Contacts of the helix formed by residues 152 - 165 (chain E) in PDB entry 4ZZ7
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 VAL 152 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E ILE* 3.9 12.1 - - + -
86E ILE* 3.5 26.0 - - + -
100E GLU* 2.7 16.1 + - - +
101E LEU* 3.8 30.1 - - + -
151E PRO* 1.3 76.5 - - - +
153E MET* 1.3 66.0 + - - +
154E VAL 3.5 0.2 - - - -
155E PRO* 3.5 3.5 - - - +
156E LEU* 3.1 46.8 + - + +
180E SER* 3.9 15.5 - - - +
184E ILE* 4.2 19.2 - - + +
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Residues in contact with MET 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E GLU* 3.0 36.9 + - + +
103E ARG* 3.1 52.9 - - - +
104E GLY* 3.9 15.7 - - - +
107E ASN* 4.1 0.2 - - - +
150E PHE* 3.7 31.6 + - + -
152E VAL* 1.3 78.2 - - - +
154E VAL* 1.3 60.1 + - + +
156E LEU* 3.0 6.8 + - - +
157E TRP* 2.9 67.6 + - + +
280E CYS* 5.9 0.4 - - - -
442E VAL* 5.9 0.2 - - - -
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Residues in contact with VAL 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146E THR* 4.1 6.7 - - + -
147E PRO* 3.6 24.0 - - + -
150E PHE* 3.5 35.9 + - + +
153E MET* 1.3 76.1 - - + +
155E PRO* 1.4 75.2 - - + +
157E TRP* 2.9 49.4 + - + +
158E MET* 3.6 6.6 + - + +
223E VAL* 3.8 23.3 - - + -
501E NAD 4.4 10.1 - - + -
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Residues in contact with PRO 155 (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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146E THR* 3.8 30.3 - - + +
150E PHE 3.3 15.9 - - - +
151E PRO 3.2 19.5 - - - +
152E VAL 3.5 8.7 - - - +
154E VAL* 1.4 89.4 - - + +
156E LEU* 1.3 56.4 + - - +
158E MET* 3.0 18.4 + - + +
159E PHE* 3.0 37.7 + - + -
171E LEU* 3.9 15.3 - - + -
181E THR* 3.9 9.6 - - + -
184E ILE* 5.1 1.3 - - + -
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Residues in contact with LEU 156 (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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71E PHE* 3.6 25.6 - - + -
75E LEU* 4.6 11.0 - - + -
101E LEU* 4.9 1.6 - - + -
104E GLY* 3.6 32.5 - - - +
105E ILE 4.6 0.7 - - - +
107E ASN* 3.2 15.8 - - - +
108E VAL* 3.9 4.5 - - + -
152E VAL* 3.1 40.0 + - + +
153E MET 3.0 10.7 + - - +
155E PRO* 1.3 72.7 - - - +
157E TRP* 1.3 62.3 + - - +
159E PHE* 3.5 24.7 - - + -
160E PRO* 3.1 28.6 - - + +
184E ILE* 4.1 7.6 - - + -
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Residues in contact with TRP 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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107E ASN* 3.3 15.9 + - - +
153E MET* 2.9 54.9 + - + +
154E VAL* 2.9 30.5 + - + +
156E LEU* 1.3 76.5 - - - +
158E MET* 1.3 64.9 + - + +
161E MET* 4.7 7.8 - - - +
223E VAL* 4.1 27.1 - - + -
246E LEU* 4.2 6.7 - - + -
280E CYS* 5.0 2.0 - - - -
442E VAL* 5.4 2.2 - - + -
449E PHE* 3.8 44.0 - + - -
462E ALA* 3.9 14.8 - - + -
463E TYR* 3.3 60.1 + + + +
471E TYR* 4.7 2.9 + - - -
501E NAD 4.1 7.9 - + - -
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Residues in contact with MET 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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144E GLY* 3.8 16.6 - - - -
145E ILE 3.8 11.7 - - - +
146E THR* 3.9 20.9 - - + -
154E VAL* 3.7 9.2 - - + +
155E PRO* 3.0 7.4 + - + +
157E TRP* 1.3 81.9 - - + +
159E PHE* 1.3 60.4 + - - +
160E PRO* 3.3 3.2 - - - -
161E MET 3.4 3.3 + - - -
162E ALA* 3.0 27.0 + - - +
169E PHE* 3.7 10.1 - - + -
171E LEU* 5.0 0.7 - - - -
221E SER* 3.4 34.5 - - - +
223E VAL* 3.4 33.4 - - + -
244E GLN* 5.7 1.3 - - - +
471E TYR* 3.4 25.4 - - - +
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Residues in contact with PHE 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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68E MET* 5.7 0.2 - - + -
