Contacts of the helix formed by residues 154 - 165 (chain B) in PDB entry 4BL8
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 GLU 154 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151B ASN* 3.5 28.3 + - - +
152B LEU 4.5 3.0 - - - -
153B GLN* 1.3 85.0 - - + +
155B PRO* 1.3 78.2 - - + +
156B TYR* 3.0 10.7 + - + +
157B PHE* 3.3 28.7 + - + +
158B THR* 4.1 3.5 + - - -
345B ARG* 5.1 4.3 - - - +
348B VAL* 6.1 0.4 - - - -
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Residues in contact with PRO 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B GLN 4.0 2.0 - - - +
154B GLU* 1.3 93.7 - - - +
156B TYR* 1.3 57.3 + - - +
157B PHE 3.1 0.2 - - - -
158B THR* 3.6 10.3 + - - +
159B TRP* 3.0 34.5 + - - +
341B TRP* 3.6 43.5 - - + +
344B VAL* 3.7 29.3 - - + +
345B ARG* 3.7 22.4 - - + +
348B VAL* 4.9 3.8 - - + -
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Residues in contact with TYR 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLU* 4.5 15.0 + - - +
113B ALA* 4.5 1.6 - - - -
114B LEU* 3.1 52.4 + - + +
154B GLU* 3.0 6.8 + - + +
155B PRO* 1.3 80.1 - - - +
157B PHE* 1.3 81.7 + + + +
159B TRP* 4.3 2.9 - - - +
160B PRO* 3.8 7.4 - - - +
231B TRP* 4.0 24.2 - + - -
259B PHE* 3.7 30.5 + - + +
261B GLY* 4.9 2.1 + - - -
331B MET* 4.7 14.6 - - + -
341B TRP* 4.0 27.7 - + + -
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Residues in contact with PHE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B LEU* 3.7 25.1 - - + +
130B TRP* 6.1 0.5 - - - -
150B PHE* 3.2 19.6 - + + -
151B ASN* 3.2 53.2 - - + +
154B GLU* 3.3 18.1 + - + +
155B PRO 3.1 0.6 - - - -
156B TYR* 1.3 97.8 - + + +
158B THR* 1.3 60.1 + - - +
159B TRP 3.5 0.9 - - - -
160B PRO* 3.5 11.5 - - - +
211B TYR* 4.1 21.1 - + - -
227B ILE* 3.7 32.7 - - + +
228B ASN* 3.9 14.8 - - - -
231B TRP* 4.9 5.6 - + - -
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Residues in contact with THR 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B PHE* 3.7 11.4 - - + -
151B ASN 4.2 6.1 - - - +
152B LEU* 3.6 35.7 - - + -
154B GLU 4.6 1.8 - - - +
155B PRO* 3.3 10.3 + - - +
157B PHE* 1.3 76.2 - - - +
159B TRP* 1.3 64.6 + - - +
160B PRO* 3.3 3.4 - - - -
161B LEU* 3.4 10.2 + - - +
162B ILE* 3.3 24.6 + - - +
196B LEU* 3.7 24.0 - - + +
348B VAL* 3.6 27.9 - - + +
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Residues in contact with TRP 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B PRO 3.0 18.8 + - - +
156B TYR 4.5 2.9 - - - +
158B THR* 1.3 76.8 - - - +
160B PRO* 1.3 64.9 - - + +
162B ILE* 4.0 29.2 - - + -
163B ALA* 2.8 41.1 + - + +
167B GLY 3.9 7.9 - - - -
168B TYR* 3.6 45.3 - - - -
169B ALA 3.9 0.4 - - - -
184B VAL* 4.5 7.9 - - + -
257B LYS 3.9 13.3 + - - -
259B PHE* 2.9 49.6 - + + -
340B PHE* 3.7 24.7 - + - -
341B TRP* 4.6 6.5 - + + -
344B VAL* 4.5 16.6 - - + -
362B LEU* 6.6 0.4 - - + -
