B LEU* 3.3 7.3 + - - +
140B HIS* 1.3 85.3 - - + +
142B LYS* 1.3 80.8 + - - +
143B TYR 3.8 0.2 - - - -
144B PRO* 4.1 6.0 - - - +
167B MSE 6.4 0.4 - - + -
172B ILE* 6.5 0.9 - - + -
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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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138B LEU* 2.6 34.0 + - + +
141B THR* 1.3 92.0 + - - +
143B TYR* 1.3 81.7 + - + +
144B PRO* 3.3 6.7 - - - +
145B GLN* 4.0 5.4 + - - +
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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