Contacts of the helix formed by residues 159 - 170 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40C LYS 3.4 12.0 - - - +
41C TYR* 3.4 14.2 - - - -
42C VAL 4.9 0.2 + - - -
45C SER* 4.1 16.0 + - - +
105C ARG* 3.0 43.8 + - - -
154C ALA* 2.8 16.5 + - + +
155C THR* 5.8 0.4 - - - -
157C ASN* 3.3 3.9 - - + +
158C GLY* 1.3 73.6 - - - +
160C VAL* 1.3 61.9 + - - +
161C GLN* 3.4 3.8 + - - +
162C LEU* 3.0 21.2 + - + -
163C ALA* 3.2 22.3 + - - +
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Residues in contact with VAL 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C GLY 3.2 11.9 + - - +
159C ASP* 1.3 73.0 + - - +
161C GLN* 1.3 58.3 + - - +
163C ALA* 3.4 5.0 + - - +
164C ASP* 3.0 25.3 + - - +
148R LEU* 4.1 19.4 - - + +
151R HIS* 3.4 41.3 - - + +
167R GLU* 4.0 7.8 - - + +
171R LEU* 3.5 22.9 - - + -
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Residues in contact with GLN 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C TYR* 2.5 35.0 + - - -
105C ARG* 3.8 10.2 + - - +
159C ASP* 3.4 2.2 + - - +
160C VAL* 1.3 78.2 - - - +
162C LEU* 1.3 60.1 + - - +
164C ASP* 3.7 9.7 + - + +
165C PHE* 2.8 40.4 + - - +
148R LEU* 5.2 4.4 - - + +
171R LEU* 3.7 37.9 - - + +
172R GLY* 3.6 18.3 - - - +
175R VAL* 3.7 23.4 - - + +
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Residues in contact with LEU 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C TYR* 4.5 2.5 - - + -
45C SER* 3.7 32.8 - - - +
49C VAL* 4.0 21.5 - - + -
101C TYR* 3.2 34.1 + - + +
105C ARG* 4.0 1.6 - - - +
150C LEU* 4.5 10.8 - - + -
153C VAL* 5.8 0.4 - - + -
154C ALA* 3.6 22.9 - - + +
159C ASP* 3.0 22.4 + - - +
161C GLN* 1.3 78.3 - - - +
163C ALA* 1.3 62.3 + - - +
165C PHE* 3.2 4.6 + - + +
166C VAL* 3.0 36.5 + - + +
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Residues in contact with ALA 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C HIS* 3.4 29.6 - - + +
154C ALA* 3.7 13.6 - - + +
155C THR* 4.2 8.1 - - - +
159C ASP 3.2 15.5 + - - +
160C VAL* 3.7 6.3 - - - +
162C LEU* 1.3 79.4 - - - +
164C ASP* 1.3 62.5 + - - +
166C VAL* 3.3 3.0 + - - -
167C GLU* 3.1 30.2 + - - +
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Residues in contact with ASP 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C VAL 3.0 18.2 + - - +
161C GLN* 3.7 14.4 + - + +
162C LEU 3.2 0.4 - - - -
163C ALA* 1.3 76.2 - - - +
165C PHE* 1.3 58.3 + - - +
167C GLU* 3.8 8.1 + - - +
168C THR* 2.9 48.1 + - - -
321C CA 3.9 11.6 - - - -
167R GLU* 3.6 51.8 - - + +
168R THR* 4.4 5.9 + - - -
171R LEU* 6.0 0.7 - - + -
172R GLY* 5.4 1.6 + - - -
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Residues in contact with PHE 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C LYS* 4.2 17.3 - - + -
98C LEU* 3.8 14.8 - - + -
101C TYR* 3.5 62.8 - + + -
104C LYS* 6.1 3.1 - - - -
161C GLN* 2.8 25.0 + - - +
162C LEU* 3.5 4.9 - - + +
164C ASP* 1.3 77.2 - - - +
166C VAL* 1.3 66.1 - - + +
168C THR* 4.7 2.7 - - - -
169C GLU* 2.8 55.6 + - + +
170C TYR* 3.6 28.3 - + - -
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Residues in contact with VAL 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C LEU* 5.8 0.2 - - + -
147C LEU* 3.8 35.4 - - + +
150C LEU* 3.6 30.7 - - + -
151C HIS* 4.3 12.6 - - + +
162C LEU* 3.0 24.7 + - + +
163C ALA* 3.3 6.9 + - - +
165C PHE* 1.3 84.8 - - + +
167C GLU* 1.3 62.8 + - - +
170C TYR* 3.0 24.5 + - + +
171C LEU* 3.2 20.9 + - + -
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Residues in contact with GLU 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C HIS* 2.4 41.0 + - + +
163C ALA* 3.1 14.7 + - - +
164C ASP* 3.8 6.5 - - - +
166C VAL* 1.3 77.1 - - - +
168C THR* 1.3 64.0 + - - +
171C LEU* 3.4 26.7 + - + +
172C GLY 4.0 4.2 + - - -
321C CA 3.3 16.6 - - - -
323C CA 2.5 30.1 - - - -
160S VAL* 3.8 17.0 - - + +
164S ASP* 3.5 31.5 + - + +
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Residues in contact with THR 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C ASP* 2.9 40.4 + - - -
165C PHE* 4.1 2.7 - - - -
167C GLU* 1.3 78.8 - - - +
169C GLU* 1.3 75.3 + - + +
173C GLU* 3.7 0.9 - - - +
215C CA 2.5 29.1 - - - -
164S ASP* 4.6 8.6 + - - -
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Residues in contact with GLU 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C HIS* 6.1 0.5 - - - -
97C LYS* 2.7 42.9 + - + +
165C PHE* 2.8 39.5 + - + +
168C THR* 1.3 97.6 - - + +
170C TYR* 1.3 81.8 + - + +
173C GLU* 3.3 21.6 - - - +
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Residues in contact with TYR 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C GLU* 4.3 5.6 - - - -
94C HIS* 2.7 52.7 + + + -
97C LYS* 3.3 22.1 - - + +
98C LEU* 3.2 26.1 + - + +
147C LEU* 3.9 34.2 - - + +
165C PHE* 3.6 32.1 - + - -
166C VAL* 3.0 17.8 + - + +
168C THR 3.5 0.4 - - - -
169C GLU* 1.3 93.1 - - + +
171C LEU* 1.3 62.1 + - - +
172C GLY 3.5 1.8 - - - -
173C GLU* 3.4 7.4 + - - +
174C 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