Contacts of the helix formed by residues 129 - 136 (chain Z) in PDB entry 5JPQ
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 GLY 129 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97Z GLY* 5.5 2.1 - - - -
122Z THR 4.4 9.9 - - - -
123Z ALA* 5.3 7.0 - - - -
124Z SER 6.1 0.4 - - - -
127Z ASP 3.4 5.3 + - - -
128Z ALA* 1.3 76.2 - - - +
130Z ILE* 1.3 66.9 + - - -
131Z GLU 3.3 2.7 - - - -
132Z ALA* 3.3 10.6 + - - +
133Z ILE* 3.2 20.8 + - - +
259Z GLU* 5.8 4.6 - - - +
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Residues in contact with ILE 130 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122Z THR* 4.3 16.4 + - - +
129Z GLY* 1.3 68.9 - - - -
131Z GLU* 1.3 58.3 + - - +
133Z ILE* 3.2 8.1 + - - +
134Z LYS* 3.0 27.8 + - - +
151Z LEU* 5.4 2.6 - - - +
153Z THR* 5.5 11.7 - - - -
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Residues in contact with GLU 131 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129Z GLY 3.3 0.2 - - - -
130Z ILE* 1.3 75.5 - - - +
132Z ALA* 1.3 60.4 + - - +
134Z LYS* 4.4 6.1 - - - +
135Z TRP* 2.8 39.4 + - + +
194Z VAL* 4.8 15.9 - - + +
244Z THR* 3.6 27.4 - - - -
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Residues in contact with ALA 132 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128Z ALA* 4.3 11.4 - - + -
129Z GLY* 3.3 24.5 + - - +
131Z GLU* 1.3 76.9 - - - +
133Z ILE* 1.3 58.4 + - - +
136Z GLY* 2.9 26.5 + - - +
137Z LEU* 3.0 10.8 + - - +
244Z THR* 4.9 3.9 - - - -
257Z PHE* 5.8 6.5 - - - -
259Z GLU* 5.2 12.7 - - + +
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Residues in contact with ILE 133 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97Z GLY* 6.4 1.6 - - - -
100Z VAL* 5.7 9.9 - - + -
101Z GLU* 6.4 1.1 - - - +
128Z ALA* 5.2 6.2 - - + +
129Z GLY 3.2 9.5 + - - +
130Z ILE* 3.5 9.4 - - - +
132Z ALA* 1.3 80.8 - - - +
134Z LYS* 1.3 59.4 + - - +
137Z LEU* 3.4 10.4 + - + +
138Z MET* 2.8 32.1 + - - +
151Z LEU* 5.2 10.8 - - + -
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Residues in contact with LYS 134 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130Z ILE 3.0 15.9 + - - +
131Z GLU* 4.2 5.6 - - - +
133Z ILE* 1.3 75.9 - - - +
135Z TRP* 1.3 58.3 + - + +
138Z MET* 3.8 17.4 - - - +
139Z PRO* 4.4 3.8 - - - +
151Z LEU* 5.1 18.8 - - + +
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Residues in contact with TRP 135 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131Z GLU* 2.8 21.6 + - + +
134Z LYS* 1.3 74.1 - - + +
136Z GLY* 1.3 59.9 + - - +
139Z PRO* 4.3 9.2 - - - +
246Z VAL* 4.7 17.5 - - + -
255Z SER* 3.7 22.0 - - - -
257Z PHE* 5.5 3.0 - - - +
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Residues in contact with GLY 136 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131Z GLU 3.7 0.8 + - - -
132Z ALA* 2.9 17.1 + - - -
135Z TRP* 1.3 79.9 - - - +
137Z LEU* 1.3 61.1 + - - +
138Z MET 3.7 0.2 - - - -
139Z PRO* 4.3 3.1 - - - +
140Z VAL* 4.0 14.9 + - - +
255Z SER* 5.2 9.3 - - - +
257Z PHE* 5.1 12.1 - - - +
293Z GLN* 4.7 10.7 - - - +
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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