Contacts of the helix formed by residues 140 - 154 (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 GLY 140 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C GLY 3.4 6.7 + - - -
139C GLY* 1.3 80.6 - - - +
141C THR* 1.3 66.4 + - - -
142C ALA 3.4 2.2 - - - -
143C ALA* 4.1 2.3 - - - +
144C PHE* 3.2 22.3 + - - +
169C PRO* 4.1 5.6 - - - +
170C TYR 5.3 4.5 - - - -
172C ARG* 5.1 2.9 - - - -
205C PHE* 4.8 1.6 - - - -
259C ALA 5.0 0.8 + - - -
1612C FAD 3.5 26.4 + - - -
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Residues in contact with THR 141 (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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140C GLY* 1.3 71.9 - - - -
142C ALA* 1.3 67.7 + - - +
144C PHE* 3.3 3.3 + - - +
145C ALA* 3.0 21.8 + - - +
170C TYR 4.0 8.1 + - - -
171C MET* 4.5 1.9 - - - -
172C ARG* 5.0 0.9 + - - +
205C PHE* 3.6 32.7 - - + -
455C HIS* 3.9 17.9 - - + +
458C ALA* 4.1 13.0 - - + -
459C VAL* 3.7 27.6 - - + -
1612C FAD 2.8 25.8 + - - -
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Residues in contact with ALA 142 (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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141C THR* 1.3 77.9 - - - +
143C ALA* 1.3 55.8 + - - +
145C ALA 3.3 0.3 + - - -
146C ALA* 2.9 26.5 + - - +
257C LEU* 4.7 1.1 - - - -
259C ALA* 3.7 19.3 - - + -
436C ALA* 4.2 21.5 - - + -
437C GLY* 4.2 2.0 - - - +
458C ALA* 3.4 21.0 - - + +
462C GLY* 3.5 9.5 - - - -
1612C FAD 2.9 22.9 + - - +
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Residues in contact with ALA 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C LEU* 3.6 18.8 - - + +
138C GLY 3.0 28.5 - - - +
139C GLY* 4.5 0.7 - - - -
140C GLY 3.7 10.2 + - - +
141C THR 3.3 0.2 - - - -
142C ALA* 1.3 73.4 - - - +
144C PHE* 1.3 67.7 + - - +
146C ALA* 2.9 6.1 + - - +
147C ALA* 2.8 21.5 + - - +
161C ILE* 4.3 17.0 - - + -
257C LEU* 4.5 4.7 - - - -
259C ALA* 3.9 8.5 - - + +
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Residues in contact with PHE 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C GLY 3.2 16.0 + - - +
141C THR 3.3 3.1 + - - +
143C ALA* 1.3 77.8 - - - +
145C ALA* 1.3 66.7 + - - +
147C ALA* 3.7 7.9 - - + +
148C ARG* 3.0 62.8 + - + +
161C ILE* 4.6 5.5 - - + +
169C PRO* 4.2 8.3 - - + -
205C PHE* 3.5 52.7 - + + -
206C GLN* 3.8 30.5 - - + -
211C TYR* 3.5 30.7 - + - -
225C VAL* 6.0 2.0 - - + -
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Residues in contact with ALA 145 (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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141C THR 3.0 16.3 + - - +
142C ALA 3.8 3.4 - - - +
144C PHE* 1.3 81.9 - - + +
146C ALA* 1.3 56.9 + - - +
148C ARG* 4.1 4.7 - - - +
149C SER* 3.2 27.0 + - - -
459C VAL* 3.5 44.0 - - + +
462C GLY* 4.2 0.4 - - - -
463C ARG* 3.7 16.5 + - + +
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Residues in contact with ALA 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C LEU* 4.0 8.1 - - + -
142C ALA 2.9 12.4 + - - +
143C ALA 2.9 7.5 + - - +
145C ALA* 1.3 74.7 - - - +
147C ALA* 1.3 54.1 + - - +
149C SER* 3.1 4.0 + - - -
150C ILE* 2.7 42.6 + - + +
257C LEU* 3.6 24.5 - - + -
462C GLY 3.4 20.6 - - - +
465C ALA 5.2 0.2 - - - -
466C GLY* 4.3 8.1 - - - +
469C MET* 5.4 0.9 - - - -
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Residues in contact with ALA 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C LEU* 3.7 9.2 - - + +
