Contacts of the helix formed by residues 146 - 155 (chain A) in PDB entry 4B6L
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 SER 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A LYS* 1.3 80.5 - - - +
147A LEU* 1.3 57.8 + - - +
148A ALA* 3.2 18.0 + - - +
149A HIS* 2.9 25.3 + - - +
150A ILE* 3.0 27.5 + - - +
188A LEU 3.8 0.9 - - - -
189A GLY* 3.6 11.4 + - - -
191A PHE 3.2 13.5 - - - -
192A PHE* 3.7 22.9 - - - -
193A ILE* 4.3 7.0 - - - +
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Residues in contact with LEU 147 (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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146A SER* 1.3 72.9 - - - +
148A ALA* 1.3 51.5 + - - +
150A ILE* 3.7 28.2 - - + +
151A TRP* 2.7 35.2 + - - +
157A LEU* 4.5 7.0 - - + -
165A TYR* 3.9 38.1 - - + -
169A ILE* 4.5 1.6 - - + -
188A LEU* 3.2 23.8 + - + +
191A PHE* 2.9 22.3 + - + +
193A ILE* 4.0 10.7 - - + +
199A LEU* 3.6 25.8 - - + -
253A LEU* 4.3 18.3 - - + +
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Residues in contact with ALA 148 (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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146A SER* 3.1 5.1 - - - +
147A LEU* 1.3 74.1 - - - +
149A HIS* 1.4 55.8 + - + +
151A TRP* 3.3 8.6 + - + +
152A LYS* 2.8 55.6 + - - +
188A LEU* 3.2 14.0 + - + -
189A GLY* 3.4 30.3 - - - +
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Residues in contact with HIS 149 (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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68A LEU 4.6 3.8 + - - -
145A LYS* 3.5 41.5 - - + -
146A SER* 2.9 39.2 + - - +
148A ALA* 1.4 75.3 - - + +
150A ILE* 1.3 65.4 + - + +
152A LYS* 3.3 28.9 + - + +
153A ALA* 3.2 21.1 + - - +
328A CYS 5.1 0.2 - - - -
1333A 9ZP 4.0 45.2 + + + -
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Residues in contact with ILE 150 (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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144A ARG 4.3 5.8 - - - +
146A SER 3.0 12.4 + - - +
147A LEU* 3.8 22.7 - - + +
149A HIS* 1.3 75.3 - - + +
151A TRP* 1.4 53.2 + - - +
153A ALA* 3.1 2.6 + - - +
154A ARG* 2.7 52.1 + - + +
157A LEU* 4.1 15.3 - - + -
165A TYR* 4.1 13.2 - - - +
193A ILE* 3.6 32.1 - - + -
327A SER 3.8 8.7 - - - +
328A CYS* 3.7 41.5 - - + +
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Residues in contact with TRP 151 (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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147A LEU 2.7 23.4 + - - +
148A ALA* 3.6 11.9 - - + +
150A ILE* 1.4 73.1 - - - +
152A LYS* 1.3 88.4 + - + +
154A ARG* 4.7 2.2 - - - -
155A HIS* 2.6 67.6 + + - +
157A LEU* 5.9 1.8 - - - -
188A LEU* 3.5 26.9 - - + -
252A THR* 3.9 16.9 - - + +
253A LEU* 4.8 8.3 - - + -
256A GLY 2.8 31.5 + - - -
257A SER* 4.9 4.7 - - - -
258A PRO* 5.4 3.4 - - + -
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Residues in contact with LYS 152 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A ALA* 2.8 34.9 + - - +
149A HIS* 3.7 43.5 + - + +
150A ILE 3.3 0.2 - - - -
151A TRP* 1.3 94.2 - - + +
153A ALA* 1.3 60.9 + - - +
155A HIS* 4.6 2.6 + - - +
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Residues in contact with ALA 153 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A HIS 3.2 10.3 + - - +
150A ILE 3.1 7.6 + - - +
152A LYS* 1.3 77.9 - - - +
154A ARG* 1.3 59.1 + - - +
328A CYS 3.4 20.2 - - - +
329A VAL* 3.8 25.4 - - + +
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Residues in contact with ARG 154 (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 ILE* 2.7 29.4 + - + +
151A TRP* 4.7 0.7 - - - -
153A ALA* 1.3 77.0 - - - +
155A HIS* 1.4 57.4 + - - +
156A THR* 2.8 39.2 + - - +
157A LEU* 3.7 14.2 - - + +
158A LEU* 4.0 3.6 - - - +
161A GLU* 2.7 41.4 + - - -
327A SER 2.7 36.5 + - - +
328A CYS 4.1 3.8 - - - +
329A VAL 3.7 1.6 - - - -
330A THR* 3.2 43.3 + - - +
331A VAL* 3.7 19.7 - - - +
332A PRO* 3.6 9.5 - - - +
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Residues in contact with HIS 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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151A TRP* 2.6 51.5 + + - +
152A LYS 4.6 2.4 - - - +
153A ALA 3.9 0.2 - - - -
154A ARG* 1.4 72.2 - - - +
156A THR* 1.3 63.5 + - + +
252A THR 3.9 1.2 - - - +
255A CYS 4.3 3.3 + - - -
256A GLY* 3.0 59.9 + - - -
257A SER* 5.2 3.1 - - - -
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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