Contacts of the helix formed by residues 159 - 170 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154D GLU* 3.0 28.3 - - + +
155D SER 2.8 15.0 + - - +
156D GLN* 3.4 31.9 - - - +
157D PRO 4.1 7.4 - - - +
158D ASP* 1.3 78.7 - - - +
160D SER* 1.3 54.7 + - - +
161D GLY 2.9 12.3 + - - -
162D LYS* 2.9 43.0 + - + +
163D LYS* 3.7 2.4 + - - +
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Residues in contact with SER 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D ALA* 3.6 13.3 - - - +
130D TYR* 3.4 25.6 - - - +
154D GLU 3.4 0.6 + - - -
155D SER* 3.6 1.3 + - - -
158D ASP* 3.0 19.2 + - - -
159D LEU* 1.3 74.8 - - - +
161D GLY* 1.3 62.5 + - - +
162D LYS 3.2 0.2 - - - -
163D LYS* 3.4 17.9 + - - +
164D MSE 3.2 15.8 + - - -
209D LYS* 3.4 22.3 + - - -
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Residues in contact with GLY 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D ALA* 4.0 13.7 - - - -
152D VAL* 3.9 8.7 - - - +
153D THR 3.1 27.6 - - - -
154D GLU* 2.6 17.6 + - - -
155D SER* 4.1 0.4 - - - -
160D SER* 1.3 73.3 + - - +
162D LYS* 1.3 58.1 + - - +
164D MSE 3.1 5.6 + - - +
165D ALA* 3.0 26.2 + - - +
177D VAL* 5.3 1.1 - - - -
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Residues in contact with LYS 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D GLU* 3.8 33.0 + - + +
159D LEU* 2.9 37.6 + - + +
161D GLY* 1.3 78.8 - - - +
163D LYS* 1.3 60.4 + - - +
165D ALA* 3.0 19.7 + - - +
166D LYS* 3.2 19.7 + - - +
177D VAL* 4.5 13.7 - - + +
266E LEU* 5.6 0.2 - - - +
268E GLU* 3.6 24.2 + - - -
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Residues in contact with LYS 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D TYR* 3.8 33.2 - - + -
159D LEU 3.7 1.9 + - - +
160D SER* 3.4 18.4 + - - +
161D GLY 3.3 0.2 - - - -
162D LYS* 1.3 78.6 - - - +
164D MSE 1.3 61.5 + - - +
166D LYS* 3.4 12.2 + - + +
167D ALA* 3.2 20.6 + - - +
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Residues in contact with MSE 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D THR* 5.1 7.4 - - + +
129D ALA 3.6 17.0 - - - +
130D TYR* 3.3 28.0 - - + -
131D SER 3.8 25.1 - - - +
134D VAL* 3.2 29.4 - - + -
135D LEU* 4.0 20.2 - - + +
138D LEU* 4.4 9.6 - - + -
150D VAL* 6.1 0.2 - - + -
152D VAL* 4.2 10.1 - - + -
160D SER 3.2 9.1 + - - +
161D GLY* 3.1 11.0 + - - +
163D LYS* 1.3 78.6 - - - +
165D ALA* 1.3 60.8 + - - +
167D ALA* 3.3 3.8 + - - +
168D LEU* 3.1 49.2 + - + +
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Residues in contact with ALA 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D VAL* 4.2 1.8 - - + +
161D GLY 3.0 8.8 + - - +
162D LYS* 3.0 10.5 + - - +
164D MSE 1.3 78.7 - - - +
166D LYS* 1.3 55.6 - - - +
168D LEU 3.4 0.7 + - - -
169D CYS* 2.8 27.0 + - - +
175D VAL* 3.4 24.4 - - + +
177D VAL* 3.5 21.3 - - + -
266E LEU* 3.3 27.6 - - + -
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Residues in contact with LYS 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D LYS* 3.2 14.9 + - - +
163D LYS* 3.8 10.5 - - + +
164D MSE 3.3 0.2 - - - -
165D ALA* 1.3 72.8 - - - +
167D ALA* 1.3 58.5 + - - +
169D CYS* 2.8 9.0 + - - +
170D HIS* 2.6 59.2 + - + +
266E LEU* 4.4 16.4 - - + -
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Residues in contact with ALA 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D TYR* 4.2 9.9 - - + +
135D LEU* 4.0 28.5 - - + -
163D LYS 3.2 10.6 + - - +
164D MSE 3.5 9.6 - - - +
166D LYS* 1.3 79.8 - - - +
168D LEU* 1.3 62.6 + - - +
170D HIS* 3.2 15.5 + - - +
171D LEU* 3.3 20.4 + - - +
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Residues in contact with LEU 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D LEU* 4.2 17.9 - - + -
138D LEU* 3.9 25.8 - - + -
150D VAL* 3.9 30.7 - - + -
152D VAL* 5.1 0.7 - - + -
164D MSE 3.1 36.5 + - + +
165D ALA* 3.6 6.7 - - - +
166D LYS 3.1 0.6 - - - -
167D ALA* 1.3 78.6 - - - +
169D CYS* 1.3 64.1 + - - +
171D LEU* 3.0 10.6 + - + -
172D ASN 3.1 2.9 + - - -
173D VAL* 2.9 45.7 + - + +
175D VAL* 4.0 17.9 - - + -
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Residues in contact with CYS 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D ALA 2.8 15.2 + - - +
166D LYS* 2.8 13.2 + - + +
168D LEU* 1.3 75.8 - - - +
170D HIS* 1.3 65.9 + - + +
172D ASN* 3.0 21.9 + - - +
173D VAL 4.3 8.1 - - - -
175D VAL* 4.2 2.0 - - + +
265E ASP* 4.6 7.8 + - - +
266E LEU* 3.8 37.9 - - + -
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Residues in contact with HIS 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D LYS* 2.6 43.1 + - + +
167D ALA* 3.6 9.8 - - - +
168D LEU 3.2 0.2 - - - -
169D CYS* 1.3 81.2 - - + +
171D LEU* 1.3 63.2 + - + +
172D ASN* 3.4 1.9 - - - +
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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