Contacts of the helix formed by residues 175 - 181 (chain E) in PDB entry 3MX4
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 175 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158E ASP 3.5 12.8 + - - -
159E GLY* 3.5 16.4 - - - -
162E ASN* 4.1 8.1 - - - -
173E ALA 3.6 1.9 + - - -
174E LYS* 1.3 77.5 - - - +
176E ASP* 1.3 63.7 + - - +
177E TRP* 3.3 4.0 + - - +
178E ASP* 2.7 36.7 + - - +
179E VAL* 2.9 25.4 + - - +
186E TRP* 5.9 1.2 - - - -
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Residues in contact with ASP 176 (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 VAL 4.3 10.7 - - - +
157E VAL* 4.0 13.3 - - + +
158E ASP* 3.7 17.2 + - + +
174E LYS 3.9 1.4 + - - +
175E SER* 1.3 71.8 - - - +
177E TRP* 1.3 61.7 + - - +
179E VAL* 3.3 14.2 + - - -
180E ILE* 3.3 10.7 + - - +
195E SER* 2.8 32.0 + - - -
199E PHE* 4.8 8.0 - - - -
200E ILE* 3.8 27.9 - - + +
203E ARG* 4.8 4.7 + - - -
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Residues in contact with TRP 177 (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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111E ASN* 4.2 10.8 - - + -
112E ILE* 4.7 1.8 - - + -
115E THR* 3.7 24.0 - - + -
118E LEU* 4.5 2.0 - - + -
153E TRP* 3.2 57.3 - + - -
157E VAL* 3.8 13.0 - - + +
158E ASP 3.0 21.0 + - - +
160E PHE* 3.4 43.5 - + + +
175E SER* 3.1 4.0 - - - +
176E ASP* 1.3 75.8 - - - +
178E ASP* 1.3 73.0 + - - +
180E ILE 3.4 0.7 + - - -
181E HIS* 2.7 64.9 + + + +
184E ARG* 3.8 26.5 - - + -
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Residues in contact with ASP 178 (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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159E GLY 4.6 0.2 - - - +
174E LYS* 3.5 24.7 - - + +
175E SER* 2.7 28.7 + - - +
177E TRP* 1.3 82.6 - - - +
179E VAL* 1.3 64.1 + - - +
181E HIS 4.4 2.8 - - - +
182E PRO* 3.2 24.1 - - + +
183E GLY 5.8 0.2 + - - -
184E ARG* 2.9 49.1 + - - +
186E TRP* 3.7 11.3 - - - -
187E ALA* 3.6 19.8 - - + +
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Residues in contact with VAL 179 (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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174E LYS* 4.2 14.6 - - + -
175E SER 2.9 20.3 + - - +
176E ASP* 3.3 9.2 + - - +
177E TRP 3.1 0.4 - - - -
178E ASP* 1.3 80.7 - - - +
180E ILE* 1.3 66.4 + - + +
182E PRO* 3.3 11.8 - - - +
194E HIS* 4.2 18.6 - - + +
195E SER 3.9 21.5 - - - +
197E PRO* 4.3 16.8 - - + -
200E ILE* 3.5 21.8 - - + -
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Residues in contact with ILE 180 (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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57E TYR* 4.2 6.7 + - - +
59E LEU* 4.0 11.9 - - + -
60E TYR* 3.2 25.6 - - - +
117E ASN* 2.7 31.4 + - - -
157E VAL* 4.3 7.2 - - + -
176E ASP 3.3 6.2 + - - +
177E TRP 4.1 2.7 - - - +
179E VAL* 1.3 75.4 - - + +
181E HIS* 1.3 73.2 + - + +
182E PRO* 3.2 7.0 - - - +
197E PRO* 4.8 8.3 - - + -
200E ILE* 3.7 33.9 - - + -
201E GLU* 4.8 12.1 - - + +
204E ILE* 3.7 22.2 - - + -
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Residues in contact with HIS 181 (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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57E TYR* 3.7 20.0 - + - -
60E TYR* 2.6 44.3 + + - -
115E THR* 3.7 25.1 - - + +
117E ASN* 2.9 22.7 + - - +
118E LEU* 3.5 15.8 - - + +
153E TRP* 4.0 0.8 - - - -
177E TRP* 2.7 61.8 + + + +
178E ASP* 3.5 5.5 - - - +
180E ILE* 1.3 94.7 + - + +
182E PRO* 1.3 67.0 - - - +
183E GLY* 3.6 1.6 + - - -
184E ARG 4.7 0.5 + - - -
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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