Contacts of the helix formed by residues 154 - 165 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LYS* 5.4 4.7 - - - -
151A ASN* 3.6 30.6 + - - +
152A LEU 4.5 2.9 - - - -
153A GLN* 1.3 85.7 - - + +
155A PRO* 1.3 78.8 - - - +
156A TYR* 3.0 9.0 + - + +
157A PHE* 3.3 25.2 + - + +
158A THR* 4.1 4.0 + - - -
345A ARG* 4.5 19.0 + - - -
348A VAL* 6.2 0.4 - - - -
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Residues in contact with PRO 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A GLN 4.0 0.7 - - - +
154A GLU* 1.3 95.8 - - - +
156A TYR* 1.3 62.1 - - + +
157A PHE 3.1 0.4 - - - -
158A THR* 3.6 10.4 + - - +
159A TRP* 3.0 29.0 + - + +
341A TRP* 3.5 44.2 - - + +
344A VAL* 3.8 28.4 - - + +
345A ARG* 3.8 24.5 - - + +
348A VAL* 5.1 4.5 - - + -
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Residues in contact with TYR 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLU* 4.4 15.1 + - - +
113A ALA* 4.5 1.2 - - - -
114A LEU* 3.1 52.6 + - + +
154A GLU* 3.0 6.6 + - + +
155A PRO* 1.3 80.9 - - + +
157A PHE* 1.3 80.6 + + + +
159A TRP* 4.3 2.0 - - - +
160A PRO* 3.8 7.6 - - - +
231A TRP* 4.0 23.5 - + - -
259A PHE* 3.7 30.5 + - + +
261A GLY* 4.8 2.1 + - - -
331A MET* 4.6 14.6 - - + -
341A TRP* 4.1 26.9 - + + -
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Residues in contact with PHE 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A LEU* 3.7 27.1 - - + +
130A TRP* 6.0 0.5 - - - -
150A PHE* 3.2 19.0 - + + -
151A ASN* 3.2 52.0 - - + +
154A GLU* 3.8 19.3 - - + +
155A PRO 3.1 1.2 - - - -
156A TYR* 1.3 96.7 - + + +
158A THR* 1.3 59.4 + - - +
159A TRP 3.5 0.7 - - - -
160A PRO* 3.6 11.4 - - - +
161A LEU 5.6 0.2 + - - -
211A TYR* 4.1 20.4 - + - -
227A ILE* 3.7 32.9 - - + +
228A ASN* 4.0 12.3 - - - -
231A TRP* 4.9 5.4 - + - -
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Residues in contact with THR 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A PHE* 3.7 10.8 - - + -
151A ASN 4.2 5.2 - - - +
152A LEU* 3.6 36.1 - - + -
154A GLU 4.1 2.0 + - - +
155A PRO* 3.3 10.2 + - - +
157A PHE* 1.3 75.9 - - - +
159A TRP* 1.3 65.0 + - - +
160A PRO* 3.3 3.1 - - - -
161A LEU* 3.4 10.6 + - - +
162A ILE* 3.4 23.3 + - - +
196A LEU* 3.8 23.1 - - + +
348A VAL* 3.6 28.2 - - + +
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Residues in contact with TRP 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A PRO 3.0 18.2 + - - +
156A TYR 4.5 3.4 - - - +
158A THR* 1.3 77.5 - - - +
160A PRO* 1.3 64.1 - - + +
162A ILE* 3.9 30.7 - - + -
163A ALA* 2.8 42.7 + - + +
167A GLY 3.9 7.9 - - - -
168A TYR* 3.7 43.5 - - - -
169A ALA 3.9 0.4 - - - -
184A VAL* 4.0 12.6 - - + -
257A LYS 3.9 12.0 + - - -
259A PHE* 2.9 50.9 - + + +
340A PHE* 3.6 26.5 - + - -
341A TRP* 4.5 7.6 - + + -
344A VAL* 4.5 12.6 - - + -
