Contacts of the helix formed by residues 159 - 170 (chain C) in PDB entry 3ECS
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 LEU 159 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154C GLU* 3.0 53.4 - - + +
155C SER 3.1 5.8 + - - -
156C GLN* 3.8 19.1 - - - +
157C PRO 3.3 7.4 - - - +
158C ASP* 1.3 80.9 - - - +
160C SER* 1.3 60.2 + - - +
161C GLY 3.1 3.1 - - - -
162C LYS* 3.0 44.9 + - + +
163C LYS* 3.5 4.3 + - - +
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Residues in contact with SER 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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129C ALA* 3.4 22.7 - - - +
130C TYR* 3.4 27.0 + - - +
154C GLU 3.5 0.8 + - - -
155C SER* 3.8 0.9 + - - -
158C ASP* 3.2 18.4 + - - -
159C LEU* 1.3 77.2 - - - +
161C GLY* 1.3 63.2 + - - +
162C LYS 3.2 0.2 - - - -
163C LYS* 3.2 15.9 + - - +
164C MSE 3.0 17.0 + - - -
209C LYS* 3.6 11.6 + - - +
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Residues in contact with GLY 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C ALA* 3.8 16.4 - - - -
152C VAL* 3.8 9.9 - - - +
153C THR 3.2 26.5 - - - -
154C GLU* 3.0 7.9 + - - -
155C SER* 3.9 0.6 - - - -
160C SER* 1.3 80.9 + - - +
162C LYS* 1.3 57.0 + - - +
164C MSE 3.1 4.7 + - - +
165C ALA* 2.9 27.0 + - - +
177C VAL* 5.3 0.2 - - - -
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Residues in contact with LYS 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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268A GLU* 4.7 17.1 + - - -
154C GLU* 3.7 35.6 + - + +
159C LEU* 3.0 33.3 + - + +
161C GLY* 1.3 78.1 - - - +
163C LYS* 1.3 60.0 + - - +
165C ALA* 3.4 9.6 - - - +
166C LYS* 3.2 40.8 + - - +
177C VAL* 4.3 13.5 - - + -
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Residues in contact with LYS 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C TYR* 3.6 28.8 - - + +
159C LEU 3.5 3.5 + - - +
160C SER* 3.2 20.2 + - - +
161C GLY 3.1 0.4 - - - -
162C LYS* 1.3 76.4 - - - +
164C MSE 1.3 65.9 + - - +
166C LYS* 3.3 15.1 + - + +
167C ALA* 3.2 21.1 + - + +
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Residues in contact with MSE 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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127C THR* 4.5 11.7 - - + +
129C ALA 3.7 16.4 - - - +
130C TYR* 3.5 14.3 - - + -
131C SER* 3.7 26.0 - - - +
134C VAL* 3.4 36.6 - - + -
135C LEU* 3.6 31.6 - - + +
138C LEU* 4.7 1.3 - - + -
152C VAL* 4.4 8.7 - - + -
160C SER 3.0 11.9 + - - +
161C GLY* 3.2 9.9 - - - +
163C LYS* 1.3 77.5 - - - +
165C ALA* 1.3 63.4 + - - +
167C ALA* 3.1 5.2 + - - +
168C LEU* 3.0 41.6 + - + +
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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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267A LYS* 6.4 1.1 - - + -
152C VAL* 4.2 4.9 - - + +
161C GLY 2.9 9.2 + - - +
162C LYS 3.4 9.9 - - - +
164C MSE 1.3 75.5 - - - +
166C LYS* 1.3 52.3 + - + +
168C LEU* 3.2 2.3 + - - +
169C CYS* 2.8 36.1 + - - +
175C VAL* 3.6 23.6 - - + +
177C VAL* 3.4 33.4 - - + -
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Residues in contact with LYS 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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162C LYS* 3.2 30.1 + - - +
163C LYS* 3.3 14.5 + - + +
165C ALA* 1.3 78.0 - - + +
167C ALA* 1.3 54.4 + - - +
169C CYS* 3.3 9.3 - - - +
170C HIS* 2.7 50.1 + - + -
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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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130C TYR* 4.8 7.0 - - + +
135C LEU* 4.3 24.7 - - + -
163C LYS* 3.2 9.4 + - + +
164C MSE 3.1 11.2 + - - +
166C LYS* 1.3 76.3 - - - +
168C LEU* 1.3 64.0 + - - +
169C CYS 3.1 1.3 - - - -
170C HIS* 3.3 16.8 + - - +
171C LEU* 3.3 19.9 + - - +
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Residues in contact with LEU 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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127C THR* 5.3 0.4 - - + -
135C LEU* 3.8 23.1 - - + -
138C LEU* 3.5 37.9 - - + -
150C VAL* 4.0 26.7 - - + -
152C VAL* 5.8 0.9 - - + -
164C MSE 3.0 36.2 + - + +
165C ALA 3.9 2.9 - - - +
167C ALA* 1.3 73.5 - - - +
169C CYS* 1.3 65.4 + - - +
171C LEU* 3.0 24.2 + - + +
173C VAL* 3.0 34.1 + - + +
175C VAL* 4.4 14.6 - - + -
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Residues in contact with CYS 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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267A LYS* 3.8 24.7 - - + +
165C ALA 2.8 18.4 + - - +
166C LYS* 3.3 12.3 - - - +
168C LEU* 1.3 80.3 - - - +
170C HIS* 1.3 59.4 + - + +
171C LEU 3.1 0.2 - - - -
172C ASN* 2.8 22.8 + - - +
173C VAL 4.3 7.9 - - - -
175C VAL* 4.3 6.7 - - + +
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Residues in contact with HIS 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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166C LYS* 2.7 37.9 + - + +
167C ALA* 3.7 10.7 - - - +
168C LEU 3.1 0.6 - - - -
169C CYS* 1.3 76.4 - - + +
171C LEU* 1.3 60.1 + - + +
172C ASN* 3.0 9.8 + - - -
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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