Contacts of the helix formed by residues 159 - 169 (chain C) in PDB entry 1Z6T
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 GLY 159 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C ARG* 4.0 2.3 + - - -
157C GLY 3.2 1.6 - - - -
158C CYS* 1.3 78.8 - - - +
160C LYS* 1.3 59.4 + - - +
162C VAL* 3.6 2.8 + - - +
163C LEU* 3.1 35.2 + - - +
902C ADP 3.1 44.4 + - - -
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Residues in contact with LYS 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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152C ILE* 3.7 26.7 - - + +
153C HIS 3.9 0.9 - - - -
154C GLY 2.9 41.4 + - - +
155C MET 3.0 13.9 + - - -
156C ALA* 4.0 5.3 - - - +
158C CYS* 3.5 13.5 - - - -
159C GLY* 1.3 75.7 - - - +
161C SER* 1.3 61.8 + - - +
163C LEU* 3.4 10.4 + - - +
164C ALA* 2.9 28.9 + - - +
244C ASP* 5.2 5.0 + - - +
263C THR* 3.6 14.6 - - + +
264C THR* 3.5 24.9 - - - +
265C ARG* 4.4 5.0 - - - +
282C VAL* 4.4 4.0 - - + -
902C ADP 3.0 30.4 + - - +
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Residues in contact with SER 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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120C PRO* 5.4 5.0 - - - +
160C LYS* 1.3 74.7 - - - +
162C VAL* 1.3 69.5 + - - +
164C ALA 4.4 0.2 - - - +
165C ALA* 3.2 20.3 + - - +
184C TRP* 3.4 20.8 - - - -
243C ASP* 3.2 35.8 + - - -
263C THR* 4.3 2.7 - - - +
902C ADP 3.1 27.0 + - - -
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Residues in contact with VAL 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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123C PRO* 4.0 30.5 - - + -
126C PHE* 4.2 10.8 - - + -
129C ARG* 6.4 0.2 - - - -
159C GLY 3.9 1.8 - - - +
160C LYS 3.3 0.2 - - - -
161C SER* 1.3 80.3 + - - +
163C LEU* 1.3 58.3 + - + +
165C ALA* 3.6 4.4 + - - +
166C GLU* 3.1 28.0 + - + +
169C ARG* 4.7 1.2 + - - +
902C ADP 3.0 74.2 + - + +
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Residues in contact with LEU 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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129C ARG* 4.0 27.4 - - + +
132C LEU* 3.9 23.3 - - + -
133C VAL* 3.7 26.7 - - + +
136C ILE* 4.0 16.4 - - + +
152C ILE* 4.7 1.1 - - + -
159C GLY 3.1 25.8 + - - +
160C LYS* 3.5 6.7 - - - +
162C VAL* 1.3 75.6 - - + +
164C ALA* 1.3 65.2 + - - +
166C GLU* 3.2 5.8 + - + +
167C ALA* 3.0 24.3 + - - +
282C VAL* 3.5 39.9 - - + -
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Residues in contact with ALA 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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152C ILE* 3.6 22.6 - - + +
160C LYS 2.9 16.9 + - - +
161C SER 4.0 4.3 - - - +
162C VAL 3.4 0.2 - - - -
163C LEU* 1.3 76.7 - - - +
165C ALA* 1.3 63.0 + - - +
167C ALA* 3.6 14.4 + - - +
168C VAL* 3.7 10.2 + - - +
184C TRP* 4.3 6.5 - - + -
241C ILE* 4.3 11.9 - - + +
261C LEU* 3.7 21.1 - - + +
263C THR* 4.1 11.2 - - + -
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Residues in contact with ALA 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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114C LEU* 4.3 0.9 - - - +
119C VAL* 3.5 30.5 - - + -
120C PRO* 4.1 8.1 - - + +
121C GLN 5.9 0.2 - - - +
161C SER 3.2 14.4 + - - +
162C VAL* 3.9 5.2 - - - +
164C ALA* 1.3 76.5 - - - +
166C GLU* 1.3 64.3 + - - +
168C VAL* 3.3 8.5 + - - +
169C ARG* 3.2 39.0 + - - +
184C TRP* 3.9 7.1 - - + -
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Residues in contact with GLU 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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122C ARG* 2.7 44.8 + - - +
126C PHE* 3.3 33.8 - - + -
133C VAL* 3.9 24.2 - - + +
137C GLN* 4.0 4.9 + - - -
162C VAL* 3.1 21.4 + - + +
163C LEU* 3.2 5.3 + - + +
165C ALA* 1.3 75.9 - - - +
167C ALA* 1.3 64.9 + - - +
169C ARG* 2.8 44.7 + - - +
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Residues in contact with ALA 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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133C VAL* 4.0 5.8 - - + +
136C ILE* 3.6 34.1 - - + -
137C GLN* 2.8 33.7 + - + +
140C LEU* 4.4 7.2 - - + -
163C LEU 3.0 15.3 + - - +
164C ALA* 3.6 7.6 - - - +
165C ALA 3.2 0.2 - - - -
166C GLU* 1.3 78.5 - - - +
168C VAL* 1.3 58.4 + - - +
170C ASP* 4.2 0.3 - - - +
173C LEU* 3.2 15.1 - - - +
261C LEU* 5.1 0.4 - - + -
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Residues in contact with VAL 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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114C LEU* 3.7 20.0 - - + +
119C VAL* 4.5 4.3 - - + -
140C LEU* 4.4 11.2 - - + -
164C ALA 3.7 13.9 + - - +
165C ALA* 3.3 15.7 - - - +
167C ALA* 1.3 77.0 - - + +
169C ARG* 1.3 55.9 + - - +
170C ASP* 2.9 13.8 + - - -
173C LEU* 4.1 9.4 - - + -
174C LEU* 3.3 33.9 - - + +
178C PHE* 5.3 0.9 - - + -
182C VAL* 4.3 6.7 - - + -
239C LEU* 3.7 29.6 - - + -
241C ILE* 4.1 15.5 - - + -
261C LEU* 4.8 1.1 - - + -
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Residues in contact with ARG 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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104C SER 5.1 2.3 - - - +
105C GLY 4.2 1.2 - - - +
106C ILE* 3.8 32.1 - - + +
110C VAL* 3.8 15.3 - - + -
114C LEU* 3.7 25.9 - - + +
119C VAL* 4.3 2.0 + - - +
120C PRO 2.6 31.5 + - - -
121C GLN* 3.7 3.0 - - - +
122C ARG* 3.6 33.8 - - - +
123C PRO* 5.9 0.2 - - - +
137C GLN* 5.3 0.2 + - - -
162C VAL* 4.7 1.8 + - - +
165C ALA* 3.2 38.3 + - - +
166C GLU* 2.8 56.9 + - - +
168C VAL* 1.3 75.8 - - - +
170C ASP* 1.3 57.7 + - - +
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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