Contacts of the helix formed by residues 152 - 165 (chain C) in PDB entry 3BFT
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 ILE 152 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A GLU 5.8 0.9 - - - +
244A GLN 4.1 21.8 - - - +
245A GLY* 4.9 6.7 - - - -
249A LYS* 5.3 11.7 - - - +
146C PHE* 5.8 2.2 - - + -
150C SER* 3.3 17.0 + - - +
151C LYS* 1.3 82.3 - - + +
153C ALA* 1.3 68.9 + - + +
154C VAL* 4.0 15.7 - - + +
155C PHE* 3.0 29.7 + - + +
156C ASP* 2.8 20.9 + - - -
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Residues in contact with ALA 153 (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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151C LYS 3.3 5.9 + - - -
152C ILE* 1.3 71.9 - - + +
154C VAL* 1.3 60.8 + - + +
156C ASP* 3.7 7.2 - - - +
157C LYS* 2.8 33.2 + - - +
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Residues in contact with VAL 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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124C ALA* 4.0 7.4 - - + +
125C GLU* 3.9 46.7 - - + +
128C SER* 3.9 10.2 - - - +
129C LYS* 6.4 0.2 - - - -
152C ILE* 3.3 10.7 - - + +
153C ALA* 1.3 78.8 - - + +
155C PHE* 1.3 77.8 + - + +
157C LYS* 3.4 6.8 + - - +
158C MET* 3.1 25.0 + - - +
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Residues in contact with PHE 155 (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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124C ALA* 4.1 11.7 - - + -
146C PHE* 3.7 24.7 - + + -
147C PHE* 3.8 25.6 - + + +
150C SER* 3.3 30.3 - - - +
152C ILE* 3.0 28.7 + - + +
154C VAL* 1.3 84.1 - - + +
156C ASP* 1.3 67.0 + - - +
158C MET* 3.1 8.6 + - - +
159C TRP* 2.9 22.8 + - - +
215C LEU* 3.9 43.3 - - + -
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Residues in contact with ASP 156 (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 PHE 4.9 1.6 - - - -
150C SER* 4.1 20.8 + - - +
151C LYS* 4.7 3.8 - - - +
152C ILE 2.8 18.1 + - - +
153C ALA* 3.7 6.0 - - - +
155C PHE* 1.3 77.1 - - - +
157C LYS* 1.3 59.0 + - - +
159C TRP* 3.2 16.3 + - - +
160C THR* 2.9 40.0 + - - -
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Residues in contact with LYS 157 (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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128C SER* 3.4 37.3 + - - +
129C LYS* 4.7 10.7 - - - +
135C TYR* 4.8 0.4 + - - +
153C ALA 2.8 18.6 + - - +
154C VAL* 3.5 7.0 - - - +
156C ASP* 1.3 80.2 - - - +
158C MET* 1.3 61.2 + - - +
160C THR* 3.3 10.0 + - - -
161C TYR* 3.2 21.3 + - - +
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Residues in contact with MET 158 (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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124C ALA* 3.7 32.3 - - + +
127C LEU* 4.1 14.4 - - + -
128C SER* 3.9 12.3 - - - -
135C TYR* 3.6 32.3 - - + +
147C PHE* 3.7 14.1 - - + -
154C VAL* 3.1 22.6 + - - +
155C PHE* 3.1 8.7 + - - +
157C LYS* 1.3 76.1 - - - +
159C TRP* 1.3 57.5 + - - +
161C TYR* 3.4 2.9 + - - +
162C MET* 2.9 40.1 + - + +
191C LEU* 3.4 36.8 - - + -
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Residues in contact with TRP 159 (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 LYS* 4.0 30.7 - - + -
147C PHE* 3.6 24.5 - - + +
148C ARG* 3.5 57.4 + - + +
155C PHE 2.9 12.4 + - - +
156C ASP* 3.4 17.7 - - - +
157C LYS 3.1 0.2 - - - -
158C MET* 1.3 75.1 - - - +
160C THR* 1.3 67.3 + - - +
162C MET* 4.1 10.0 - - + +
163C ARG* 3.0 75.2 + - + +
170C PHE* 3.8 23.1 - + - -
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Residues in contact with THR 160 (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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156C ASP* 2.9 27.8 + - - -
157C LYS* 3.3 11.8 + - - -
159C TRP* 1.3 78.0 - - - +
161C TYR* 1.3 65.2 + - - +
163C ARG* 3.5 33.2 + - - +
164C SER* 3.7 11.4 + - - +
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Residues in contact with TYR 161 (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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130C GLN 6.1 0.9 - - - -
131C THR* 5.4 14.7 + - + -
133C ILE 5.0 1.1 - - - -
134C ALA* 3.2 33.4 - - - +
135C TYR* 3.3 63.6 + + - +
157C LYS 3.2 9.6 + - - +
158C MET 3.6 4.3 - - - +
159C TRP 3.1 0.6 - - - -
160C THR* 1.3 80.5 - - - +
162C MET* 1.3 71.5 + - + +
164C SER* 3.3 3.6 + - - -
165C ALA* 2.9 44.4 + - + +
169C VAL* 3.7 6.8 - - - +
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Residues in contact with MET 162 (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 TYR* 3.3 25.6 - - + +
136C GLY* 3.7 23.3 - - - -
137C THR* 3.9 13.0 - - + -
147C PHE* 3.6 48.7 - - + -
158C MET* 2.9 33.8 + - + +
159C TRP* 3.3 6.7 + - + +
161C TYR* 1.3 83.4 - - + +
163C ARG* 1.3 62.1 + - - +
164C SER 3.2 0.9 + - - -
165C ALA* 3.3 9.9 + - - +
168C SER* 6.0 0.2 - - - -
169C VAL* 3.6 13.5 + - + +
170C PHE* 3.5 28.5 - - + -
191C LEU* 4.1 4.5 - - + -
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Residues in contact with ARG 163 (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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159C TRP* 3.0 62.5 + - + +
160C THR* 3.5 26.1 + - - +
162C MET* 1.3 77.5 - - - +
164C SER* 1.3 68.7 + - - +
165C ALA 4.9 1.6 - - - +
170C PHE* 4.1 12.4 - - - -
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Residues in contact with SER 164 (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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160C THR* 3.7 15.4 + - - +
161C TYR 3.3 2.7 + - - -
162C MET 3.2 0.6 - - - -
163C ARG* 1.3 86.9 + - - +
165C ALA* 1.3 68.2 + - - +
166C GLU* 3.5 17.5 + - - +
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Residues in contact with ALA 165 (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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161C TYR* 2.9 35.4 + - + +
162C MET 3.3 12.2 + - - +
163C ARG 4.9 1.6 - - - +
164C SER* 1.3 79.9 - - - +
166C GLU* 1.3 63.0 + - - +
167C PRO 3.4 8.9 - - - +
168C SER* 4.0 6.6 + - - -
169C VAL* 3.7 27.8 - - + -
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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