Contacts of the helix formed by residues 143 - 161 (chain C) in PDB entry 3BQM
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 GLN 143 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C SER 3.3 7.7 + - - +
142C LEU* 1.3 72.7 - - - +
144C PRO* 1.4 81.3 - - + +
145C ASP* 3.2 17.9 - - - +
146C GLU* 2.9 33.9 + - - +
147C PHE* 3.0 11.7 + - - +
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Residues in contact with PRO 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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142C LEU 3.8 2.4 - - - +
143C GLN* 1.4 94.1 - - + +
145C ASP* 1.3 62.8 + - - +
147C PHE* 3.4 8.4 + - + +
148C GLN* 3.1 22.9 + - - +
201C HIS* 5.0 7.6 - - - +
203C LEU* 6.5 0.9 - - + -
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Residues in contact with ASP 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C GLN* 3.2 16.1 + - - +
144C PRO* 1.3 79.9 - - - +
146C GLU* 1.3 67.1 + - - +
148C GLN* 3.4 6.7 + - - +
149C LYS* 2.9 61.9 + - - +
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Residues in contact with GLU 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C SER 3.9 3.6 - - - +
142C LEU* 3.6 9.2 - - + -
143C GLN* 2.9 38.7 + - + +
145C ASP* 1.3 89.1 - - - +
147C PHE* 1.3 64.6 + - - +
149C LYS* 3.3 1.7 + - - +
150C ILE* 3.2 18.9 + - - +
239C ASP* 4.7 1.4 - - - +
292C PHE* 3.4 64.1 - - + -
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Residues in contact with PHE 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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136C PHE* 3.7 20.6 - + - -
137C ASP 3.8 18.2 - - - -
142C LEU* 4.0 5.9 - - + +
143C GLN 3.0 10.8 + - - +
144C PRO* 3.6 8.7 - - + +
146C GLU* 1.3 76.1 - - - +
148C GLN* 1.3 62.5 + - - +
150C ILE* 3.2 13.4 + - + +
151C LEU* 3.2 32.5 + - + +
172C GLN* 3.5 29.8 - - - -
199C VAL* 3.6 30.3 - - + -
200C LYS* 5.3 0.2 - - - -
201C HIS* 3.7 50.5 - + + +
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Residues in contact with GLN 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 PRO 3.1 16.4 + - - +
145C ASP* 3.8 8.1 - - - +
146C GLU 3.3 0.2 - - - -
147C PHE* 1.3 74.5 - - + +
149C LYS* 1.3 61.1 + - + +
151C LEU* 3.0 28.3 + - - +
152C ASP* 2.8 58.4 + - - +
155C LYS* 4.1 12.9 - - - +
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Residues in contact with LYS 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 ASP* 2.9 49.5 + - - +
146C GLU 3.3 5.6 + - - +
148C GLN* 1.3 75.8 - - + +
150C ILE* 1.3 61.1 + - - +
152C ASP* 3.7 14.6 - - - +
153C PHE* 3.1 23.7 + - - +
292C PHE* 3.9 35.7 - - + +
293C GLU* 3.3 35.7 - - - +
295C LEU* 3.6 7.1 - - + +
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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
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136C PHE* 3.7 34.3 - - + -
137C ASP* 4.1 17.0 - - + +
142C LEU* 3.9 16.8 - - + -
146C GLU 3.2 11.6 + - - +
147C PHE* 3.4 10.3 - - + +
148C GLN 3.2 0.6 - - - -
149C LYS* 1.3 77.2 - - - +
151C LEU* 1.3 62.5 + - - +
153C PHE* 3.2 5.2 + - - +
154C MET* 3.0 24.4 + - - +
237C ILE* 4.1 35.7 - - + +
238C THR* 6.1 1.6 - - - -
292C PHE* 3.8 27.1 - - + -
295C LEU* 4.0 8.5 - - + -
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Residues in contact with LEU 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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136C PHE* 3.7 27.1 - - + -
147C PHE* 3.2 32.5 + - + +
148C GLN* 3.0 32.5 + - - +
150C ILE* 1.3 74.7 - - - +
152C ASP* 1.3 57.8 + - - +
154C MET* 3.3 29.7 + - + +
155C LYS* 2.9 40.4 + - - +
196C LEU* 4.7 9.6 - - + +
199C VAL* 4.3 20.0 - - + -
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Residues in contact with ASP 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 GLN* 2.8 47.3 + - - +
149C LYS* 3.7 16.5 - - - +
150C ILE 3.3 0.2 - - - -
151C LEU* 1.3 74.9 - - - +
153C PHE* 1.3 53.2 + - - +
155C LYS* 3.3 12.8 + - - +
156C ASP* 2.8 48.6 + - - +
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Residues in contact with PHE 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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1C BQM 3.4 43.5 - - + -
134C PHE* 5.3 1.8 - + - -
149C LYS 3.1 15.4 + - - +
150C ILE 3.2 3.8 + - - +
