Contacts of the helix formed by residues 149 - 157 (chain A) in PDB entry 1ULH
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 THR 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A GLY* 6.1 0.4 - - - -
115A ARG 3.1 18.5 + - - +
116A GLY* 3.5 8.5 - - - -
117A PRO* 3.2 10.3 - - - +
147A GLN* 3.0 37.5 - - + +
148A MET* 1.3 70.7 - - - +
150A ASP* 1.3 61.8 + - - +
151A ASP* 3.4 2.7 - - - -
152A GLU* 2.8 30.2 + - - +
153A LYS* 3.2 16.6 + - - +
190A ASP* 3.4 15.9 - - - +
233A PHE* 3.7 9.4 - - + -
237A GLN* 5.3 2.2 - - + +
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Residues in contact with ASP 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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117A PRO* 3.5 10.7 - - + +
148A MET 3.1 3.4 - - - +
149A THR* 1.3 71.4 - - - +
151A ASP* 1.3 57.2 + - - +
153A LYS* 3.2 2.2 + - - +
154A TYR* 2.9 28.8 + - - +
164A ALA* 3.5 27.4 - - - +
165A TYR* 3.2 17.9 - - - -
168A ALA* 4.0 6.6 - - + +
189A SER* 2.5 23.4 + - - -
190A ASP* 3.0 25.8 + - - +
191A LEU* 3.4 25.9 + - + +
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Residues in contact with ASP 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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149A THR 3.6 1.9 - - - -
150A ASP* 1.3 75.1 + - - +
152A GLU* 1.3 57.5 + - - -
154A TYR* 3.0 8.7 + - - +
155A LEU* 2.7 43.7 + - + +
190A ASP* 2.5 44.0 - - - +
191A LEU* 3.5 22.7 - - + +
233A PHE* 3.3 10.3 - - + -
236A ILE* 3.6 8.0 - - - +
201B TYR* 2.9 27.5 + - - +
205B VAL* 3.9 10.8 - - + -
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Residues in contact with GLU 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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116A GLY* 4.8 2.1 - - - -
149A THR* 2.8 34.0 + - - +
151A ASP* 1.3 82.1 + - - +
153A LYS* 1.3 80.1 + - + +
155A LEU* 3.0 4.0 + - - -
156A TRP* 2.8 59.3 + - + +
233A PHE* 3.3 36.7 - - + -
237A GLN* 4.2 8.0 + - - -
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Residues in contact with LYS 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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116A GLY* 3.4 39.3 - - - -
117A PRO* 3.4 21.8 - - + +
118A SER* 3.4 18.3 - - - +
149A THR 3.2 14.1 + - - +
150A ASP 3.2 8.1 + - - +
152A GLU* 1.3 96.5 + - - +
154A TYR* 1.3 55.9 + - - +
156A TRP* 4.7 1.8 - - - +
157A LYS* 2.6 68.6 + - + +
159A LEU* 4.0 13.4 - - + +
164A ALA* 4.7 1.8 - - + -
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Residues in contact with TYR 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 ASP 2.9 13.8 + - - +
151A ASP 3.0 7.2 + - - +
153A LYS* 1.3 76.0 - - - +
155A LEU* 1.3 59.4 + - + +
157A LYS 3.1 4.9 - - - +
159A LEU* 3.5 26.2 - - - -
160A THR* 3.8 3.4 - - - -
161A LEU* 3.5 37.0 - - + -
164A ALA* 4.3 8.4 - - + +
205B VAL* 3.5 42.0 - - + -
206B LYS* 3.4 37.7 + - + +
209B LYS* 2.6 59.9 + - + +
210B HIS* 3.8 10.0 + - - -
280B ILE* 4.3 2.8 - - - +
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Residues in contact with LEU 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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151A ASP* 2.7 30.0 + - + +
152A GLU* 3.0 7.4 + - - +
154A TYR* 1.3 76.5 - - + +
156A TRP* 1.3 69.2 + - + +
227A CYS* 4.3 5.6 - - - -
229A GLY* 3.5 42.6 - - - +
230A LYS* 4.0 19.0 - - + +
233A PHE* 4.3 15.5 - - + -
201B TYR* 6.0 0.7 - - - +
205B VAL* 3.9 28.5 - - + +
208B GLN* 4.3 6.1 - - - +
209B LYS* 3.9 33.5 - - + +
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Residues in contact with TRP 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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152A GLU* 2.8 60.1 + - + +
153A LYS* 4.7 1.6 - - - +
155A LEU* 1.3 82.8 - - + +
157A LYS* 1.3 78.5 + - + +
222A PHE* 3.6 33.8 - + - -
230A LYS* 3.4 55.4 + - + +
233A PHE* 4.1 22.2 - + + -
237A GLN* 6.1 0.7 - - - -
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Residues in contact with LYS 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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118A SER* 3.4 18.6 - - - +
153A LYS* 2.6 53.0 + - + +
154A TYR 3.1 4.2 - - - +
156A TRP* 1.3 89.0 + - + +
158A ASP* 1.3 52.1 + - - +
159A LEU* 2.7 30.9 + - + -
209B LYS* 2.8 24.4 + - - -
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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