71E PHE* 4.0 12.8 - + - -
155E PRO* 3.0 49.1 + - + -
156E LEU* 3.5 26.2 - - + -
158E MET* 1.3 75.1 - - - +
160E PRO* 1.4 67.4 - - + +
163E ILE* 2.8 48.4 + - + +
169E PHE* 3.7 36.6 - + + -
171E LEU* 4.5 4.9 - - + -
181E THR 6.0 0.2 - - - -
184E ILE* 4.1 16.2 - - + -
185E ALA* 5.1 4.5 - - + -
188E LEU* 3.8 19.1 - - + -
198E MET* 3.4 31.4 - - + -
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Residues in contact with PRO 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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68E MET* 3.5 30.5 - - + +
107E ASN* 4.5 4.3 - - + +
108E VAL* 4.1 10.5 - - + -
111E ALA* 4.0 11.5 - - + +
155E PRO 3.6 0.2 - - - +
156E LEU* 3.1 55.0 - - + +
158E MET 3.3 2.5 - - - -
159E PHE* 1.4 102.7 - - + +
161E MET* 1.3 63.0 + - - +
164E VAL* 3.2 22.5 + - - +
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Residues in contact with MET 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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107E ASN 5.5 2.0 - - - +
110E TYR* 3.5 38.4 - - + -
111E ALA* 4.1 13.6 - - + +
114E ALA* 5.7 0.7 - - - -
117E LEU* 3.8 10.5 - - + -
157E TRP 4.7 6.2 + - - +
158E MET 3.4 6.7 + - - +
160E PRO* 1.3 80.1 - - - +
162E ALA* 1.3 57.3 + - - +
164E VAL* 3.3 13.0 + - - +
165E CYS* 2.9 45.7 + - - -
463E TYR* 5.7 1.6 - - + -
464E GLY 4.2 5.8 - - - +
467E ALA* 3.7 27.6 - - + -
468E VAL* 3.6 23.8 - - + +
471E TYR* 4.0 4.0 - - + -
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Residues in contact with ALA 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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142E VAL* 4.7 2.5 - - + -
158E MET 3.0 19.4 + - - +
159E PHE 3.9 0.4 - - - +
161E MET* 1.3 77.6 - - - +
163E ILE* 1.3 60.5 + - - +
165E CYS 3.5 3.5 + - - -
167E ASN* 3.0 34.9 + - + +
169E PHE* 3.7 28.3 - - + -
471E TYR* 3.5 32.4 - - + -
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Residues in contact with ILE 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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56E TRP* 2.9 45.9 + - + -
64E ARG* 3.9 0.6 - - - +
67E VAL* 6.0 0.4 - - + -
68E MET* 5.0 10.3 - - - -
159E PHE* 2.8 48.7 + - + +
160E PRO* 4.1 2.9 - - + +
162E ALA* 1.3 70.5 - - - +
164E VAL* 1.3 61.7 + - - +
166E GLY* 2.9 12.1 + - - -
167E ASN 3.6 7.9 - - - +
169E PHE* 4.3 8.1 - - + -
188E LEU* 3.9 17.0 - - + -
193E LEU* 3.8 10.3 - - + -
197E VAL* 3.7 24.2 - - + +
198E MET* 4.0 15.9 - - + -
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Residues in contact with VAL 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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56E TRP* 5.1 0.2 - - - -
61E PRO* 5.0 0.5 - - - +
64E ARG* 2.9 32.5 + - + +
65E ALA* 3.7 30.5 - - - +
68E MET* 4.0 9.6 - - + -
111E ALA* 3.5 29.2 - - + +
114E ALA* 3.5 22.9 - - + +
118E LEU* 4.1 6.1 - - - +
160E PRO 3.2 14.0 + - - +
161E MET* 3.4 20.6 - - - +
163E ILE* 1.3 80.8 - - - +
165E CYS* 1.3 59.2 + - - +
166E GLY 3.1 0.4 - - - -
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Residues in contact with CYS 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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64E ARG* 3.6 7.8 + - - +
118E LEU* 4.2 18.2 - - + +
136E PHE 5.2 0.3 - - - +
138E PRO* 3.4 22.7 - - - +
161E MET* 2.9 47.3 + - - +
162E ALA 3.7 6.5 - - - +
163E ILE 3.1 0.2 - - - -
164E VAL* 1.3 77.4 - - - +
166E GLY* 1.3 57.2 + - - +
167E ASN* 3.5 10.3 + - - +
468E VAL* 4.1 18.2 - - - -
471E TYR* 3.9 10.8 - - + +
472E THR* 3.9 15.9 - - + +
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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