Contacts of the helix formed by residues 132 - 149 (chain C) in PDB entry 4BPU
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 TRP 132 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C MET* 4.0 9.0 - - + -
127C ILE* 4.1 17.0 - - + -
128C CYS 3.1 15.8 + - - +
129C PRO* 4.0 9.4 + - + +
130C LYS 3.7 0.4 - - - -
131C CYS* 1.3 78.4 - - - +
133C THR* 1.3 53.9 + - - +
134C LEU 2.9 0.2 - - - -
135C MET* 2.7 56.4 + - + +
136C THR* 3.2 20.4 + - - +
139C ILE* 5.9 1.7 - - + +
159C TYR* 3.6 31.6 - + - -
163C ARG 4.5 2.5 - - - -
164C GLY 4.2 11.9 - - - -
165C VAL* 3.9 15.0 - - + -
334C ILE* 5.2 0.4 - - + -
339C VAL 5.6 0.2 + - - -
342C PHE* 3.5 48.1 + + - +
344C PRO* 3.7 29.5 - - + +
345C PHE* 5.7 0.2 - - + -
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Residues in contact with THR 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C PRO 3.9 12.9 + - - -
130C LYS* 4.1 4.3 + - - -
131C CYS 3.0 0.2 - - - -
132C TRP* 1.3 78.7 - - - +
134C LEU* 1.3 55.7 + - - +
136C THR* 3.3 11.1 + - - -
137C MET* 2.9 33.5 + - + +
222C TYR* 3.9 28.7 - - + -
226C TYR* 3.7 34.0 - - + +
230C ASN* 5.2 4.9 + - - -
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Residues in contact with LEU 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C MET* 3.8 19.5 - - - -
115C TYR* 3.7 48.6 + - + -
118C VAL* 5.1 1.3 - - + -
119C ARG* 4.7 9.6 - - + -
131C CYS* 3.0 13.0 + - + +
132C TRP 2.9 0.4 - - - -
133C THR* 1.3 78.8 - - - +
135C MET* 1.3 58.6 + - - +
137C MET* 3.4 17.6 + - + +
138C ALA* 3.0 27.8 + - - +
226C TYR* 3.2 33.4 - - + +
300C TYR 3.4 20.6 - - - +
301C CYS* 3.9 8.5 - - - +
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Residues in contact with MET 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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110C ILE* 3.7 22.0 - - + +
111C ASP 4.0 0.7 - - - -
112C MET* 3.7 37.0 - - + +
115C TYR* 3.6 31.2 - - + -
132C TRP* 2.7 56.6 + - + +
134C LEU* 1.3 71.3 - - - +
136C THR* 1.3 55.3 + - - +
138C ALA* 3.0 2.9 + - - +
139C ILE* 2.8 42.2 + - + +
163C ARG 4.2 0.7 - - - +
164C GLY* 3.8 18.6 - - - -
165C VAL* 4.0 14.6 - - + -
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Residues in contact with THR 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C TRP* 3.2 22.3 + - - +
133C THR* 3.4 15.4 - - + -
135C MET* 1.3 79.0 - - - +
137C MET* 1.3 61.7 + - - +
139C ILE* 3.6 6.6 + - - +
140C ARG* 3.1 27.8 + - - +
222C TYR* 3.9 32.3 - - + +
339C VAL* 4.2 17.6 + - + +
340C ASP* 4.1 21.4 + - - +
342C PHE 5.5 0.3 + - - -
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Residues in contact with MET 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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133C THR* 2.9 26.0 + - + +
134C LEU* 3.7 25.4 - - + +
136C THR* 1.3 73.3 - - - +
138C ALA* 1.3 60.5 + - - +
140C ARG* 4.0 4.8 - - - +
141C ILE* 2.8 45.0 + - + +
218C ILE* 5.1 3.1 - - + +
219C ILE* 4.4 13.7 - - + +
222C TYR* 3.7 41.7 - - + -
226C TYR* 4.1 12.6 - - + -
301C CYS* 3.7 46.2 - - + +
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Residues in contact with ALA 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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110C ILE* 3.9 26.7 - - + -
115C TYR* 4.0 7.4 - - - +
134C LEU 3.0 18.0 + - - +
135C MET* 3.0 9.4 + - - +
137C MET* 1.3 74.7 - - - +
139C ILE* 1.3 66.1 + - + +
142C ILE* 3.0 30.8 + - - +
301C CYS 5.3 0.2 + - - -
303C PRO* 3.9 24.9 - - + -
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Residues in contact with ILE 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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132C TRP* 5.9 1.3 - - + +
135C MET* 2.8 26.4 + - + +
136C THR* 3.9 4.9 - - - +
138C ALA* 1.3 72.5 - - - +
140C ARG* 1.3 57.6 + - + +
143C ASP* 2.9 36.6 + - - +
157C TRP* 3.8 35.6 - - + -
165C VAL* 4.0 17.5 - - + -
334C ILE* 4.0 29.2 - - + -
336C LEU* 3.5 30.5 - - + -
339C VAL* 3.8 22.7 - - + -
342C PHE* 6.2 0.4 - - + -
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Residues in contact with ARG 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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136C THR* 3.1 18.6 + - - +
137C MET 4.0 0.7 - - - +
139C ILE* 1.3 77.1 - - + +
141C ILE* 1.3 63.0 + - - +
143C ASP* 4.5 2.6 - - - +
144C ARG* 3.1 27.4 + - - +
