Contacts of the helix formed by residues 134 - 140 (chain C) in PDB entry 3RBQ
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 134 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C PHE* 1.3 78.0 - - - +
135C PRO* 1.3 70.0 - - - +
136C ALA* 3.3 21.6 + - - +
137C PHE* 2.9 29.4 + - - +
236C TYR* 3.6 9.4 - - - +
238C GLY* 4.0 7.4 - - - +
237D SER* 3.7 14.6 - - - +
238D GLY 4.4 6.5 - - - +
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Residues in contact with PRO 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C THR* 1.3 85.0 - - - +
136C ALA* 1.3 61.7 + - - +
138C LEU* 3.2 19.6 + - - +
139C ARG* 4.1 7.7 + - - +
208C ILE* 3.6 20.3 - - + +
236C TYR* 3.1 22.6 - - + +
237C SER 4.5 0.2 - - - -
238C GLY 4.0 4.0 - - - +
135D PRO* 3.8 16.2 - - + -
208D ILE* 3.4 33.4 - - + -
237D SER* 3.3 27.4 - - - +
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Residues in contact with ALA 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C THR* 3.1 13.2 + - - +
135C PRO* 1.3 76.8 - - - +
137C PHE* 1.3 67.1 + - - +
139C ARG* 2.9 26.6 + - + +
140C LEU* 3.6 13.0 + - + +
237D SER* 5.9 5.0 - - - -
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Residues in contact with PHE 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C ILE* 4.7 2.2 - - + -
102C LEU* 3.7 37.9 - - + -
133C PHE* 3.6 53.8 - + + -
134C THR* 2.9 21.3 + - - +
136C ALA* 1.3 78.9 - - - +
138C LEU* 1.3 60.4 + - + +
140C LEU* 3.2 23.9 + - + +
143C VAL* 4.7 1.6 - - + -
196C PHE* 3.2 43.7 - + - -
234C TYR* 5.7 1.1 - + - -
236C TYR* 3.6 24.2 - + + -
500I DAO 4.1 26.7 - - + -
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Residues in contact with LEU 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C PRO 3.2 8.7 + - - +
136C ALA 3.0 1.8 + - - -
137C PHE* 1.3 77.6 - - + +
139C ARG* 1.3 60.3 + - - +
140C LEU 3.4 1.0 + - - +
196C PHE* 4.5 7.8 - - + -
199C LEU* 3.8 22.9 - - + +
204C ILE* 3.8 38.6 - - + +
207C MET* 3.8 32.1 - - + -
208C ILE* 3.5 32.8 - - + -
236C TYR* 3.7 41.1 - - + -
500I DAO 6.0 2.2 - - + -
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Residues in contact with ARG 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C PRO 4.1 9.9 + - - +
136C ALA* 2.9 16.9 + - + +
138C LEU* 1.3 76.7 - - - +
140C LEU* 1.3 66.8 + - - +
141C ARG* 3.8 0.7 + - - +
201C GLU* 2.8 43.0 + - - -
204C ILE* 3.6 34.5 - - - +
208C ILE* 6.0 0.4 - - - +
205D SER* 3.3 16.6 + - - -
209D ARG* 3.3 50.6 - - + +
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Residues in contact with LEU 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ASP* 3.5 33.7 - - + +
97C ASP* 6.1 0.7 - - + -
102C LEU* 3.7 21.8 - - + -
136C ALA* 3.8 11.4 - - + +
137C PHE* 3.2 30.0 + - + +
138C LEU 3.4 1.1 - - - +
139C ARG* 1.3 84.3 - - - +
141C ARG* 1.3 60.9 + - - +
142C GLN 4.5 2.9 - - - +
143C VAL* 3.7 24.9 - - + -
196C PHE* 3.4 30.8 - - + +
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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