Contacts of the helix formed by residues 145 - 159 (chain A) in PDB entry 3UMO
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 LYS 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A GLU* 5.3 9.9 + - - +
140A LEU* 4.8 0.2 - - - -
143A GLY 4.0 3.4 + - - +
144A VAL* 1.3 77.7 - - - +
146A LEU* 1.3 66.9 + - - +
147A GLU* 3.4 33.4 - - + +
148A LYS* 2.9 30.5 + - + +
149A LEU* 3.6 3.1 + - - +
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Residues in contact with LEU 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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140A LEU* 3.8 24.2 - - + -
144A VAL 3.6 1.8 + - - +
145A LYS* 1.3 71.2 - - - +
147A GLU* 1.3 61.7 + - - +
149A LEU* 3.1 17.8 + - + +
150A THR* 3.1 14.0 + - - -
170A GLU* 3.6 62.4 - - + +
171A ALA* 3.7 8.3 - - - +
174A ALA* 3.9 12.6 - - + +
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Residues in contact with GLU 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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145A LYS* 3.4 34.4 - - + +
146A LEU* 1.3 80.7 - - - +
148A LYS* 1.3 62.2 + - + +
150A THR* 3.3 10.2 + - - -
151A GLN* 2.9 50.5 + - - +
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Residues in contact with LYS 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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115A GLU* 6.0 9.6 - - + +
118A PHE* 3.3 38.0 - - + -
119A ARG* 5.2 15.2 - - - +
122A GLU* 3.5 25.7 + - - -
144A VAL* 4.1 6.5 - - + -
145A LYS* 2.9 29.8 + - + +
147A GLU* 1.3 79.6 - - + +
149A LEU* 1.3 60.3 + - - +
151A GLN* 3.1 31.5 + - - +
152A LEU 3.0 22.0 + - - -
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Residues in contact with LEU 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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7A LEU* 5.8 0.2 - - + -
9A LEU* 4.2 22.7 - - + -
118A PHE* 4.2 6.8 - - + -
136A ILE* 4.5 14.8 - - + -
140A LEU* 4.4 17.5 - - + -
144A VAL* 4.8 0.8 - - + +
145A LYS 3.6 3.2 + - - +
146A LEU* 3.1 12.2 + - + +
148A LYS* 1.3 75.6 - - - +
150A THR* 1.3 66.2 + - - +
152A LEU* 3.3 9.2 + - + +
153A ILE* 3.2 39.4 + - + +
167A SER* 5.8 1.1 - - - +
171A ALA* 3.5 42.0 - - + +
174A ALA* 4.6 2.2 - - + -
175A ALA* 4.3 9.9 - - + +
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Residues in contact with THR 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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146A LEU 3.1 11.2 + - - -
147A GLU* 3.4 13.8 - - - +
149A LEU* 1.3 77.6 - - - +
151A GLN* 1.3 54.1 + - + +
153A ILE* 3.3 1.6 + - - -
154A SER* 2.5 39.2 + - - +
174A ALA* 2.7 30.3 + - - +
177A ALA* 4.2 10.7 - - + +
178A ILE* 3.5 26.5 - - + +
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Residues in contact with GLN 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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122A GLU* 4.0 6.4 - - - +
147A GLU* 2.9 41.4 + - - +
148A LYS* 3.1 38.0 + - - +
149A LEU 3.3 0.2 - - - -
150A THR* 1.3 78.2 - - + +
152A LEU* 1.3 58.3 + - - +
154A SER* 3.7 6.5 - - - -
155A ALA* 2.9 30.3 + - - +
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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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7A LEU* 3.9 31.2 - - + -
118A PHE* 3.7 24.2 - - + -
121A LEU* 4.8 2.5 - - + -
122A GLU* 3.7 43.5 - - + +
125A VAL* 4.5 19.1 - - + -
126A LEU* 5.1 0.9 - - + +