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Residues in contact with PRO 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B LEU* 4.1 15.9 - - + -
130B TRP* 6.1 2.7 - - + -
156B TYR 3.8 4.3 - - - +
157B PHE 3.5 15.3 - - - +
158B THR 3.3 4.9 - - - -
159B TRP* 1.3 95.4 - - + +
161B LEU* 1.3 55.4 + - - +
163B ALA 3.9 0.2 - - - -
164B ALA* 3.1 23.7 + - - +
227B ILE* 5.7 3.4 - - + -
248B LEU* 4.3 9.2 - - + -
256B SER* 3.5 17.9 - - - -
257B LYS 3.2 24.6 + - - +
258B PRO* 3.8 31.2 - - + -
259B PHE 5.6 0.2 - - - +
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Residues in contact with LEU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B TRP* 3.8 52.6 - - + +
150B PHE* 6.1 0.2 - - + -
158B THR* 3.4 12.4 + - - +
159B TRP 3.2 0.4 - - - -
160B PRO* 1.3 78.8 - - - +
162B ILE* 1.3 64.7 + - + +
164B ALA* 3.2 17.9 + - - +
165B ASP 4.2 1.4 + - - -
192B GLY* 3.5 31.3 - - - +
195B PHE* 4.2 9.0 - - + -
196B LEU* 4.1 21.3 - - + -
251B PHE* 3.6 39.3 - - + -
256B SER* 4.8 0.4 + - - -
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Residues in contact with ILE 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B THR* 3.4 20.6 - - - +
159B TRP* 3.2 34.2 + - + +
161B LEU* 1.3 77.3 - - + +
163B ALA* 1.3 59.2 + - - +
164B ALA 3.6 0.2 + - - -
165B ASP 4.2 0.2 + - - -
167B GLY* 3.7 5.5 + - - -
184B VAL* 6.3 0.2 - - - -
188B GLY 3.6 5.9 - - - +
189B ALA* 3.4 44.4 - - + +
192B GLY* 4.1 8.1 - - - +
193B LEU* 4.2 30.1 - - + +
196B LEU* 5.8 0.9 - - + -
344B VAL* 4.8 4.3 - - + -
348B VAL* 3.9 27.8 - - + -
362B LEU* 5.4 6.7 - - + -
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Residues in contact with ALA 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B TRP* 2.8 38.2 + - + +
160B PRO 3.9 0.4 - - - +
162B ILE* 1.3 75.6 - - - +
164B ALA* 1.3 66.0 + - - +
165B ASP 3.3 1.1 - - - -
166B GLY* 2.9 13.9 + - - -
167B GLY 3.3 21.7 - - - +
257B LYS* 3.2 36.8 - - + +
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Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B PRO 3.1 13.2 + - - +
161B LEU* 3.2 15.8 + - - +
163B ALA* 1.3 78.9 - - - +
165B ASP* 1.3 58.9 + - - +
166B GLY* 3.0 4.7 + - - -
251B PHE* 3.8 27.4 - - + +
254B GLN* 3.4 23.6 - - - +
255B PRO* 3.6 23.7 - - - +
256B SER* 4.1 4.7 - - - -
257B LYS* 4.4 4.3 - - - +
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Residues in contact with ASP 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B LEU 4.2 2.6 + - - -
162B ILE 4.2 1.0 + - - -
163B ALA 3.3 0.6 - - - -
164B ALA* 1.3 77.0 - - - +
166B GLY* 1.3 57.1 + - - +
167B GLY 3.5 2.0 - - - -
187B ALA* 4.4 1.7 - - - +
188B GLY* 3.2 39.4 + - - +
191B ALA* 3.5 8.8 - - + +
251B PHE* 4.4 9.6 - - + -
252B LYS* 3.4 30.0 + - - -
254B GLN* 3.0 33.4 + - - +
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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
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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