Contacts of the helix formed by residues 133 - 140 (chain R) in PDB entry 1RZZ
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 LEU 133 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129R LEU* 2.7 40.9 + - + +
132R VAL* 1.3 77.4 - - + +
134R PHE* 1.3 85.6 + - + +
135R ARG 3.3 1.3 - - - -
136R PRO* 3.1 3.3 - - - +
137R VAL* 2.8 52.6 + - + +
142R TRP* 4.5 13.7 - - + -
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Residues in contact with PHE 134 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126R LEU* 4.1 20.6 - - + -
129R LEU* 3.0 45.3 + - + +
130R THR* 3.4 17.3 - - + -
133R LEU* 1.3 94.9 - - + +
135R ARG* 1.3 57.8 + - - +
137R VAL* 3.9 2.8 - - - +
138R MET* 3.0 35.1 + - - +
249R ILE* 3.9 17.9 - - + -
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Residues in contact with ARG 135 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130R THR* 2.9 25.0 + - + +
131R LEU* 4.5 7.8 + - - +
134R PHE* 1.3 70.6 - - - +
136R PRO* 1.3 71.6 - - + +
138R MET* 3.2 3.4 + - - +
139R MET* 2.8 58.8 + - + +
144R TYR* 3.8 27.0 + - - +
156R TRP* 4.0 7.7 - - - +
160R THR* 3.6 24.4 - - - +
164R TYR* 4.5 3.8 + - - -
248R MET* 3.3 44.6 + - - +
249R ILE* 4.0 13.6 - - + +
251R THR* 2.6 41.3 + - - +
253R THR* 4.9 3.4 - - + -
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Residues in contact with PRO 136 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75R LEU* 4.3 0.2 - - - -
131R LEU 3.4 22.7 - - - +
132R VAL 3.5 14.1 - - - +
133R LEU 3.1 14.6 - - - +
135R ARG* 1.3 94.4 - - + +
137R VAL* 1.3 56.2 + - - +
139R MET 3.1 2.0 + - - +
140R GLY 2.8 24.9 + - - -
141R ALA 2.9 31.2 + - - +
142R TRP* 4.0 15.7 - - + -
144R TYR* 4.3 9.9 - - + +
145R ALA* 3.8 17.5 - - + +
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Residues in contact with VAL 137 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75R LEU* 3.7 27.2 - - + +
133R LEU* 2.8 43.9 + - + +
134R PHE* 3.9 3.6 - - - +
136R PRO* 1.3 71.8 - - - +
138R MET* 1.3 65.6 + - + +
140R GLY* 3.0 13.9 + - - -
142R TRP* 4.2 22.7 - - + -
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Residues in contact with MET 138 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134R PHE* 3.0 18.5 + - + +
135R ARG 3.6 3.1 - - - +
137R VAL* 1.3 79.7 - - + +
139R MET* 1.3 61.6 + - - +
140R GLY 3.2 1.0 + - - -
249R ILE* 3.7 33.2 - - + +
253R THR* 3.7 36.6 - - + +
254R ILE* 5.7 3.6 - - + -
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Residues in contact with MET 139 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135R ARG* 2.8 58.6 + - - +
136R PRO 3.7 0.7 - - - +
138R MET* 1.3 76.5 - - - +
140R GLY* 1.3 59.1 + - - +
141R ALA 3.6 0.2 - - - -
144R TYR* 3.4 56.8 - - + -
164R TYR* 4.3 6.5 - - - +
251R THR 4.1 1.3 - - - +
252R GLY* 3.6 33.2 - - - +
253R THR* 3.8 17.7 - - + -
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Residues in contact with GLY 140 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74R GLY* 3.6 13.9 - - - -
75R LEU* 3.6 17.0 + - - +
136R PRO 2.8 5.5 + - - -
137R VAL 3.0 13.6 + - - -
138R MET 3.2 1.0 + - - -
139R MET* 1.3 78.7 - - - +
141R ALA* 1.3 61.9 + - - +
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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