Contacts of the helix formed by residues 135 - 144 (chain A) in PDB entry 1U5H
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 GLY 135 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LEU* 3.8 5.3 - - - +
111A VAL 3.1 8.9 + - - +
112A GLU* 3.5 23.9 - - - +
133A MET* 6.0 0.7 - - - -
134A TRP* 1.3 80.9 - - - +
136A ALA* 1.3 63.4 + - - -
137A GLU 3.5 2.9 - - - -
138A ASP 4.7 0.7 - - - -
139A LEU* 3.4 16.5 - - - +
162A VAL* 5.7 0.3 - - - +
180A ALA* 4.6 4.0 - - - -
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Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A TRP* 3.6 19.5 - - + -
135A GLY* 1.3 73.1 - - - -
137A GLU* 1.3 67.7 + - + +
139A LEU* 3.5 6.1 - - - +
140A ILE* 3.0 28.1 + - + +
148A SER* 3.8 13.0 - - - +
155A TYR* 3.5 36.3 - - + +
159A ALA* 4.2 4.5 - - + -
180A ALA* 5.0 2.6 - - - +
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Residues in contact with GLU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLY 3.5 0.6 - - - -
136A ALA* 1.3 80.0 - - + +
138A ASP* 1.3 64.9 + - - +
140A ILE* 3.9 3.0 - - - +
141A ALA* 3.0 26.7 + - - +
148A SER* 3.6 21.4 + - - -
183A LEU* 3.3 38.9 - - + +
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Residues in contact with ASP 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLU* 5.5 0.2 - - - +
37A ASP* 4.1 10.3 - - - +
92A LYS* 2.5 39.8 + - - -
112A GLU* 3.1 28.4 + - - +
113A THR* 5.7 0.4 - - + -
135A GLY 4.5 1.8 + - - -
136A ALA 3.5 0.2 - - - -
137A GLU* 1.3 83.0 - - - +
139A LEU* 1.3 59.6 - - - +
141A ALA* 3.7 10.2 - - - +
142A THR* 2.8 34.0 + - - +
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Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLU* 3.0 12.8 + - - +
113A THR* 3.7 29.4 - - - +
114A ALA* 3.8 5.8 - - - +
134A TRP* 5.1 0.7 - - + -
135A GLY 3.4 19.1 + - - +
136A ALA* 3.3 9.5 + - - +
137A GLU 3.2 1.0 - - - -
138A ASP* 1.3 77.6 - - - +
140A ILE* 1.3 64.9 + - + +
142A THR* 3.2 3.2 - - - +
143A LEU* 3.0 42.4 + - + +
158A VAL* 4.2 15.9 - - + +
159A ALA* 4.2 13.7 - - + +
162A VAL* 3.6 40.6 - - + -
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Residues in contact with ILE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ALA* 3.0 19.7 + - + +
137A GLU* 4.0 3.4 - - - +
139A LEU* 1.3 79.1 - - + +
141A ALA* 1.3 63.1 + - - +
143A LEU* 3.3 10.7 + - + +
144A GLY 3.2 3.8 + - - -
145A GLY* 2.9 28.3 + - - +
146A SER 3.6 27.1 - - - +
147A SER* 3.6 24.0 - - - +
148A SER* 3.5 24.0 - - - +
156A ARG* 5.2 5.8 - - + -
158A VAL* 3.7 30.5 - - + -
159A ALA* 5.4 2.2 - - + +
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Residues in contact with ALA 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A GLU 3.0 18.0 + - - +
138A ASP* 3.9 11.7 - - - +
139A LEU 3.3 0.2 - - - -
140A ILE* 1.3 76.9 - - - +
142A THR* 1.3 56.8 + - - +
144A GLY* 3.1 19.4 + - - -
145A GLY 4.4 7.7 - - - +
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Residues in contact with THR 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLU 3.7 13.2 - - - +
113A THR* 3.7 27.4 - - + +
114A ALA 4.5 4.0 - - - +
138A ASP 2.8 30.3 + - - +
139A LEU 3.2 9.2 - - - +
141A ALA* 1.3 69.9 - - - +
143A LEU* 1.3 63.2 + - - +
144A GLY* 3.1 2.8 + - - -
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Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ALA* 3.9 26.2 - - + -
139A LEU* 3.0 42.8 + - + +
140A ILE* 3.6 12.8 - - + +
142A THR* 1.3 76.2 - - + +
144A GLY* 1.3 57.3 + - - +
145A GLY* 4.4 2.0 - - - +
158A VAL* 4.1 30.3 - - + -
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Residues in contact with GLY 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ALA 3.1 14.0 + - - -
142A THR 3.1 2.3 + - - -
143A LEU* 1.3 79.4 - - - +
145A GLY* 1.3 63.2 + - - +
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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