Contacts of the helix formed by residues 133 - 144 (chain D) in PDB entry 5HZZ
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 133 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104D GLU* 2.8 23.0 + - - +
130D ARG* 6.1 1.8 - - - +
131D PRO 4.3 4.5 - - - +
132D ALA* 1.3 70.5 - - - +
134D VAL* 1.3 60.8 + - - +
135D ARG* 3.8 7.8 + - - +
136D GLY* 3.1 24.3 + - - -
137D VAL* 3.2 20.4 + - - +
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Residues in contact with VAL 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ALA* 3.5 28.0 - - + +
77B ALA* 3.9 13.2 - - + -
78B HIS* 3.6 47.1 + - + +
101D VAL* 3.9 22.2 - - + -
104D GLU* 4.9 4.0 - - + -
105D VAL* 4.7 3.6 - - + -
132D ALA* 3.6 10.5 + - + -
133D ASP* 1.3 70.1 + - - +
135D ARG* 1.3 66.4 + - - +
137D VAL* 3.0 8.6 + - - +
138D ILE* 3.0 24.5 + - + +
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Residues in contact with ARG 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B GLY* 3.2 38.5 + - - +
72B ASP* 4.9 6.1 + - - +
74B ALA* 3.6 17.0 - - + +
75B PRO* 4.2 20.8 - - - +
133D ASP* 4.0 6.5 - - - +
134D VAL* 1.3 79.0 - - - +
136D GLY* 1.3 61.0 + - - +
138D ILE* 3.3 4.6 + - - +
139D GLU* 3.1 41.6 + - + +
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Residues in contact with GLY 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ASP* 3.1 28.7 + - - -
134D VAL 3.2 0.2 - - - -
135D ARG* 1.3 73.4 - - - +
137D VAL* 1.3 64.8 - - - +
139D GLU* 3.4 11.7 + - - +
140D ARG* 3.2 33.0 + - - +
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Residues in contact with VAL 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ALA* 3.8 38.6 - - + +
101D VAL* 3.9 11.0 - - + +
104D GLU* 3.7 30.7 - - + +
133D ASP 3.2 14.7 + - - +
134D VAL* 3.0 12.4 + - - +
136D GLY* 1.3 74.8 - - - +
138D ILE* 1.3 64.6 + - - +
140D ARG* 3.3 11.3 + - - +
141D LEU* 2.9 35.1 + - + +
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Residues in contact with ILE 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ALA 3.8 18.8 - - - +
71B GLY* 4.7 3.4 - - - +
73B LEU 4.1 4.7 - - - -
74B ALA* 3.5 42.4 - - + +
77B ALA* 4.2 6.7 - - + -
29D PRO* 3.9 16.1 - - + +
96D ILE* 4.2 30.5 - - + -
101D VAL* 5.3 0.2 - - + -
134D VAL* 3.0 14.1 + - + +
135D ARG* 3.3 6.9 + - - +
137D VAL* 1.3 77.6 - - + +
139D GLU* 1.3 64.9 + - + +
141D LEU* 3.2 9.1 + - + +
142D GLN* 3.0 37.1 + - - +
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Residues in contact with GLU 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B GLY* 6.4 2.0 - - - -
135D ARG* 3.1 33.2 + - + +
136D GLY* 3.8 9.2 - - - +
137D VAL 3.2 0.4 - - - -
138D ILE* 1.3 79.0 - - + +
140D ARG* 1.3 63.6 + - + +
142D GLN* 3.1 24.5 + - - +
143D HIS* 3.2 31.5 + - + +
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Residues in contact with ARG 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D GLY 3.2 20.4 + - - +
137D VAL* 3.7 10.3 - - - +
139D GLU* 1.3 76.7 - - + +
141D LEU* 1.3 63.0 + - + +
143D HIS* 3.3 7.7 + - - +
144D ALA* 3.1 23.7 + - - +
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Residues in contact with LEU 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ARG* 3.0 27.4 + - - +
29D PRO* 4.0 17.4 - - + +
96D ILE* 4.2 12.1 - - + -
97D ASP* 3.7 47.6 - - + +
100D ALA* 4.1 9.9 - - + -
137D VAL* 2.9 37.5 + - + +
138D ILE* 3.5 10.3 - - - +
139D GLU 3.2 0.2 - - - -
140D ARG* 1.3 79.2 - - + +
142D GLN* 1.3 55.8 + - - +
144D ALA* 3.5 10.4 + - + +
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Residues in contact with GLN 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ALA* 3.7 29.3 - - - +
71B GLY* 4.8 3.2 - - - +
28D ARG* 3.0 27.5 + - + +
29D PRO* 4.1 20.5 - - + +
138D ILE* 3.0 27.2 + - - +
139D GLU* 3.1 17.7 + - - +
141D LEU* 1.3 76.3 - - - +
143D HIS* 1.3 72.2 + - + +
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Residues in contact with HIS 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ARG* 3.7 0.2 - - - -
139D GLU* 3.2 29.6 + - + +
140D ARG* 3.7 6.7 - - - +
141D LEU 3.2 0.8 - - - -
142D GLN* 1.3 90.1 + - + +
144D ALA* 1.3 62.9 + - - +
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Residues in contact with ALA 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ARG* 3.1 37.0 + - - +
140D ARG 3.1 14.4 + - - +
141D LEU* 3.8 10.8 - - + +
143D HIS* 1.3 81.2 - - - +
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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