Contacts of the helix formed by residues 155 - 164 (chain B) in PDB entry 5XMA
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 155 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LYS* 6.1 3.8 - - - +
110B PRO* 3.4 9.8 - - - +
154B THR* 1.3 84.5 + - + +
156B GLU* 1.3 64.5 + - - +
157B LYS* 3.5 9.3 + - - +
158B GLU* 2.8 41.3 + - - +
159B LEU* 3.2 16.6 + - - +
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Residues in contact with GLU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ARG* 3.6 15.5 + - - +
110B PRO* 3.7 16.1 - - + +
113B ILE* 3.8 26.6 - - + +
114B PHE* 3.3 36.4 - - + +
155B THR* 1.3 74.7 - - - +
157B LYS* 1.3 62.5 + - - +
159B LEU* 3.2 4.0 + - - +
160B ILE* 3.1 25.2 + - + +
167B TYR* 3.8 13.7 + - - -
173B ARG* 2.5 48.8 + - - -
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Residues in contact with LYS 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B THR* 3.2 9.5 + - - +
156B GLU* 1.3 79.6 + - - +
158B GLU* 1.3 64.1 + - + +
160B ILE* 3.1 5.0 + - - +
161B LYS* 3.1 23.3 + - + +
167B TYR* 3.6 55.1 - - + +
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Residues in contact with GLU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B LYS 4.9 2.8 - - - +
153B ILE* 3.6 19.6 - - + +
154B THR* 3.0 20.0 + - - -
155B THR* 2.8 44.8 + - - +
157B LYS* 1.3 79.6 - - + +
159B LEU* 1.3 58.1 + - - +
161B LYS* 3.4 6.2 + - - +
162B GLU* 2.8 31.2 + - - +
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Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B PRO* 3.6 25.8 - - + +
111B TYR* 3.7 49.6 - - + +
114B PHE* 4.6 11.4 - - + -
137B LEU* 5.7 2.2 - - + -
151B LEU* 4.2 12.6 - - + -
153B ILE* 3.8 18.0 - - + +
155B THR 3.2 10.0 + - - +
156B GLU 3.2 9.3 + - - +
157B LYS 3.2 0.6 - - - -
158B GLU* 1.3 78.3 - - - +
160B ILE* 1.3 51.8 + - + +
162B GLU 3.0 2.1 + - - -
163B LEU* 2.5 66.6 + - + +
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Residues in contact with ILE 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B PHE* 3.6 39.9 - - + -
122B TYR* 4.9 5.8 - - - +
156B GLU* 3.1 12.9 + - + +
157B LYS 3.1 5.6 + - - +
159B LEU* 1.3 74.3 - - + +
161B LYS* 1.3 63.7 + - - +
163B LEU* 3.1 15.1 + - + +
164B GLY 3.0 17.3 + - - -
165B PHE* 3.2 36.9 + - + +
166B THR 4.2 2.2 - - - +
167B TYR* 3.5 41.7 - - + +
168B ARG 5.1 0.4 - - - +
173B ARG* 3.7 14.6 - - - +
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Residues in contact with LYS 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B LYS* 3.1 13.6 + - + +
158B GLU* 3.7 9.6 - - - +
160B ILE* 1.3 77.0 - - - +
162B GLU* 1.3 58.7 + - - +
164B GLY* 3.0 18.5 + - - -
165B PHE 4.4 7.6 - - - -
167B TYR* 5.5 3.5 - - + +
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Residues in contact with GLU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B LEU* 3.6 46.2 - - + +
152B LYS 5.5 1.6 - - - +
153B ILE* 3.8 13.6 - - + +
158B GLU 2.8 21.6 + - - +
159B LEU 3.5 3.6 - - - +
161B LYS* 1.3 70.1 - - - +
163B LEU* 1.3 64.4 + - - +
164B GLY* 3.4 0.9 + - - -
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Residues in contact with LEU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B TYR* 6.1 0.2 - - + -
114B PHE* 4.8 16.2 - - + -
126B ILE* 5.1 1.3 - - + -
130B LEU* 4.6 24.8 - - + +
137B LEU* 5.0 14.4 - - + -
142B LEU* 4.6 18.8 - - + -
151B LEU* 5.2 3.1 - - + -
159B LEU* 2.5 54.6 + - + +
160B ILE* 3.1 22.0 + - + +
162B GLU* 1.3 72.9 - - - +
164B GLY* 1.3 60.6 + - - +
165B PHE* 3.5 28.5 - - + -
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Residues in contact with GLY 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B ILE 3.0 3.0 + - - -
161B LYS 3.0 13.8 + - - -
162B GLU 3.1 1.3 - - - -
163B LEU* 1.3 78.9 - - - +
165B PHE* 1.3 68.7 + - - +
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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