Contacts of the helix formed by residues 183 - 189 (chain X) in PDB entry 4MXV
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 LYS 183 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125X LEU* 3.2 44.6 + - + +
126X LYS* 5.4 2.2 - - - +
128X GLY* 2.8 33.1 + - - +
129X THR* 4.0 1.7 - - - +
130X ALA* 4.7 4.3 - - - -
181X LEU 3.8 0.2 + - - -
182X SER* 1.3 69.4 - - - +
184X ALA* 1.3 67.5 + - - +
186X TYR* 3.6 6.8 - - - +
187X GLU* 3.1 47.1 + - + +
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Residues in contact with ALA 184 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128X GLY 4.7 0.2 + - - -
182X SER* 3.4 12.3 - - - +
183X LYS* 1.3 82.0 - - - +
185X ASP* 1.3 65.2 + - - +
187X GLU* 3.0 13.1 + - - +
188X LYS* 3.4 19.9 + - - +
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Residues in contact with ASP 185 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181X LEU* 4.1 14.7 - - + +
182X SER* 3.0 21.8 + - - +
184X ALA* 1.3 78.9 - - - +
186X TYR* 1.3 58.9 + - - +
188X LYS* 3.2 35.7 + - - +
189X HIS* 2.9 36.3 + - + -
192X TYR* 3.9 0.5 + - - -
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Residues in contact with TYR 186 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119X PRO* 4.6 1.4 - - - +
120X PRO* 3.2 33.2 - - + +
125X LEU* 4.2 25.4 - - + -
130X ALA* 3.8 16.2 - - + -
132X VAL* 4.4 5.6 - - + -
181X LEU* 3.7 9.2 - - + -
182X SER 3.0 17.5 + - - +
183X LYS 3.6 5.2 - - - +
184X ALA 3.0 0.4 - - - -
185X ASP* 1.3 79.1 - - - +
187X GLU* 1.3 78.8 + - - +
189X HIS 3.3 2.8 - - - +
192X TYR* 2.7 59.9 + + - -
209X PHE* 3.7 15.3 - + - -
211X ARG* 3.3 35.8 + - + +
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Residues in contact with GLU 187 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125X LEU* 4.4 8.5 - - - +
183X LYS* 3.1 32.8 + - + +
184X ALA* 3.0 9.4 + - - +
186X TYR* 1.3 95.3 - - - +
188X LYS* 1.3 65.7 + - + +
189X HIS 3.1 3.9 + - - -
211X ARG* 2.7 53.3 + - - +
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Residues in contact with LYS 188 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151X ASP* 4.8 0.3 - - - +
184X ALA* 3.8 14.8 - - - +
185X ASP* 3.2 32.3 + - - +
186X TYR 3.4 0.6 - - - -
187X GLU* 1.3 78.6 - - - +
189X HIS* 1.3 81.0 + - + +
190X LYS* 5.6 1.4 - - - +
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Residues in contact with HIS 189 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150X VAL* 3.6 31.9 - - + +
151X ASP* 3.1 28.3 - - + +
185X ASP* 2.9 32.5 + - + -
186X TYR 3.3 4.2 + - - +
187X GLU 3.1 0.6 - - - -
188X LYS* 1.3 103.5 - - + +
190X LYS* 1.3 61.8 + - - +
192X TYR* 3.6 9.2 - - + +
211X ARG* 3.2 27.4 + - - -
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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