152C ASP* 1.3 79.8 - - - +
154C MET* 1.3 64.1 + - + +
156C ASP* 3.3 7.7 + - - +
157C VAL* 3.0 34.5 + - + +
235C ILE* 5.0 0.2 - - + -
237C ILE* 4.1 20.2 - - + -
259C ILE* 4.0 12.6 - - + -
295C LEU* 3.6 46.0 - - + -
298C LEU* 3.8 19.3 - - + -
299C PHE* 3.9 26.7 - - + -
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Residues in contact with MET 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* 3.6 48.5 - - + -
136C PHE* 3.6 40.2 - - + -
150C ILE* 3.0 14.2 + - - +
151C LEU* 3.3 43.3 + - + +
153C PHE* 1.3 75.0 - - + +
155C LYS* 1.3 63.0 + - - +
157C VAL* 3.3 3.5 + - - +
158C MET* 3.0 30.2 + - - +
170C ALA* 4.8 1.8 - - + -
196C LEU* 3.9 19.1 - - + -
237C ILE* 4.3 11.2 - - + -
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Residues in contact with LYS 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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148C GLN* 4.1 14.4 - - - +
151C LEU* 2.9 31.0 + - - +
152C ASP* 3.8 13.7 + - - +
154C MET* 1.3 76.8 - - - +
156C ASP* 1.3 63.5 + - - +
158C MET* 3.3 1.9 + - - +
159C LYS* 2.9 45.2 + - - +
192C PRO* 3.8 33.9 - - + +
193C ASP* 3.2 32.5 + - + +
196C LEU* 3.6 23.5 - - + +
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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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152C ASP* 2.8 35.6 + - - +
153C PHE* 3.6 7.9 - - - +
155C LYS* 1.3 74.3 - - - +
157C VAL* 1.3 62.2 + - - +
159C LYS* 3.9 12.3 + - - +
160C LYS 3.1 17.0 + - - -
299C PHE* 3.2 47.6 - - + +
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Residues in contact with VAL 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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1C BQM 3.2 55.0 - - + -
134C PHE* 3.9 15.7 - - + -
153C PHE* 3.0 22.7 + - + +
154C MET 3.7 6.7 - - - +
156C ASP* 1.3 76.0 - - - +
158C MET* 1.3 63.3 + - - +
160C LYS* 3.2 4.6 + - - +
161C LEU* 3.2 32.1 + - + +
168C PHE* 4.7 2.7 - - + -
299C PHE* 3.9 11.7 - - + -
302C LEU* 3.7 12.1 - - + -
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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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134C PHE* 3.7 16.4 - - + -
154C MET* 3.0 21.0 + - - +
155C LYS* 3.3 0.9 + - - +
157C VAL* 1.3 75.2 - - - +
159C LYS* 1.3 57.4 + - - +
161C LEU 3.4 2.6 + - - -
162C SER* 3.0 27.7 + - - -
168C PHE* 3.6 35.0 - - + -
181C PHE* 3.5 31.6 - - + -
186C TYR* 3.5 36.5 + - + -
192C PRO* 3.7 37.9 - - + +
195C LEU* 4.0 1.8 - - + -
196C LEU* 5.5 3.8 - - - -
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Residues in contact with LYS 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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160B LYS* 4.3 1.2 + - - -
155C LYS* 2.9 39.1 + - - +
156C ASP* 3.9 12.1 + - - +
158C MET* 1.3 75.1 - - - +
160C LYS* 1.3 63.0 + - - +
162C SER* 3.2 23.2 + - - -
191C ASP* 6.0 0.2 - - - -
192C PRO* 3.9 28.9 - - + -
193C ASP* 4.9 11.6 + - - +
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Residues in contact with LYS 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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159B LYS 4.3 0.8 + - - -
160B LYS* 3.2 45.8 + - - +
162B SER* 2.5 48.0 + - - -
164B THR* 4.2 11.4 - - - -
306B ILE* 5.7 1.2 - - - +
156C ASP 3.1 18.9 + - - +
157C VAL* 3.2 5.4 + - - +
159C LYS* 1.3 77.5 - - - +
161C LEU* 1.3 59.6 + - + +
162C SER 3.4 0.4 - - - -
299C PHE* 4.2 8.7 - - + -
303C GLN* 3.5 24.6 - - + +
306C ILE* 3.6 26.9 - - + -
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Residues in contact with LEU 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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306B ILE* 4.3 24.2 - - + +
308B VAL* 4.2 17.0 - - + +
1C BQM 4.1 22.4 - - - -
157C VAL* 3.2 26.5 + - + +
158C MET 3.5 4.0 - - - -
160C LYS* 1.3 81.7 - - + +
162C SER* 1.3 62.5 + - - +
164C THR* 2.6 34.3 + - + +
166C TYR* 4.1 33.8 - - + +
168C PHE* 4.0 19.5 - - + -
186C TYR* 4.5 1.2 + - - -
302C LEU* 6.1 0.4 - - + -
306C ILE* 4.4 11.2 - - + -
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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
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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