Contacts of the strand formed by residues 131 - 137 (chain C) in PDB entry 4BUR
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 HIS 131 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129C PRO* 3.5 18.4 - - - +
130C SER* 1.3 81.3 + - - +
132C VAL* 1.3 82.7 + - - +
133C PRO* 4.2 3.6 - - + -
218C PRO* 5.2 4.9 - - - +
252C THR* 3.0 33.5 + - - +
253C TYR 4.0 10.3 - - - -
254C GLU* 3.2 40.6 + - + +
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Residues in contact with VAL 132 (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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129C PRO* 5.5 3.6 - - + +
131C HIS* 1.3 80.1 + - - +
133C PRO* 1.3 79.7 - - + +
134C PHE 3.4 24.0 - - - +
135C LEU* 4.4 12.6 - - + -
158C ARG 3.9 6.1 - - - +
160C LEU* 3.9 26.7 - - + +
217C LEU* 4.4 10.8 - - + -
251C ILE* 3.3 29.8 - - + -
252C THR 3.0 3.9 + - - +
253C TYR* 3.2 22.9 - - - +
254C GLU 3.4 0.7 + - - -
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Residues in contact with PRO 133 (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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131C HIS* 4.6 5.6 - - + -
132C VAL* 1.3 89.8 - - + +
134C PHE* 1.3 71.0 + - + +
158C ARG* 3.4 43.7 - - + +
254C GLU* 3.1 32.8 + - + +
255C LYS 3.0 27.5 + - - +
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Residues in contact with PHE 134 (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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132C VAL* 3.4 5.8 - - - +
133C PRO* 1.3 88.9 - - + +
135C LEU* 1.3 57.6 + - - +
136C LEU* 4.2 2.7 - - + -
150C ILE* 3.8 42.2 - - + -
154C ASP* 4.7 10.3 - - - -
157C ALA* 4.2 13.0 - - + -
158C ARG 3.3 17.7 + - - +
159C VAL* 3.5 10.7 - - + +
160C LEU 2.8 31.5 + - - +
254C GLU* 6.1 0.4 - - + -
255C LYS* 3.7 36.6 - - + +
469C MET* 3.8 14.4 - - + -
470C THR* 4.0 21.1 - - + -
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Residues in contact with LEU 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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132C VAL* 4.4 7.4 - - + -
133C PRO 4.1 1.0 + - - -
134C PHE* 1.3 71.0 - - - +
136C LEU* 1.3 66.0 + - - +
137C ILE* 4.6 12.6 - - + -
160C LEU* 3.5 28.0 - - + +
162C VAL* 3.6 27.8 - - + -
233C VAL* 5.7 0.2 - - + -
243C VAL* 3.7 35.0 - - + -
251C ILE* 4.7 7.2 - - + -
253C TYR* 3.8 35.0 - - + -
255C LYS 3.1 8.6 + - - +
256C CYS* 3.2 8.3 - - - -
257C LEU 2.9 24.8 + - - -
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Residues in contact with LEU 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 PHE 4.4 4.7 - - - +
135C LEU* 1.3 85.0 - - - +
137C ILE* 1.3 64.8 + - - +
138C GLY 3.4 1.6 + - - +
143C ALA* 3.6 31.4 - - + +
146C ALA* 4.0 4.9 - - + -
147C ALA* 3.7 14.6 - - + +
150C ILE* 4.3 10.1 - - + -
159C VAL* 4.0 12.1 - - + -
160C LEU 2.8 13.5 + - - +
161C ILE* 3.4 24.2 - - + +
162C VAL 3.1 23.5 + - - -
257C LEU* 3.6 19.7 - - + +
259C ALA* 6.2 0.2 - - - -
469C MET* 3.9 23.6 - - + -
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Residues in contact with ILE 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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135C LEU* 4.6 8.3 - - + -
136C LEU* 1.3 71.0 - - - +
138C GLY* 1.3 61.2 + - - +
162C VAL* 4.0 4.3 - - - +
233C VAL* 3.9 34.8 - - + -
236C LEU* 5.1 5.4 - - + -
243C VAL* 4.2 11.7 - - + -
256C CYS* 4.1 21.3 - - - -
257C LEU 2.7 18.7 + - - +
258C ILE* 4.4 12.3 - - + -
259C ALA* 2.9 30.8 + - - +
260C THR* 3.8 15.0 + - + -
406C LEU* 4.1 13.7 - - + -
1612C FAD 3.9 22.0 - - - +
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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