Contacts of the helix formed by residues 152 - 163 (chain A) in PDB entry 1HMU
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 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A PHE* 4.7 3.8 - - - -
110A SER* 5.4 1.0 + - - -
150A PRO 3.6 1.7 + - - -
151A LEU* 1.3 71.5 - - - +
153A GLU* 1.3 61.6 + - - +
154A ALA* 3.2 19.3 + - - -
155A LEU* 3.0 25.6 + - + +
156A VAL* 3.0 26.9 + - - +
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Residues in contact with GLU 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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151A LEU 3.2 5.6 + - - +
152A ASP* 1.3 75.7 + - - +
154A ALA* 1.3 57.2 + - - +
156A VAL* 3.8 8.9 - - - +
157A HIS* 3.0 28.8 + - - +
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Residues in contact with ALA 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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152A ASP* 3.2 13.1 + - - -
153A GLU* 1.3 77.4 - - - +
155A LEU* 1.3 60.3 + - - +
157A HIS* 3.6 5.1 + - - +
158A LYS* 3.1 36.4 + - - +
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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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110A SER* 4.0 31.2 - - - +
113A PHE* 4.1 10.5 - - + +
114A LYS* 4.5 31.6 - - + +
117A TYR* 5.3 3.8 - - + -
151A LEU* 4.5 15.7 - - + -
152A ASP* 3.0 25.9 + - + +
154A ALA* 1.3 76.6 - - - +
156A VAL* 1.3 59.8 + - + +
158A LYS* 3.3 14.1 + - + +
159A LEU* 3.0 51.3 + - + +
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Residues in contact with VAL 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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141A LEU* 4.8 13.9 - - + -
151A LEU* 3.7 33.9 - - + +
152A ASP 3.0 17.0 + - - +
153A GLU* 3.8 8.5 - - - +
155A LEU* 1.3 77.9 - - + +
157A HIS* 1.3 57.4 + - - +
159A LEU* 3.3 8.1 + - - +
160A THR* 2.9 46.5 + - + +
189A LEU* 5.4 11.2 - - + +
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Residues in contact with HIS 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 GLU 3.0 18.5 + - - +
154A ALA* 3.9 6.1 - - - +
155A LEU 3.2 0.2 - - - -
156A VAL* 1.3 75.6 - - - +
158A LYS* 1.3 69.5 + - + +
160A THR* 2.9 25.1 + - - -
161A GLU* 3.0 44.2 + - + +
190A THR* 5.8 3.7 - - + +
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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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114A LYS* 3.8 27.9 - - - +
117A TYR* 3.3 55.8 - - + +
154A ALA 3.1 25.8 + - - +
155A LEU* 3.6 12.2 - - + +
157A HIS* 1.3 82.1 - - + +
159A LEU* 1.3 58.3 + - + +
161A GLU* 3.5 7.7 + - - +
162A ARG 3.1 19.6 + - - -
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Residues in contact with LEU 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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113A PHE* 3.7 43.1 - - + +
116A TRP* 5.1 4.3 - - + -
117A TYR* 4.1 30.3 - - + +
137A LEU* 4.3 22.5 - - + +
141A LEU* 3.9 26.5 - - + -
155A LEU* 3.0 33.2 + - + +
156A VAL* 3.7 4.7 - - + +
157A HIS 3.1 0.2 - - - -
158A LYS* 1.3 74.7 - - - +
160A THR* 1.3 65.1 + - - +
161A GLU 3.1 1.8 - - - -
162A ARG* 3.0 14.8 + - + +
163A MET* 3.0 18.4 + - - +
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Residues in contact with THR 160 (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 LEU* 4.4 3.1 - - + -
156A VAL* 2.9 33.5 + - + +
157A HIS* 2.9 27.0 + - - -
159A LEU* 1.3 75.5 - - - +
161A GLU* 1.3 63.9 + - - +
163A MET* 3.1 16.8 + - - +
164A LYS* 3.7 1.7 + - - +
186A ARG* 3.1 30.0 - - + -
189A LEU* 4.3 23.1 - - + -
190A THR* 4.0 31.3 - - + +
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Residues in contact with GLU 161 (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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157A HIS* 3.0 51.9 + - + +
158A LYS* 3.6 7.9 - - - +
160A THR* 1.3 76.9 + - - +
162A ARG* 1.3 56.5 + - - +
163A MET 3.0 4.9 - - - -
164A LYS* 3.0 67.2 + - - +
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Residues in contact with ARG 162 (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 TRP* 4.7 4.2 + - + +
117A TYR* 2.9 70.1 + - + +
120A ASP* 3.5 24.4 + - - +
133A THR* 6.3 1.3 - - + -
134A PRO* 5.2 1.6 - - - +
137A LEU* 4.7 14.9 - - + +
158A LYS 3.1 14.7 + - - +
159A LEU* 3.0 14.9 + - + +
161A GLU* 1.3 76.2 - - - +
163A MET* 1.3 58.4 + - - +
164A LYS 3.2 1.7 + - - -
165A ARG* 3.3 48.8 + - - +
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Residues in contact with MET 163 (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* 3.5 30.8 - - + +
137A LEU* 4.0 19.5 - - + -
138A GLY* 3.6 25.4 - - - -
141A LEU* 4.3 11.7 - - - -
159A LEU 3.0 11.5 + - - +
160A THR* 3.2 26.5 - - - +
161A GLU 3.0 0.6 - - - -
162A ARG* 1.3 75.9 - - - +
164A LYS* 1.3 50.4 + - - +
165A ARG* 2.7 19.7 + - - +
182A HIS* 3.5 47.3 + - + +
186A ARG* 3.9 22.8 + - + +
189A LEU* 4.3 5.6 - - - -
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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