143C ALA 2.8 18.1 + - - +
144C PHE* 3.7 7.2 - - + +
146C ALA* 1.3 71.6 - - - +
148C ARG* 1.3 63.4 + - + +
150C ILE* 3.1 6.5 + - - +
151C ARG* 2.9 29.5 + - - +
159C VAL* 4.0 24.4 - - + +
161C ILE* 4.2 12.1 - - + -
225C VAL* 4.0 15.9 - - + -
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Residues in contact with ARG 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C PHE* 3.0 53.4 + - + +
145C ALA* 4.2 5.4 - - - +
147C ALA* 1.3 76.4 - - + +
149C SER* 1.3 57.2 + - - +
151C ARG* 3.6 8.4 + - - +
152C ALA* 3.1 28.1 + - - +
205C PHE 5.5 3.6 + - - -
206C GLN* 4.7 15.1 - - - +
225C VAL* 6.0 0.9 - - + -
463C ARG* 5.6 8.0 - - - +
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Residues in contact with SER 149 (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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145C ALA 3.2 20.6 + - - -
146C ALA 3.1 5.9 + - - -
148C ARG* 1.3 75.4 - - - +
150C ILE* 1.3 65.9 + - - +
152C ALA* 3.6 6.6 + - - +
153C ARG* 3.4 24.4 + - - +
463C ARG* 2.9 41.3 + - - +
466C GLY* 4.0 6.0 - - - -
467C GLU* 3.4 16.1 + - - +
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Residues in contact with ILE 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C PHE* 3.8 54.7 - - + -
136C LEU* 4.3 10.5 - - + -
146C ALA* 2.7 25.6 + - + +
147C ALA 3.6 4.5 - - - +
149C SER* 1.3 72.5 - - - +
151C ARG* 1.3 56.6 + - - +
153C ARG* 3.1 2.9 + - - +
154C ASP* 2.9 27.4 + - + +
157C ALA* 3.8 11.9 - - + -
159C VAL* 4.0 9.6 - - + -
466C GLY* 3.9 17.9 - - - +
469C MET* 4.1 24.2 - - + -
470C THR* 4.0 14.5 - - + +
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Residues in contact with ARG 151 (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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147C ALA 2.9 21.6 + - - +
148C ARG* 4.0 7.9 - - - +
150C ILE* 1.3 74.1 - - - +
152C ALA* 1.3 63.3 + - - +
153C ARG 3.3 0.5 + - - -
154C ASP 3.3 20.6 - - - +
155C PRO* 3.3 34.0 + - - +
157C ALA* 2.8 40.8 + - - +
159C VAL* 4.5 3.4 - - + -
222C ASN* 3.5 4.4 + - - +
223C GLY 3.4 8.3 + - - -
224C GLY* 3.1 26.6 - - - +
225C VAL* 3.9 23.7 - - + +
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Residues in contact with ALA 152 (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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148C ARG 3.1 18.4 + - - +
149C SER* 3.9 7.2 - - - +
150C ILE 3.3 0.4 - - - -
151C ARG* 1.3 77.6 - - - +
153C ARG* 1.3 62.9 + - + +
155C PRO* 4.8 5.7 - - - +
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Residues in contact with ARG 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C SER 3.4 10.4 + - - +
150C ILE 3.1 3.1 + - - +
152C ALA* 1.3 84.8 - - + +
154C ASP* 1.3 59.0 + - - +
155C PRO* 3.8 6.5 - - - +
467C GLU* 3.5 32.1 + - - +
470C THR* 2.7 52.4 + - - +
471C GLY 3.9 1.6 - - - -
472C ALA* 3.4 31.5 - - - +
474C LYS* 6.1 1.0 - - - +
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Residues in contact with ASP 154 (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* 4.7 9.4 - - + -
150C ILE* 2.9 10.9 + - + +
151C ARG* 3.3 7.4 - - - +
153C ARG* 1.3 76.0 - - - +
155C PRO* 1.3 65.5 - - - +
156C GLY* 2.8 20.5 + - - -
157C ALA* 3.1 29.4 + - + +
470C THR* 4.9 13.4 - - + +
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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
------------------------------------------------------------
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