Contacts of the helix formed by residues 159 - 170 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40X LYS 3.3 12.8 - - - +
41X TYR* 3.4 14.4 - - - -
42X VAL 4.9 0.3 + - - -
45X SER* 4.2 11.4 + - - +
105X ARG* 2.9 43.1 + - - -
154X ALA* 2.8 19.2 + - - +
155X THR* 5.9 0.4 - - - -
157X ASN* 3.2 5.1 - - + +
158X GLY* 1.3 73.7 - - - +
160X VAL* 1.3 64.4 + - - +
161X GLN* 3.5 2.4 + - - +
162X LEU* 3.0 20.0 + - + +
163X ALA* 3.2 22.2 + - - +
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Residues in contact with VAL 160 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A LEU* 4.1 21.0 - - + +
151A HIS* 3.4 44.6 - - + +
167A GLU* 4.0 6.9 - - + +
171A LEU* 3.5 20.2 - - + -
158X GLY* 3.3 12.2 + - - +
159X ASP* 1.3 73.3 + - - +
161X GLN* 1.3 57.7 + - - +
163X ALA* 3.4 6.9 + - - +
164X ASP* 3.0 26.0 + - - +
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Residues in contact with GLN 161 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A LEU* 5.1 4.8 - - + +
171A LEU* 3.7 38.3 - - + +
172A GLY* 3.6 17.6 - - - +
175A VAL* 3.7 22.2 - - + +
101X TYR* 2.5 40.8 + - - -
105X ARG* 3.7 9.1 + - - +
159X ASP* 3.4 1.6 + - - +
160X VAL* 1.3 78.4 - - - +
162X LEU* 1.3 61.9 + - - +
164X ASP* 3.3 11.5 + - + +
165X PHE* 2.9 34.2 + - - +
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Residues in contact with LEU 162 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41X TYR* 4.5 2.7 - - + -
45X SER* 3.8 32.1 - - - +
49X VAL* 4.0 20.4 - - + -
101X TYR* 3.2 35.5 + - + +
105X ARG* 4.0 1.6 - - - +
150X LEU* 4.5 11.7 - - + -
153X VAL* 5.6 0.2 - - + -
154X ALA* 3.6 22.0 - - + +
159X ASP* 3.0 23.8 + - - +
161X GLN* 1.3 74.9 - - - +
163X ALA* 1.3 65.3 + - - +
165X PHE* 3.2 4.5 + - + +
166X VAL* 3.0 36.2 + - + +
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Residues in contact with ALA 163 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151X HIS* 3.5 27.5 - - + +
154X ALA* 3.7 14.3 - - + +
155X THR* 4.5 8.1 - - + -
159X ASP 3.2 13.0 + - - +
160X VAL* 3.5 10.1 - - - +
162X LEU* 1.3 81.4 - - - +
164X ASP* 1.3 57.0 + - - +
166X VAL* 3.3 1.7 + - - -
167X GLU* 3.0 38.8 + - - +
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Residues in contact with ASP 164 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLU* 3.5 55.5 - - + +
168A THR* 4.4 5.4 + - - -
172A GLY* 5.4 1.9 + - - -
351A CA 3.9 6.8 - - - -
164H ASP* 5.2 0.3 - - - +
160X VAL 3.0 17.6 + - - +
161X GLN* 3.7 13.7 + - + +
162X LEU 3.2 0.2 - - - -
163X ALA* 1.3 75.4 - - - +
165X PHE* 1.3 57.9 + - - +
167X GLU* 4.4 9.4 + - - +
168X THR* 2.9 49.0 + - - -
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Residues in contact with PHE 165 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97X LYS* 4.1 19.1 - - + -
98X LEU* 3.8 15.0 - - + -
101X TYR* 3.5 62.1 - + + -
104X LYS* 6.2 1.8 - - - -
161X GLN* 2.9 24.8 + - - +
162X LEU* 3.5 4.0 - - + +
164X ASP* 1.3 76.4 - - - +
166X VAL* 1.3 68.8 + - + +
168X THR* 4.8 2.5 - - - -
169X GLU* 2.8 54.7 + - + +
170X TYR* 3.6 26.9 - + - -
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Residues in contact with VAL 166 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147X LEU* 3.8 33.9 - - + +
150X LEU* 3.6 30.5 - - + -
151X HIS* 4.3 13.7 - - + +
162X LEU* 3.0 26.9 + - + +
163X ALA* 3.8 4.5 - - - +
165X PHE* 1.3 84.1 - - + +
167X GLU* 1.3 63.0 + - - +
170X TYR* 3.0 25.3 + - + +
171X LEU* 3.2 23.9 + - + +
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Residues in contact with GLU 167 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLU* 5.1 6.8 - - - +
353A CA 4.2 9.7 - - - -
160H VAL* 3.8 17.0 - - + +
163H ALA* 6.0 0.5 - - - +
164H ASP* 3.4 46.5 + - + +
167H GLU* 5.1 5.5 - - - +
151X HIS* 2.7 33.9 + - + +
163X ALA* 3.0 25.9 + - - +
164X ASP* 3.7 9.7 + - - +
166X VAL* 1.3 78.0 - - - +
168X THR* 1.3 63.4 + - - +
171X LEU* 3.5 23.6 + - + +
172X GLY 4.0 4.2 + - - -
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Residues in contact with THR 168 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164H ASP* 4.7 7.8 + - - -
164X ASP* 2.9 37.7 + - - -
165X PHE* 4.1 2.2 - - - -
167X GLU* 1.3 77.8 - - - +
169X GLU* 1.3 75.7 + - - +
173X GLU* 3.7 0.9 - - - +
243X CA 2.4 29.2 - - - -
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Residues in contact with GLU 169 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94X HIS* 6.1 0.5 - - - -
97X LYS* 2.9 34.4 + - + -
165X PHE* 2.8 43.8 + - + +
168X THR* 1.3 93.1 - - - +
170X TYR* 1.3 82.2 + - + +
173X GLU* 3.3 20.6 - - - +
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Residues in contact with TYR 170 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56X GLU* 4.2 6.3 - - - -
94X HIS* 2.8 53.3 + + + -
97X LYS* 3.3 23.0 - - + +
98X LEU* 3.3 24.6 + - + +
147X LEU* 3.8 34.7 - - + +
165X PHE* 3.6 30.7 - + - -
166X VAL* 3.0 20.1 + - + +
168X THR 3.5 0.4 - - - -
169X GLU* 1.3 92.7 - - + +
171X LEU* 1.3 61.5 + - - +
172X GLY 3.5 2.0 - - - -
173X GLU* 3.4 7.1 + - + +
174X GLN* 2.9 31.6 + - - +
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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