218C ILE* 3.8 29.1 - - + +
221C LYS* 4.6 16.8 - - - +
222C TYR* 2.9 36.9 + - - -
336C LEU* 6.2 0.2 - - - -
339C VAL* 4.1 19.0 - - + +
340C ASP* 3.6 18.2 + - - -
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Residues in contact with ILE 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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137C MET* 2.8 34.1 + - + +
138C ALA 3.9 2.2 - - - +
140C ARG* 1.3 76.5 - - - +
142C ILE* 1.3 64.2 + - + +
144C ARG* 3.7 7.4 + - - +
145C ALA* 3.5 17.3 + - - +
211C PHE* 4.5 5.2 - - + -
215C SER* 3.4 34.5 + - - +
218C ILE* 4.1 15.5 - - + -
219C ILE* 3.7 33.9 - - + -
301C CYS 4.6 0.4 - - - +
302C PHE* 3.8 17.9 - - + -
303C PRO* 3.7 27.6 - - + -
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Residues in contact with ILE 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C PHE* 4.9 7.6 - - + -
110C ILE* 3.6 29.4 - - + -
138C ALA 3.0 14.8 + - - +
141C ILE* 1.3 75.5 - - + +
143C ASP* 1.3 59.6 + - - +
144C ARG 3.1 1.8 - - - -
145C ALA* 2.7 27.0 + - - +
146C LEU* 2.8 35.4 + - + +
157C TRP* 4.0 13.0 - - + -
189C LEU* 4.4 22.2 - - + +
211C PHE* 6.0 0.7 - - + -
302C PHE* 6.2 0.2 - - + -
303C PRO* 3.9 20.9 - - + -
305C LEU* 3.8 26.5 - - + -
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Residues in contact with ASP 143 (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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139C ILE 2.9 21.4 + - - +
140C ARG* 4.5 2.2 - - - +
142C ILE* 1.3 78.4 - - - +
144C ARG* 1.3 62.5 + - - +
146C LEU* 3.4 6.5 + - - +
147C LYS* 3.0 26.7 + - - +
155C ARG* 2.6 37.7 + - - -
157C TRP* 2.9 32.5 + - - +
336C LEU* 3.3 21.7 - - + +
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Residues in contact with ARG 144 (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 ARG 3.1 21.2 + - - +
141C ILE 3.7 6.5 + - - +
143C ASP* 1.3 80.4 + - - +
145C ALA* 1.3 59.9 + - - +
147C LYS* 4.7 5.6 - - - +
148C GLU* 2.9 68.4 + - - +
149C ASP* 3.0 39.0 + - - -
211C PHE* 3.3 31.5 + - - +
214C LYS* 3.4 34.4 - - - +
215C SER* 4.9 1.6 + - - +
218C ILE* 3.9 20.1 - - + +
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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 ILE 3.5 4.1 + - - +
142C ILE 2.7 15.5 + - - +
144C ARG* 1.3 83.9 - - - +
146C LEU* 1.3 64.0 + - - +
149C ASP* 3.0 27.4 + - - +
150C PHE* 3.1 11.7 + - - -
188C TYR* 4.7 1.8 - - + -
189C LEU* 3.5 29.2 - - + -
211C PHE* 3.5 20.9 - - + -
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Residues in contact with LEU 146 (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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108C PHE* 3.7 31.9 - - + -
142C ILE* 2.8 29.2 + - + +
143C ASP* 3.8 4.9 - - - +
145C ALA* 1.3 76.5 - - - +
147C LYS* 1.3 56.8 + - - +
150C PHE* 3.5 8.3 - - + +
151C GLY 3.2 7.1 + - - -
152C PHE* 2.8 53.6 + - + +
155C ARG* 3.8 17.5 - - - -
167C CYS* 3.9 13.5 - - - -
169C VAL* 3.7 23.6 - - + -
185C ILE* 4.5 5.6 - - + -
189C LEU* 4.5 10.8 - - + -
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Residues in contact with LYS 147 (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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143C ASP* 3.0 20.1 + - - +
144C ARG* 4.1 3.8 - - - +
146C LEU* 1.3 78.4 - - - +
148C GLU* 1.3 80.6 + - + +
151C GLY* 3.2 22.6 - - - -
152C PHE 3.6 9.3 + - - +
155C ARG* 3.4 33.2 - - - +
204D ASP* 4.5 3.6 - - - +
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Residues in contact with GLU 148 (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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144C ARG* 2.9 52.9 + - + +
147C LYS* 1.3 102.0 + - + +
149C ASP* 1.3 58.9 + - - +
214C LYS* 4.5 11.2 + - - +
203D GLU* 3.7 6.9 - - - +
204D ASP* 2.7 32.4 + - - +
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Residues in contact with ASP 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C ARG* 3.0 38.9 + - - -
145C ALA* 3.0 12.5 + - - +
148C GLU* 1.3 79.3 - - - +
150C PHE* 1.3 62.6 + - + +
188C TYR* 2.6 41.1 + - + +
211C PHE* 3.7 3.5 - - - +
214C LYS* 4.5 8.0 + - - -
188D PHE* 5.7 0.3 - - - +
201D TYR* 5.9 0.7 - - - -
202D LEU* 3.4 36.8 - - + +
203D GLU 3.4 8.3 + - - -
204D ASP 3.9 0.4 - - - -
205D GLY* 3.4 9.2 + - - -
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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