Contacts of the helix formed by residues 155 - 164 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A LYS* 6.5 1.1 - - - +
110A PRO* 3.7 7.9 - - - +
113A ILE* 6.5 0.2 - - - -
153A ILE* 3.9 0.9 - - - +
154A THR* 1.3 85.5 - - + +
156A GLU* 1.3 64.0 + - - +
157A LYS* 3.6 9.0 + - - +
158A GLU* 2.7 40.7 + - - +
159A LEU* 3.2 16.1 + - - +
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Residues in contact with GLU 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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41A ARG* 3.9 13.8 + - - -
110A PRO* 3.8 16.1 - - - +
113A ILE* 4.1 26.4 - - + +
114A PHE* 3.5 32.9 - - + +
155A THR* 1.3 71.2 - - - +
157A LYS* 1.3 65.5 + - - +
159A LEU* 3.1 6.6 + - + +
160A ILE* 2.9 37.7 + - + +
167A TYR* 4.0 9.7 + - - -
173A ARG* 2.6 47.6 + - - -
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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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155A THR* 3.3 8.6 + - - +
156A GLU* 1.3 80.3 + - - +
158A GLU* 1.3 63.5 + - + +
160A ILE* 3.1 4.2 + - - +
161A LYS* 2.9 25.9 + - + +
167A TYR* 3.6 53.2 - - + +
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Residues in contact with GLU 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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152A LYS 4.8 3.3 - - - +
153A ILE* 3.5 22.5 - - + +
154A THR* 2.8 19.7 + - - -
155A THR* 2.7 42.5 + - - +
157A LYS* 1.3 77.7 - - + +
159A LEU* 1.3 57.3 + - - +
161A LYS* 3.3 7.5 + - - +
162A GLU* 2.8 30.7 + - - +
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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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110A PRO* 3.9 22.2 - - + +
111A TYR* 3.7 43.1 - - + -
114A PHE* 4.9 11.4 - - + -
137A LEU* 5.7 4.3 - - + -
142A LEU* 5.6 0.4 - - + -
151A LEU* 3.9 21.1 - - + -
153A ILE* 3.7 22.6 - - + +
155A THR 3.2 5.0 + - - +
156A GLU* 3.1 10.6 + - - +
158A GLU* 1.3 78.7 - - - +
160A ILE* 1.3 52.4 + - + +
162A GLU* 3.0 2.5 + - - -
163A LEU* 2.6 60.8 + - + +
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Residues in contact with ILE 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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114A PHE* 4.2 20.2 - - + -
122A TYR* 5.4 5.8 - - - +
156A GLU* 2.9 31.5 + - + +
157A LYS 3.6 5.4 - - - +
159A LEU* 1.3 75.7 - - + +
161A LYS* 1.3 62.5 + - - +
163A LEU* 3.1 17.0 + - + +
164A GLY 2.9 18.0 + - - -
165A PHE* 3.4 30.5 + - + +
166A THR 4.6 1.1 - - - +
167A TYR* 3.6 34.3 - - + -
168A ARG 5.3 0.4 - - - +
173A ARG* 3.5 28.9 - - - +
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Residues in contact with LYS 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 LYS* 2.9 17.0 + - + +
158A GLU* 3.6 7.2 - - - +
160A ILE* 1.3 78.8 - - - +
162A GLU* 1.3 56.6 + - - +
164A GLY* 3.0 19.0 + - - +
165A PHE 4.9 4.3 - - - -
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Residues in contact with GLU 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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151A LEU* 3.7 41.3 - - + +
152A LYS 6.1 0.7 - - - -
153A ILE* 4.0 12.6 - - + +
158A GLU 2.8 21.2 + - - +
159A LEU 3.5 3.6 - - - +
161A LYS* 1.3 71.3 - - - +
163A LEU* 1.3 63.7 + - - +
164A GLY* 3.4 0.9 + - - -
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Residues in contact with LEU 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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114A PHE* 5.2 15.9 - - + -
126A ILE* 5.7 3.1 - - + -
130A LEU* 4.9 16.5 - - + +
137A LEU* 5.6 11.0 - - + -
142A LEU* 4.5 20.9 - - + -
151A LEU* 5.4 1.8 - - + -
159A LEU* 2.6 51.0 + - + +
160A ILE* 3.1 24.4 + - + +
162A GLU* 1.3 72.5 - - - +
164A GLY* 1.3 61.2 + - - +
165A PHE* 3.4 33.3 - - + -
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Residues in contact with GLY 164 (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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160A ILE 2.9 4.4 + - - -
161A LYS* 3.0 14.0 + - - -
162A GLU 3.2 1.1 - - - -
163A LEU* 1.3 79.0 - - - +
165A PHE* 1.3 68.3 + - - +
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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