134A LEU* 4.7 7.2 - - + -
136A ILE* 5.0 1.8 - - + -
148A LYS 3.0 17.2 + - - +
149A LEU* 3.7 10.5 - - + +
150A THR 3.2 0.2 - - - -
151A GLN* 1.3 75.1 - - - +
153A ILE* 1.3 71.5 + - + +
155A ALA* 3.3 4.0 + - - +
156A ALA* 2.9 28.1 + - + +
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Residues in contact with ILE 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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136A ILE* 3.9 27.1 - - + -
149A LEU* 3.2 29.1 + - + +
152A LEU* 1.3 81.5 - - + +
154A SER* 1.3 63.6 + - - +
156A ALA* 3.3 5.1 + - - +
157A GLN* 3.0 34.6 + - + +
163A CYS* 4.4 6.7 - - + -
165A VAL* 4.6 3.4 - - + -
175A ALA* 3.6 37.5 - - + +
178A ILE* 3.5 20.4 - - + -
181A ILE* 3.8 20.2 - - + -
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Residues in contact with SER 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 THR* 2.5 27.8 + - - +
151A GLN* 3.7 6.8 - - - -
153A ILE* 1.3 75.9 - - - +
155A ALA* 1.3 63.2 + - - +
157A GLN* 3.4 4.3 + - - +
158A LYS* 3.1 42.9 + - - +
178A ILE* 3.2 33.6 - - - +
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Residues in contact with ALA 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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122A GLU* 4.4 7.2 - - + +
126A LEU* 3.7 27.0 - - + +
151A GLN 2.9 18.7 + - - +
152A LEU* 3.4 7.4 - - - +
153A ILE 3.2 0.2 - - - -
154A SER* 1.3 79.3 - - - +
156A ALA* 1.3 62.3 + - - +
158A LYS* 3.5 20.3 + - - +
159A GLN* 3.7 14.2 - - - +
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Residues in contact with ALA 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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125A VAL* 4.0 15.3 - - + -
126A LEU* 3.8 9.8 - - - +
134A LEU* 4.8 2.2 - - + -
152A LEU* 2.9 16.8 + - + +
153A ILE* 3.3 5.8 + - - +
155A ALA* 1.3 77.0 - - - +
157A GLN* 1.3 61.2 + - - +
159A GLN* 3.3 10.7 - - - +
161A ILE* 3.2 40.0 + - + +
163A CYS* 4.0 18.6 - - - -
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Residues in contact with GLN 157 (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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153A ILE* 3.0 31.7 + - - +
154A SER* 4.0 4.0 - - - +
155A ALA 3.4 0.2 - - - -
156A ALA* 1.3 72.2 - - - +
158A LYS* 1.3 64.4 + - + +
159A GLN 3.0 4.3 + - - -
160A GLY* 3.1 12.1 + - - -
161A ILE 3.7 11.4 - - - +
163A CYS* 3.9 21.0 + - + +
178A ILE* 4.5 12.5 - - - +
179A GLY 3.0 21.6 + - - -
180A ASN* 3.0 32.6 + - - +
181A ILE* 3.6 12.1 - - - +
182A GLU* 4.7 0.5 + - - +
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Residues in contact with LYS 158 (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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154A SER* 3.1 33.7 + - - +
155A ALA* 3.8 12.4 - - - +
156A ALA 3.3 0.4 - - - -
157A GLN* 1.3 76.3 - - - +
159A GLN* 1.3 58.1 + - + +
160A GLY 3.5 0.6 + - - -
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Residues in contact with GLN 159 (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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126A LEU* 3.1 53.9 + - - +
128A ILE 3.7 15.2 + - - -
130A SER* 3.3 23.9 + - - +
155A ALA 3.7 6.8 - - - +
156A ALA 3.3 13.5 - - - +
157A GLN 3.0 0.2 - - - -
158A LYS* 1.3 78.4 - - + +
160A GLY* 1.3 59.0 + - - +
161A ILE* 3.5 8.0 + - + +
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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