Contacts of the helix formed by residues 156 - 167 (chain E) in PDB entry 1GZ0
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 ASN 156 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82E GLU* 4.4 3.5 + - - +
154E VAL* 4.4 0.4 - - - -
155E THR* 1.3 80.4 - - + +
157E LEU* 1.3 53.4 + - - +
158E ALA* 3.3 12.1 + - - +
159E ARG* 2.9 51.4 + - + +
160E THR* 2.8 34.9 + - - -
162E ARG* 4.7 6.9 - - - +
205E LEU* 5.2 4.0 - - - +
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Residues in contact with LEU 157 (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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99E ILE* 3.7 30.5 - - + -
101E ASP* 3.5 34.8 - - + +
125E ILE* 4.4 9.6 - - + -
127E PRO* 4.2 25.5 - - + +
154E VAL* 3.9 22.6 - - + +
155E THR 4.0 1.8 + - - -
156E ASN* 1.3 72.4 + - - +
158E ALA* 1.3 52.8 + - - +
160E THR* 3.0 6.4 + - - -
161E MSE 2.8 48.3 + - + +
206E THR* 3.5 18.4 - - + +
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Residues in contact with ALA 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 ASN* 3.3 9.3 + - - +
157E LEU* 1.3 79.0 - - - +
159E ARG* 1.3 63.5 + - - +
161E MSE 3.0 22.9 + - - +
162E ARG* 3.1 26.9 + - - +
205E LEU* 3.4 40.4 - - + +
206E THR* 5.6 1.7 + - - +
209E HIS* 3.8 12.9 - - + +
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Residues in contact with ARG 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E GLU* 4.4 17.1 + - - +
155E THR* 4.6 11.9 - - - +
156E ASN* 2.9 41.7 + - + +
158E ALA* 1.3 78.7 - - - +
160E THR* 1.3 62.3 + - - +
162E ARG* 3.0 38.7 + - - +
163E MSE 3.2 11.8 + - - +
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Residues in contact with THR 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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82E GLU* 3.9 8.8 + - - +
85E LEU* 3.6 28.9 - - + -
99E ILE* 6.1 0.2 - - + -
125E ILE* 4.3 16.8 - - + -
154E VAL* 3.2 34.3 - - + +
156E ASN 2.8 10.2 + - - -
157E LEU* 3.4 11.2 - - + -
159E ARG* 1.3 76.6 - - - +
161E MSE 1.3 58.7 + - + +
163E MSE 3.2 12.7 + - + +
164E LEU* 3.0 28.9 + - + +
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Residues in contact with MSE 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E ILE* 4.2 16.8 - - + -
157E LEU* 2.8 37.0 + - + +
158E ALA* 3.0 13.9 + - - +
160E THR* 1.3 76.2 - - - +
162E ARG* 1.3 60.4 + - - +
164E LEU* 3.3 6.4 + - - +
165E GLN* 3.0 34.1 + - - +
171E ILE* 3.7 39.2 - - + +
194E VAL* 4.3 6.5 - - + -
206E THR* 3.5 38.4 - - + +
209E HIS* 3.8 25.1 - - + +
210E CYS* 3.9 4.7 - - - -
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Residues in contact with ARG 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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156E ASN* 4.7 6.5 - - - +
158E ALA* 3.1 27.6 + - - +
159E ARG* 3.0 48.7 + - - +
161E MSE 1.3 73.0 - - - +
163E MSE 1.3 61.5 + - - +
165E GLN* 3.1 11.2 + - - +
166E GLU* 2.8 31.0 + - - +
205E LEU* 5.2 2.4 - - - +
209E HIS* 3.4 26.0 + - + -
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Residues in contact with MSE 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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82E GLU 5.5 0.4 - - - +
85E LEU* 3.5 41.3 - - + -
86E PRO* 4.4 21.5 - - + -
89E ILE* 3.7 18.6 - - + -
159E ARG 3.2 8.7 + - - +
160E THR* 3.4 17.9 - - + +
162E ARG* 1.3 80.4 - - - +
164E LEU* 1.3 75.0 + - + +
166E GLU* 3.2 16.0 + - - +
167E GLU* 3.2 26.9 + - + +
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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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89E ILE* 3.3 31.2 - - + -
97E LEU* 3.8 21.8 - - + -
99E ILE* 4.0 20.9 - - + -
125E ILE* 4.0 24.9 - - + -
160E THR* 3.0 20.6 + - + +
161E MSE 3.5 11.9 - - - +
163E MSE 1.3 87.1 - - + +
165E GLN* 1.3 60.4 + - - +
167E GLU* 3.2 11.4 + - - +
169E ILE* 3.1 35.1 + - + +
171E ILE* 4.6 5.4 - - + -
192E ALA* 4.2 8.7 - - + -
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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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161E MSE 3.0 22.4 + - - +
162E ARG* 3.1 12.2 + - - +
164E LEU* 1.3 73.4 - - - +
166E GLU* 1.3 64.3 + - - +
167E GLU 3.0 1.6 - - - -
168E ASN* 3.0 16.8 + - - +
169E ILE 3.8 13.9 - - - +
171E ILE* 3.6 13.9 - - + +
209E HIS* 2.9 36.4 + - - +
210E CYS 4.4 0.2 - - - -
211E ASP* 3.0 34.2 + - - +
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Residues in contact with GLU 166 (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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162E ARG 2.8 16.0 + - - +
163E MSE 3.2 8.7 + - + +
165E GLN* 1.3 77.4 - - - +
167E GLU* 1.3 65.5 + - + +
168E ASN* 3.1 11.0 + - - +
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Residues in contact with GLU 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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86E PRO* 5.2 5.3 - - + +
89E ILE* 4.4 20.6 - - + +
90E ALA* 5.0 10.9 - - - +
163E MSE 3.3 27.8 - - + +
164E LEU* 3.4 10.5 - - - +
165E GLN 3.0 0.8 - - - -
166E GLU* 1.3 85.3 - - + +
168E ASN* 1.3 63.0 + - - +
169E ILE* 3.4 2.6 + - + -
190E ARG* 2.8 39.8 + - - +
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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