Contacts of the helix formed by residues 159 - 170 (chain B) in PDB entry 3A68
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 ASP 159 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B LYS 3.4 11.3 - - - +
41B TYR* 3.3 17.3 - - - -
42B VAL 4.9 0.2 + - - -
45B SER* 4.1 10.2 + - - +
105B ARG* 2.8 44.5 + - - -
154B ALA* 2.8 21.8 + - - +
155B THR* 5.3 0.4 - - - -
157B ASN* 3.1 6.3 - - + +
158B GLY* 1.3 72.9 - - - +
160B VAL* 1.3 62.0 + - - +
161B GLN* 3.6 3.1 + - - +
162B LEU* 3.0 19.8 + - + -
163B ALA* 3.1 20.3 + - - +
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Residues in contact with VAL 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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155B THR* 6.1 0.9 - - - +
158B GLY 2.9 13.6 + - - +
159B ASP* 1.3 72.7 + - - +
161B GLN* 1.3 61.8 + - - +
163B ALA* 3.5 8.4 + - + +
164B ASP* 3.0 25.8 + - - +
148V LEU* 3.3 33.9 - - + -
151V HIS* 3.2 42.6 - - + +
167V GLU* 3.4 19.9 - - + +
171V LEU* 3.4 9.2 - - + -
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Residues in contact with GLN 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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101B TYR* 2.5 40.9 + - - -
105B ARG* 3.5 12.8 + - - +
159B ASP* 3.2 1.9 + - - +
160B VAL* 1.3 79.9 - - + +
162B LEU* 1.3 59.7 + - - +
164B ASP* 3.3 9.1 + - + +
165B PHE* 2.9 33.1 + - - +
148V LEU* 5.8 2.7 - - + -
171V LEU* 3.6 40.4 - - + +
172V GLY* 3.6 17.3 - - - +
175V VAL* 3.6 21.7 - - + +
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Residues in contact with LEU 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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41B TYR* 4.4 4.0 - - + -
45B SER* 4.0 28.3 - - - +
49B VAL* 3.9 22.7 - - + -
98B LEU* 5.9 0.2 - - + -
101B TYR* 3.1 37.8 + - + +
105B ARG* 4.0 0.9 - - - +
150B LEU* 4.3 12.3 - - + -
153B VAL* 5.7 0.2 - - + -
154B ALA* 3.6 21.3 - - + -
159B ASP* 3.0 22.6 + - - +
161B GLN* 1.3 75.1 - - - +
163B ALA* 1.3 63.2 + - - +
165B PHE* 3.2 4.8 + - + +
166B VAL* 3.0 44.2 + - + +
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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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151B HIS* 3.2 31.7 + - + +
154B ALA* 3.7 10.2 - - + +
155B THR* 3.9 22.0 - - + -
159B ASP 3.1 13.8 + - - +
160B VAL* 3.6 11.9 - - + +
162B LEU* 1.3 78.0 - - - +
164B ASP* 1.3 57.3 + - - +
166B VAL* 3.3 1.8 + - - -
167B GLU* 3.0 26.4 + - - +
167V GLU* 6.6 0.2 - - - -
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Residues in contact with ASP 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 VAL 3.0 17.1 + - - +
161B GLN* 3.6 12.5 + - + +
163B ALA* 1.3 73.8 - - - +
165B PHE* 1.3 61.8 + - - +
167B GLU* 3.5 8.1 + - - +
168B THR* 2.8 53.4 + - - +
311E CA 4.2 8.0 - - - -
167V GLU* 3.4 49.2 + - + +
168V THR* 4.2 12.3 + - - -
171V LEU* 6.0 0.2 - - + -
172V GLY* 5.4 2.4 + - - -
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Residues in contact with PHE 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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97B LYS* 4.1 20.6 - - + -
98B LEU* 3.9 13.9 - - + -
101B TYR* 3.6 59.0 - + + -
104B LYS* 6.2 2.2 - - - -
161B GLN* 2.9 25.0 + - - +
162B LEU* 3.2 5.1 + - + +
164B ASP* 1.3 78.0 + - - +
166B VAL* 1.3 68.7 + - + +
168B THR* 4.7 1.3 - - - -
169B GLU* 2.8 63.7 + - + +
170B TYR* 3.7 27.4 - + - -
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Residues in contact with VAL 166 (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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147B LEU* 3.9 32.1 - - + +
150B LEU* 3.6 33.4 - - + -
151B HIS* 4.2 13.5 - - + +
162B LEU* 3.0 30.6 + - + +
163B ALA* 3.7 4.5 - - - +
165B PHE* 1.3 83.5 - - + +
167B GLU* 1.3 62.4 + - - +
170B TYR* 3.0 29.4 + - + +
171B LEU* 3.2 20.4 + - + -
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Residues in contact with GLU 167 (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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151B HIS* 2.7 29.3 + - - +
163B ALA* 3.0 17.9 + - - +
164B ASP* 3.5 13.7 - - - +
166B VAL* 1.3 79.2 - - - +
168B THR* 1.3 67.3 + - - +
171B LEU* 3.5 37.6 + - + +
172B GLY 4.0 4.7 + - - -
160E VAL* 4.4 3.0 - - + +
164E ASP* 3.0 33.0 - - + +
311E CA 2.5 26.5 - - - -
312E CA 2.7 22.5 - - - -
167V GLU* 4.4 3.9 - - - +
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Residues in contact with THR 168 (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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164B ASP* 2.8 42.4 + - - +
165B PHE* 4.1 2.2 - - - -
167B GLU* 1.3 80.4 - - - +
169B GLU* 1.3 75.3 + - - +
173B GLU* 3.7 0.9 - - - +
215B CA 2.4 30.0 - - - -
164E ASP* 4.7 5.9 + - - -
168V THR* 5.4 6.9 + - + +
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Residues in contact with GLU 169 (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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97B LYS* 2.9 34.3 + - - +
165B PHE* 2.8 45.8 + - + +
168B THR* 1.3 92.4 - - - +
170B TYR* 1.3 79.6 + - + +
173B GLU* 3.3 21.3 - - - +
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Residues in contact with TYR 170 (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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56B GLU* 4.1 6.5 - - - -
94B HIS* 2.7 52.9 + + + -
97B LYS* 3.4 20.9 - - + +
98B LEU* 3.3 24.0 + - + +
147B LEU* 3.8 34.4 - - + +
150B LEU* 6.5 0.2 - - + -
165B PHE* 3.7 30.1 - + - -
166B VAL* 3.0 21.0 + - + +
168B THR 3.5 0.2 - - - -
169B GLU* 1.3 93.3 - - + +
171B LEU* 1.3 62.6 + - - +
172B GLY 3.5 2.0 - - - -
173B GLU* 3.5 7.1 + - - +
174B GLN* 2.9 31.0 + - - +
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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