Contacts of the helix formed by residues 151 - 159 (chain E) in PDB entry 4MNE
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 151 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150E SER* 1.3 69.3 - - - +
152E ASP* 1.3 59.0 + - - +
154E VAL* 3.8 17.6 - - + +
155E LEU* 2.9 32.1 + - - +
161E ILE* 4.5 12.2 - - + +
169E VAL* 3.7 27.4 - - + -
193E PRO* 3.2 14.8 + - + +
196E ILE* 2.8 42.5 + - + +
198E VAL* 3.6 24.7 - - + -
256E MET* 3.7 29.6 - - - +
371E PHE* 5.2 6.3 - - + -
374E TRP* 5.7 1.1 - - + -
375E LEU* 5.8 0.2 - - + -
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Residues in contact with ASP 152 (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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150E SER* 3.0 12.2 + - - +
151E LEU* 1.3 79.0 - - - +
153E GLN* 1.3 64.6 + - - +
155E LEU* 3.3 7.7 + - - +
156E LYS* 3.3 44.1 + - - +
193E PRO* 3.4 16.0 + - + +
194E SER* 3.6 27.5 - - - +
227E ARG* 3.6 24.5 + - - -
255E GLU* 4.9 5.2 - - - +
901E ACP 4.8 5.2 + - - -
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Residues in contact with GLN 153 (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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74E LEU 4.0 11.5 + - - -
148E GLY 4.8 2.3 - - - +
149E GLY* 4.1 12.2 - - - -
150E SER* 3.0 21.2 + - - +
152E ASP* 1.3 76.0 - - + +
154E VAL* 1.3 67.3 + - + +
156E LYS* 3.0 23.2 + - - +
157E LYS* 3.1 15.2 + - - +
901E ACP 2.4 40.9 + - - +
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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
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148E GLY 4.0 18.2 - - - +
150E SER 3.1 16.8 + - - +
151E LEU* 3.8 18.8 - - + +
153E GLN* 1.3 75.6 - - - +
155E LEU* 1.3 58.5 + - - +
157E LYS* 3.4 5.4 + - - +
158E ALA* 2.8 34.4 + - + +
161E ILE* 4.6 3.8 - - + -
198E VAL* 4.3 2.7 - - + -
374E TRP* 3.8 34.1 - - + -
375E LEU* 4.2 18.4 - - + -
378E THR* 4.4 9.4 - - - +
379E ILE* 6.0 3.8 - - + -
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Residues in contact with LEU 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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151E LEU 2.9 19.6 + - - +
152E ASP* 3.6 8.3 - - - +
153E GLN 3.2 0.2 - - - -
154E VAL* 1.3 74.2 - - - +
156E LYS* 1.3 62.6 + - + +
158E ALA 4.5 0.2 - - - +
159E GLY* 2.9 44.6 + - - +
161E ILE* 4.3 17.0 - - + +
193E PRO* 5.3 3.4 - - + -
255E GLU* 3.9 29.4 - - + +
256E MET* 3.6 47.1 - - + +
259E GLY* 4.0 10.3 - - - -
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Residues in contact with LYS 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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152E ASP* 3.3 46.3 + - - +
153E GLN* 3.0 14.1 + - - +
155E LEU* 1.3 82.2 - - + +
157E LYS* 1.3 63.5 + - - +
159E GLY* 3.8 5.9 + - - -
227E ARG* 5.3 3.7 - - - +
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Residues in contact with LYS 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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153E GLN 3.1 14.2 + - - +
154E VAL* 3.9 7.2 - - - +
156E LYS* 1.3 78.4 - - - +
158E ALA* 1.3 58.4 + - + +
378E THR* 3.2 31.1 + - - +
379E ILE* 4.5 19.4 - - + +
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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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154E VAL 2.8 18.3 + - - +
155E LEU* 4.6 2.5 - - - +
157E LYS* 1.3 77.3 - - - +
159E GLY* 1.3 55.9 + - - +
160E ARG 2.8 19.4 + - - +
161E ILE* 5.0 0.4 - - + -
374E TRP* 4.2 27.1 - - + -
378E THR* 4.2 18.2 - - + -
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Residues in contact with GLY 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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155E LEU* 2.9 19.7 + - - +
156E LYS 3.8 4.0 + - - -
157E LYS 3.6 2.6 + - - -
158E ALA* 1.3 72.3 - - - +
160E ARG* 1.3 61.1 + - - +
259E GLY* 3.2 26.3 - - - +
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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