Contacts of the helix formed by residues 145 - 156 (chain A) in PDB entry 3UC5
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 PRO 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A VAL* 3.5 22.9 - - + +
14A THR 3.8 7.0 - - - -
15A LEU* 3.8 13.9 - - + +
18A VAL* 4.0 18.4 - - + -
57A SER* 3.4 35.2 - - - +
144A LEU* 1.3 87.5 - - + +
146A GLU* 1.3 60.6 + - - +
147A PRO* 3.2 4.9 - - + -
148A VAL* 2.9 27.1 + - + +
149A ASN* 3.0 10.4 + - - -
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Residues in contact with GLU 146 (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 SER 4.7 3.5 - - - +
144A LEU 4.8 1.4 - - - +
145A PRO* 1.3 71.5 - - - +
147A PRO* 1.3 65.5 - - + +
149A ASN* 3.2 21.1 + - - +
150A ARG* 2.9 38.0 + - - +
153A ARG* 3.9 16.8 + - - -
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Residues in contact with PRO 147 (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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53A MET* 4.4 4.0 - - - +
56A GLU* 3.4 46.7 - - + +
57A SER* 3.7 17.0 - - - +
145A PRO* 3.3 11.0 - - + -
146A GLU* 1.3 94.4 - - + +
148A VAL* 1.3 58.8 + - - +
150A ARG* 3.5 20.8 - - - +
151A ARG* 3.2 34.3 + - - +
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Residues in contact with VAL 148 (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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12A PRO* 3.7 29.6 - - + -
13A VAL* 3.4 38.4 - - + +
45A PHE* 5.3 0.6 - - + -
53A MET* 3.9 21.1 - - + -
57A SER* 4.6 1.3 - - - +
144A LEU* 3.9 20.0 - - + -
145A PRO* 2.9 20.9 + - + +
147A PRO* 1.3 75.7 - - - +
149A ASN* 1.3 54.9 + - - +
151A ARG* 3.1 3.6 + - - +
152A LEU* 2.8 39.0 + - + +
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Residues in contact with ASN 149 (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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140A VAL* 5.4 0.2 - - - +
141A SER* 3.0 49.7 + - - -
144A LEU* 3.3 28.5 + - - +
145A PRO 3.0 6.8 + - - -
146A GLU* 3.3 25.7 + - - +
148A VAL* 1.3 75.2 - - - +
150A ARG* 1.3 63.7 + - - +
152A LEU* 3.1 7.9 + - - +
153A ARG* 2.9 48.1 + - - +
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Residues in contact with ARG 150 (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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56A GLU* 3.2 24.0 + - - -
146A GLU* 2.9 18.1 + - - +
147A PRO* 3.5 29.6 - - - +
148A VAL 3.3 0.2 - - - -
149A ASN* 1.3 76.4 - - - +
151A ARG* 1.3 74.3 + - + +
153A ARG* 3.6 18.9 + - - +
154A ASP* 3.1 36.0 + - - +
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Residues in contact with ARG 151 (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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45A PHE* 4.5 10.3 - - + -
49A GLU* 4.8 18.7 + - - +
52A ALA* 3.7 16.1 - - - +
53A MET* 3.5 36.8 - - - +
56A GLU* 2.8 44.0 + - - -
147A PRO* 3.2 18.6 + - - +
148A VAL 3.1 7.3 + - - +
150A ARG* 1.3 88.6 - - + +
152A LEU* 1.3 61.8 + - - +
154A ASP* 3.3 11.6 + - - +
155A ARG* 3.0 30.0 + - - +
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Residues in contact with LEU 152 (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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12A PRO* 5.2 3.4 - - + -
44A MET* 3.9 17.0 - - - -
45A PHE* 3.5 28.5 - - + -
130A ALA 5.3 1.6 - - - +
131A LYS* 5.5 3.8 - - + -
134A ALA* 3.8 30.5 - - + -
140A VAL* 4.1 5.6 - - + -
144A LEU* 3.8 28.3 - - + -
148A VAL* 2.8 18.6 + - + +
149A ASN* 3.6 7.4 - - - +
151A ARG* 1.3 75.6 - - - +
153A ARG* 1.3 62.9 + - + +
155A ARG* 3.3 4.7 + - + +
156A LEU* 3.1 28.5 + - + +
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Residues in contact with ARG 153 (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 SER* 5.2 6.9 - - - -
146A GLU* 3.9 19.6 + - - -
149A ASN* 2.9 39.2 + - - +
150A ARG* 3.7 16.7 - - - +
151A ARG 3.3 0.2 - - - -
152A LEU* 1.3 78.7 - - + +
154A ASP* 1.3 60.7 + - - +
156A LEU* 2.9 16.9 - - + +
157A ASN* 2.9 21.8 - - - +
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Residues in contact with ASP 154 (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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150A ARG* 3.1 25.8 - - - +
151A ARG* 3.3 9.9 + - - +
152A LEU 3.2 0.4 - - - -
153A ARG* 1.3 81.9 - - - +
155A ARG* 1.3 61.6 + - - +
156A LEU 3.2 0.4 + - - -
157A ASN* 2.9 31.0 + - - +
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Residues in contact with ARG 155 (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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43A GLY 4.6 2.2 + - - -
44A MET* 2.8 58.1 + - + +
45A PHE* 4.5 13.4 - - + +
49A GLU* 4.0 21.0 + - - -
151A ARG 3.0 17.4 + - - +
152A LEU* 3.3 8.7 + - + +
154A ASP* 1.3 77.7 - - - +
156A LEU* 1.3 60.0 + - - +
157A ASN* 3.3 2.9 + - - +
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Residues in contact with LEU 156 (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 ALA 4.8 15.0 - - - +
135A MET* 6.3 1.8 - - - -
137A GLY* 5.9 4.5 - - - -
152A LEU* 3.1 14.1 + - + +
153A ARG* 2.9 32.8 - - + +
154A ASP 3.2 0.4 - - - -
155A ARG* 1.3 78.3 - - - +
157A ASN* 1.3 72.4 + - + +
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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