Contacts of the helix formed by residues 156 - 168 (chain E) in PDB entry 6A5T
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 SER 156 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70E LYS* 4.3 33.7 - - - +
71E TYR* 4.3 11.9 - - - +
154E ARG 4.1 0.6 + - - -
155E LEU* 1.3 78.9 - - - +
157E ASP* 1.3 62.1 + - - +
158E GLY* 4.1 2.0 + - - -
159E GLU* 3.4 34.0 + - - +
160E LYS* 2.8 27.7 + - - +
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Residues in contact with ASP 157 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72E SER* 6.0 1.7 - - - -
155E LEU 5.2 1.0 - - - +
156E SER* 1.3 73.6 - - - +
158E GLY* 1.3 68.8 + - - +
160E LYS* 3.2 11.0 + - - +
161E SER* 3.0 26.3 + - - -
192E GLY 5.7 0.2 - - - +
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Residues in contact with GLY 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E SER* 3.5 3.4 + - - -
157E ASP* 1.3 77.6 - - - +
159E GLU* 1.3 58.0 + - - +
161E SER* 3.9 3.2 - - - -
162E GLN* 3.0 30.2 + - - +
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Residues in contact with GLU 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008A LEU* 5.1 2.3 - - - +
70E LYS* 4.8 11.5 - - - -
155E LEU* 3.8 26.9 - - + +
156E SER* 3.4 23.2 + - - +
157E ASP 3.2 0.4 - - - -
158E GLY* 1.3 74.7 - - - +
160E LYS* 1.3 66.1 + - - +
162E GLN* 3.3 14.3 + - - +
163E LEU* 2.9 22.0 + - - +
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Residues in contact with LYS 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E LEU* 4.2 15.6 - - + +
156E SER 2.8 20.3 + - - +
157E ASP* 3.2 12.1 + - - +
159E GLU* 1.3 76.2 - - - +
161E SER* 1.3 66.8 + - - +
163E LEU* 2.9 16.9 + - + +
164E LEU* 3.1 19.8 + - + +
171E GLU* 2.9 45.4 + - - +
192E GLY* 2.2 43.8 + - - +
193E GLN* 4.9 0.4 - - - -
194E VAL* 3.4 31.8 - - + +
212E ILE* 5.0 0.6 - - - +
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Residues in contact with SER 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157E ASP 3.0 16.0 + - - -
158E GLY* 4.2 2.9 - - - -
160E LYS* 1.3 79.2 - - - +
162E GLN* 1.3 62.9 + - - +
164E LEU* 3.3 11.1 + - - +
165E GLN* 3.0 31.2 + - - +
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Residues in contact with GLN 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006A ASN* 3.8 24.7 + - - +
1007A GLU* 4.3 21.0 + - - +
1008A LEU* 4.6 16.0 - - + +
158E GLY 3.0 19.3 + - - +
159E GLU* 3.5 16.9 - - - +
161E SER* 1.3 77.8 - - - +
163E LEU* 1.3 66.2 + - - +
165E GLN* 3.0 11.8 + - + +
166E ARG* 3.0 16.1 + - - +
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Residues in contact with LEU 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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867A PHE* 5.7 0.2 - - + -
1008A LEU* 3.7 27.1 - - + +
155E LEU* 4.7 2.0 - - + -
159E GLU 2.9 12.5 + - - +
160E LYS* 2.9 13.1 + - + +
162E GLN* 1.3 75.1 - - - +
164E LEU* 1.3 60.7 + - + +
166E ARG* 2.6 32.4 + - + +
167E TYR* 3.2 36.9 + - + -
169E LEU* 6.4 0.2 - - + -
174E LEU* 4.9 9.9 - - + -
194E VAL* 4.0 17.5 - - + -
210E TYR* 3.4 46.7 - - + -
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Residues in contact with LEU 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E LYS* 3.1 21.7 + - + +
161E SER* 3.8 11.9 - - - +
163E LEU* 1.3 83.4 - - + +
165E GLN* 1.3 60.4 + - + +
167E TYR* 4.6 2.0 - - - +
168E LYS* 2.7 33.1 + - - +
169E LEU* 3.8 34.6 + - + +
170E LYS* 5.2 2.9 - - - -
171E GLU* 3.6 45.1 - - + +
174E LEU* 4.9 13.9 - - + -
194E VAL* 6.1 1.6 - - + -
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Residues in contact with GLN 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006A ASN* 4.7 5.0 + - - -
161E SER* 3.0 20.0 + - - +
162E GLN* 3.0 13.2 + - - +
164E LEU* 1.3 77.2 - - + +
166E ARG* 1.3 63.0 + - - +
168E LYS* 4.0 17.6 - - - +
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Residues in contact with ARG 166 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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854A ASP* 5.3 11.5 + - - +
856A THR* 5.8 0.4 - - - +
867A PHE 5.2 2.4 + - - -
1002A LEU* 4.2 26.3 - - - +
1006A ASN* 4.1 18.6 - - - +
1008A LEU* 4.3 23.2 - - + +
1009A ILE* 4.2 27.6 - - + +
1012A ALA* 4.3 13.7 - - - +
162E GLN 3.0 8.7 + - - +
163E LEU* 2.6 21.7 + - - +
165E GLN* 1.3 75.3 - - - +
167E TYR* 1.3 115.3 + - - +
168E LYS* 3.5 11.3 + - - +
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Residues in contact with TYR 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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854A ASP* 4.7 7.0 - - + -
856A THR* 4.1 21.1 - - + -
858A ARG* 3.5 20.9 + - - +
864A ILE* 5.1 2.2 - - + -
867A PHE* 3.1 49.5 + + - +
1012A ALA* 5.6 2.3 - - - +
163E LEU* 3.2 36.2 + - + +
164E LEU 5.3 0.2 - - - -
166E ARG* 1.3 128.5 + - - +
168E LYS* 1.3 73.7 + - - +
169E LEU* 3.5 25.6 - - + +
174E LEU* 5.9 0.2 - - + -
210E TYR* 4.8 8.5 - + - -
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Residues in contact with LYS 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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858A ARG* 4.3 5.4 + - - +
164E LEU 2.7 19.6 + - - +
165E GLN* 4.0 17.0 - - - +
166E ARG 3.8 9.2 - - - +
167E TYR* 1.3 77.0 - - - +
169E LEU* 1.3 62.4 + - - +
173E GLN* 4.8 0.5 - - - +
74F ILE* 4.8 16.8 - - - +
138F LEU* 5.1 12.4 - - + +
140F ASP* 3.9 38.4 + - + +
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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