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Residues in contact with PRO 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A LEU* 4.1 15.7 - - + -
130A TRP* 6.1 2.2 - - + -
156A TYR 3.8 4.7 - - - +
157A PHE 3.6 14.4 - - - +
158A THR 3.3 5.4 - - - -
159A TRP* 1.3 95.7 - - + +
161A LEU* 1.3 55.7 + - - +
163A ALA 3.9 0.2 - - - -
164A ALA* 3.1 23.4 + - - +
227A ILE* 5.7 3.4 - - + -
248A LEU* 4.3 8.7 - - + -
256A SER* 3.5 16.6 - - - -
257A LYS 3.2 24.4 + - - +
258A PRO* 3.8 31.2 - - + -
259A PHE 5.6 0.2 - - - +
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Residues in contact with LEU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A TRP* 3.7 59.5 - - + +
150A PHE* 6.1 0.7 - - + -
158A THR* 3.4 10.6 + - - +
159A TRP 3.2 0.4 - - - -
160A PRO* 1.3 77.3 - - - +
162A ILE* 1.3 65.7 + - + +
164A ALA* 3.1 18.1 + - - +
165A ASP 4.2 1.4 + - - -
192A GLY* 3.5 30.9 - - - +
195A PHE* 4.3 8.7 - - + -
196A LEU* 4.2 20.6 - - + -
251A PHE* 3.7 33.9 - - + -
256A SER* 4.8 0.6 + - - -
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Residues in contact with ILE 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A THR* 3.4 20.9 - - - +
159A TRP* 3.2 35.4 + - + +
161A LEU* 1.3 76.3 - - + +
163A ALA* 1.3 59.7 + - - +
164A ALA 3.6 0.2 + - - -
165A ASP 4.2 0.3 + - - -
167A GLY* 3.7 5.4 + - - -
184A VAL* 5.8 0.2 - - - -
188A GLY 3.7 5.9 - - - +
189A ALA* 3.5 42.7 - - + +
192A GLY* 4.2 8.1 - - - -
193A LEU* 4.3 28.3 - - + +
196A LEU* 6.0 1.1 - - + -
344A VAL* 4.7 4.9 - - + -
348A VAL* 3.9 28.0 - - + -
362A LEU* 5.5 7.4 - - + -
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Residues in contact with ALA 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A TRP* 2.8 39.1 + - + +
160A PRO 3.9 0.4 - - - +
162A ILE* 1.3 75.4 - - - +
164A ALA* 1.3 60.1 + - - +
165A ASP 3.3 1.1 - - - -
166A GLY* 2.8 20.0 + - - -
167A GLY 3.3 21.2 + - - +
257A LYS* 3.2 35.5 - - + +
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Residues in contact with ALA 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A PRO 3.1 13.4 + - - +
161A LEU* 3.1 16.7 + - - +
163A ALA* 1.3 79.0 - - - +
165A ASP* 1.3 58.0 + - - +
166A GLY* 3.1 4.3 + - - -
251A PHE* 3.9 25.6 - - + +
254A GLN* 3.5 24.7 - - - +
255A PRO* 3.5 24.2 - - - +
256A SER* 4.1 4.9 - - - +
257A LYS* 4.4 4.5 - - - +
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Residues in contact with ASP 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A LEU 4.2 1.8 + - - -
162A ILE 4.2 1.2 + - - -
163A ALA 3.3 0.6 - - - -
164A ALA* 1.3 78.1 - - - +
166A GLY* 1.3 56.7 + - - +
167A GLY 3.5 2.0 - - - -
187A ALA* 4.7 0.9 - - - +
188A GLY* 3.2 34.4 - - - +
191A ALA* 3.4 13.0 - - + +
251A PHE* 4.4 9.9 - - + -
252A LYS* 3.1 35.1 + - - -
254A GLN* 3.0 31.5 + - - +
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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