Contacts of the helix formed by residues 159 - 170 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40U LYS 3.6 10.1 - - - +
41U TYR* 3.3 18.2 - - - -
42U VAL 4.9 0.2 + - - -
45U SER* 4.2 11.6 + - - +
105U ARG* 2.9 43.5 + - - -
154U ALA* 2.8 20.4 + - - +
155U THR* 5.6 0.7 - - - -
157U ASN* 3.1 4.6 - - + +
158U GLY* 1.3 73.7 - - - +
160U VAL* 1.3 62.6 + - - +
161U GLN* 3.6 3.5 + - - +
162U LEU* 3.0 18.8 + - + -
163U ALA* 3.0 22.6 + - - +
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Residues in contact with VAL 160 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148K LEU* 3.3 33.2 - - + -
151K HIS* 3.3 45.1 - - + +
167K GLU* 3.7 12.5 - - + +
171K LEU* 3.7 11.2 - - + -
158U GLY 3.1 10.6 + - - +
159U ASP* 1.3 72.7 + - - +
161U GLN* 1.3 60.7 + - - +
163U ALA* 3.5 7.1 + - + +
164U ASP* 2.9 26.2 + - - +
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Residues in contact with GLN 161 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148K LEU* 5.5 3.6 - - + -
171K LEU* 3.7 38.4 - - + +
172K GLY* 3.6 16.5 - - - +
175K VAL* 3.6 23.8 - - + +
101U TYR* 2.4 41.2 + - - -
105U ARG* 3.6 9.2 + - - +
159U ASP* 3.3 2.1 + - - +
160U VAL* 1.3 81.1 - - + +
162U LEU* 1.3 60.1 + - - +
164U ASP* 3.3 10.7 + - + +
165U PHE* 2.9 33.2 + - - +
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Residues in contact with LEU 162 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41U TYR* 4.5 2.9 - - + -
45U SER* 3.9 28.7 - - - +
49U VAL* 3.9 23.6 - - + -
101U TYR* 3.2 35.7 + - + +
105U ARG* 4.1 0.7 - - - +
150U LEU* 4.3 11.2 - - + -
154U ALA* 3.6 22.2 - - + +
159U ASP* 3.0 26.3 + - - +
161U GLN* 1.3 71.8 - - - +
163U ALA* 1.3 67.1 + - - +
165U PHE* 3.2 5.1 + - + +
166U VAL* 2.9 43.2 + - + +
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Residues in contact with ALA 163 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151U HIS* 3.5 25.1 - - + +
154U ALA* 3.7 9.1 - - + +
155U THR* 4.0 18.2 - - + -
159U ASP 3.0 17.5 + - - +
160U VAL* 3.7 7.4 - - - +
162U LEU* 1.3 77.7 - - - +
164U ASP* 1.3 58.8 + - - +
166U VAL* 3.3 2.1 + - - +
167U GLU* 2.9 37.4 + - - +
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Residues in contact with ASP 164 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167K GLU* 3.6 40.8 - - + +
168K THR* 4.7 5.6 + - - -
171K LEU* 6.3 0.2 - - + -
172K GLY* 5.6 1.4 + - - -
373K CA 2.7 25.5 - - - -
160U VAL 2.9 17.7 + - - +
161U GLN* 3.7 12.3 + - - +
163U ALA* 1.3 74.6 - - - +
165U PHE* 1.3 62.3 + - - +
167U GLU* 3.3 8.3 + - - +
168U THR* 2.8 47.0 + - - -
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Residues in contact with PHE 165 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97U LYS* 3.9 20.4 - - + -
98U LEU* 3.8 14.4 - - + -
101U TYR* 3.6 57.7 - + + -
104U LYS* 6.1 2.9 - - - -
161U GLN* 2.9 25.3 + - - +
162U LEU* 3.2 9.8 + - + +
164U ASP* 1.3 78.0 + - - +
166U VAL* 1.3 60.8 + - + +
168U THR* 4.8 2.7 - - - -
169U GLU* 2.9 54.8 + - + +
170U TYR* 3.7 28.5 - + - -
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Residues in contact with VAL 166 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147U LEU* 3.9 27.1 - - + +
150U LEU* 3.6 31.2 - - + -
151U HIS* 4.3 13.0 - - + +
162U LEU* 2.9 29.7 + - + +
163U ALA* 3.7 8.1 - - - +
165U PHE* 1.3 80.9 - - + +
167U GLU* 1.3 62.7 + - - +
170U TYR* 3.0 33.3 + - + +
171U LEU* 3.0 25.7 + - + -
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Residues in contact with GLU 167 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371K CA 3.8 14.7 - - - -
373K CA 2.6 29.5 - - - -
160P VAL* 4.0 6.6 - - + +
164P ASP* 3.6 32.1 - - + +
167P GLU* 5.4 0.8 - - - +
151U HIS* 2.7 35.0 + - + +
163U ALA* 2.9 18.9 + - - +
164U ASP* 3.3 10.7 + - - +
166U VAL* 1.3 79.0 - - - +
168U THR* 1.3 62.4 + - - +
171U LEU* 3.5 31.0 + - + +
172U GLY* 3.8 6.8 + - - -
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Residues in contact with THR 168 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164P ASP* 4.8 5.9 + - - -
164U ASP* 2.8 39.9 + - - -
165U PHE* 4.2 2.0 - - - -
167U GLU* 1.3 75.0 - - - +
169U GLU* 1.3 74.5 + - - +
173U GLU* 3.5 1.7 - - - +
214U CA 2.6 27.1 - - - -
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Residues in contact with GLU 169 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94U HIS* 6.0 1.2 - - - -
97U LYS* 2.8 39.8 + - - +
165U PHE* 2.9 45.1 + - + +
168U THR* 1.3 91.3 - - - +
170U TYR* 1.3 79.8 + - + +
173U GLU* 3.3 21.0 - - - +
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Residues in contact with TYR 170 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56U GLU* 4.3 5.6 - - - -
94U HIS* 2.7 55.2 + + + -
97U LYS* 3.4 21.8 - - + +
98U LEU* 3.2 24.5 + - + +
147U LEU* 3.8 33.7 - - + +
150U LEU* 6.3 0.2 - - + -
165U PHE* 3.7 31.6 - + - -
166U VAL* 3.0 20.5 + - + +
168U THR 3.5 0.4 - - - -
169U GLU* 1.3 92.9 - - + +
171U LEU* 1.3 61.4 + - - +
172U GLY 3.5 2.0 - - - -
173U GLU* 3.4 6.2 + - - +
174U GLN* 2.9 30.9 + - - +
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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