Contacts of the helix formed by residues 133 - 144 (chain A) in PDB entry 1UJP
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 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A LEU* 4.2 17.8 - - + +
129A PRO 3.8 2.2 + - - -
130A PRO 3.2 6.0 + - - -
132A GLU* 1.3 82.3 - - - +
134A PRO* 1.3 64.5 - - - +
135A GLY* 3.5 5.2 + - - -
136A LEU* 3.1 45.0 + - + +
137A VAL* 3.2 14.0 + - - +
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Residues in contact with PRO 134 (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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130A PRO 3.3 9.8 - - - +
131A ASP* 3.5 18.4 - - - +
132A GLU 3.7 2.0 - - - +
133A ASP* 1.3 87.9 - - - +
135A GLY* 1.3 57.7 + - - +
137A VAL* 3.2 7.6 + - + +
138A ARG* 2.8 54.7 + - + +
166A HIS* 4.1 20.9 - - + +
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Residues in contact with GLY 135 (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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133A ASP* 3.1 6.5 + - - -
134A PRO* 1.3 81.1 - - - +
136A LEU* 1.3 56.1 + - - +
138A ARG* 3.4 22.9 + - - +
139A LEU* 3.0 27.4 + - - +
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Residues in contact with LEU 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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100A LEU* 3.9 29.6 - - + -
103A VAL* 5.6 0.2 - - + -
104A LEU* 4.9 5.6 - - + -
108A PRO* 4.8 18.6 - - + -
112A PHE* 3.7 30.2 - - + -
125A LEU* 4.6 4.7 - - + -
128A LEU* 3.8 21.8 - - + -
133A ASP* 3.1 35.6 + - + +
135A GLY* 1.3 72.6 - - - +
137A VAL* 1.3 70.0 + - - +
139A LEU* 3.2 17.9 + - - +
140A ALA* 3.2 10.8 + - + +
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Residues in contact with VAL 137 (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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125A LEU* 6.1 0.4 - - - -
128A LEU* 4.6 6.3 - - + -
130A PRO* 3.9 21.8 - - + +
133A ASP 3.4 13.5 - - - +
134A PRO* 3.2 9.6 + - + +
136A LEU* 1.3 78.5 - - - +
138A ARG* 1.3 65.6 + - + +
140A ALA* 3.2 7.3 + - - +
141A GLN* 3.0 51.1 + - - +
147A THR* 3.9 2.7 - - - +
149A PHE* 3.6 37.9 - - + -
166A HIS* 4.0 12.3 - - + +
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Residues in contact with ARG 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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134A PRO* 2.8 54.8 + - + +
135A GLY* 3.7 18.3 - - - +
137A VAL* 1.3 73.9 - - + +
139A LEU* 1.3 57.4 + - - +
141A GLN* 3.8 13.8 - - - +
142A GLU* 2.8 46.0 + - + +
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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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108A PRO* 3.6 17.7 - - + -
109A GLU* 3.6 42.2 - - + +
112A PHE* 4.5 3.1 - - + -
135A GLY 3.0 14.8 + - - +
136A LEU* 3.3 13.0 - - - +
137A VAL 3.1 0.2 - - - -
138A ARG* 1.3 77.5 - - - +
140A ALA* 1.3 62.8 + - - +
142A GLU* 3.4 11.9 + - + +
143A ILE* 3.1 46.4 + - + +
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Residues in contact with ALA 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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112A PHE* 3.8 41.0 - - + -
123A VAL* 4.8 0.4 - - + -
125A LEU* 5.7 0.4 - - + -
136A LEU* 3.2 3.7 + - + +
137A VAL* 3.2 9.2 + - - +
139A LEU* 1.3 78.5 - - - +
141A GLN* 1.3 62.2 + - - +
143A ILE* 3.3 12.3 + - - +
144A GLY 3.3 0.9 + - - -
145A LEU* 3.0 27.8 + - + +
147A THR* 3.7 19.7 - - + -
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Residues in contact with GLN 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 VAL* 3.0 26.0 + - - +
138A ARG* 3.8 13.1 - - - +
140A ALA* 1.3 75.5 - - - +
142A GLU* 1.3 60.1 + - + +
144A GLY* 2.9 19.8 + - - -
145A LEU 3.4 11.6 + - - +
147A THR* 2.9 31.9 + - + +
166A HIS* 2.9 20.2 + - - +
168A THR* 3.5 20.4 - - - +
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Residues in contact with GLU 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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138A ARG* 2.8 32.0 + - + +
139A LEU* 3.7 14.1 - - + +
141A GLN* 1.3 74.8 - - + +
143A ILE* 1.3 61.6 + - + +
144A GLY* 3.0 1.6 + - - -
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Residues in contact with ILE 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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109A GLU* 3.8 22.4 - - + +
112A PHE* 3.6 32.3 - - + +
113A GLY* 3.9 7.6 - - - +
116A LYS* 3.5 36.3 - - + +
139A LEU* 3.1 33.3 + - + +
140A ALA* 3.5 9.6 - - - +
141A GLN 3.2 0.2 - - - -
142A GLU* 1.3 78.1 - - + +
144A GLY* 1.3 57.5 + - - +
145A LEU* 4.6 1.8 - - + -
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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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116A LYS* 2.8 31.1 + - - -
121A THR 4.1 2.6 - - - +
141A GLN 2.9 12.4 + - - -
142A GLU 3.0 1.7 - - - -
143A ILE* 1.3 82.5 - - - +
145A LEU* 1.3 60.5 + - - +
146A GLU* 4.0 1.4 + - - +
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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