Contacts of the helix formed by residues 151 - 158 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150H SER* 1.3 68.4 - - - +
152H ASP* 1.3 57.9 + - - +
154H VAL* 3.8 23.7 - - + +
155H LEU* 2.7 36.7 + - - +
161H ILE* 4.9 11.4 - - + -
165H ILE* 6.3 0.2 - - + -
169H VAL* 4.0 24.2 - - + -
193H PRO* 3.1 11.5 + - + +
196H ILE* 3.0 41.3 + - + +
198H VAL* 4.0 23.6 - - + -
204H ILE* 5.0 0.2 - - + -
256H MET* 3.8 28.6 - - - +
371H PHE* 5.0 8.5 - - + -
374H TRP* 5.6 0.9 - - + -
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Residues in contact with ASP 152 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150H SER* 3.2 14.3 + - - +
151H LEU* 1.3 76.1 - - - +
153H GLN* 1.3 72.5 + - - +
155H LEU* 3.4 7.1 + - - +
156H LYS* 3.3 17.3 + - - +
193H PRO* 3.2 17.3 + - + +
194H SER* 3.5 27.4 - - - +
227H ARG* 3.5 24.6 + - - -
901H ACP 4.5 4.8 + - - -
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Residues in contact with GLN 153 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74H LEU 3.3 20.0 + - - +
75H GLY* 4.9 0.7 - - - -
148H GLY 4.6 1.9 + - - +
149H GLY* 3.3 30.1 - - - -
150H SER* 2.8 13.2 + - - +
152H ASP* 1.3 85.1 + - - +
154H VAL* 1.3 63.7 + - + +
156H LYS* 3.4 19.1 + - + +
157H LYS* 3.4 19.8 + - + +
901H ACP 2.8 26.9 + - - -
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Residues in contact with VAL 154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148H GLY 3.8 19.1 - - - +
150H SER 3.0 15.7 + - - +
151H LEU* 3.4 19.9 + - + +
153H GLN* 1.3 72.9 - - - +
155H LEU* 1.3 67.6 + - - +
157H LYS* 3.1 7.8 + - - +
158H ALA* 3.1 22.7 + - + +
161H ILE* 4.6 4.5 - - + -
198H VAL* 4.2 8.5 - - + -
374H TRP* 3.8 34.1 - - + -
375H LEU* 3.9 20.0 - - + -
378H THR* 4.9 6.5 - - - +
379H ILE* 4.8 7.0 - - + -
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Residues in contact with LEU 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151H LEU 2.7 21.2 + - - +
152H ASP* 3.5 7.0 - - - +
153H GLN 3.3 0.2 - - - -
154H VAL* 1.3 73.6 - - - +
156H LYS* 1.3 62.5 + - - +
158H ALA 3.3 0.2 + - - -
159H GLY* 3.1 50.9 + - - +
160H ARG* 4.0 0.4 - - - -
161H ILE* 3.9 17.2 - - + +
193H PRO* 5.2 4.3 - - + -
255H GLU* 3.7 34.1 - - + +
256H MET* 3.7 44.6 - - + +
259H GLY* 4.4 8.5 - - - -
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Residues in contact with LYS 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152H ASP 3.3 8.6 + - - +
153H GLN* 3.4 15.3 - - + +
155H LEU* 1.3 79.9 - - - +
157H LYS* 1.3 67.3 + - + +
158H ALA 3.4 0.3 + - - -
159H GLY* 3.8 5.5 + - - -
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Residues in contact with LYS 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153H GLN* 3.5 15.5 - - + +
154H VAL* 3.1 8.5 + - - +
156H LYS* 1.3 83.8 - - + +
158H ALA* 1.3 59.2 + - + +
159H GLY 3.6 0.6 + - - -
378H THR* 4.2 13.7 + - - +
379H ILE* 3.4 38.3 - - + +
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Residues in contact with ALA 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154H VAL* 3.1 14.8 + - + +
155H LEU 3.7 1.3 - - - +
157H LYS* 1.3 79.6 - - - +
159H GLY* 1.3 54.4 + - - +
160H ARG* 2.6 30.7 + - - +
161H ILE* 4.8 7.9 - - + -
374H TRP* 4.8 6.3 - - + -
378H THR* 4.2 27.8 - - + -
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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