Contacts of the helix formed by residues 200 - 206 (chain F) in PDB entry 6H25
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 THR 200 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31F ARG* 5.9 0.9 - - - -
37F ARG* 4.9 14.1 + - - -
59F GLY* 5.9 5.6 - - - +
154F GLY* 3.4 14.8 - - - +
155F GLY* 4.1 2.5 - - - -
199F PRO* 1.3 76.1 - - - +
201F ARG* 1.3 74.0 + - + +
202F LEU* 3.3 9.4 - - + +
203F GLU* 3.1 22.5 + - - -
204F GLU* 3.0 21.8 + - - +
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Residues in contact with ARG 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C THR* 3.5 30.3 - - - +
107F GLY* 5.1 9.4 - - - -
108F ARG* 3.1 57.2 - - - +
153F ASP* 3.3 29.4 + - - +
154F GLY* 2.7 23.0 + - - +
155F GLY* 4.6 2.2 - - - +
200F THR* 1.3 75.4 - - + +
202F LEU* 1.3 62.5 + - - +
204F GLU* 3.1 14.3 + - - +
205F GLU* 2.9 26.7 + - + +
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Residues in contact with LEU 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F GLU* 5.8 8.3 - - + -
26F GLU 5.4 8.3 - - - +
28F PRO* 4.8 22.4 - - + -
108F ARG* 3.4 32.1 - - - +
200F THR* 3.3 6.1 - - + +
201F ARG* 1.3 80.9 - - + +
203F GLU* 1.3 58.0 + - + +
205F GLU* 3.1 9.1 + - + +
206F ARG* 2.9 45.0 + - + +
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Residues in contact with GLU 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F PRO* 3.9 18.4 - - + -
31F ARG* 2.8 40.6 + - - -
37F ARG* 5.1 3.6 + - - -
186F SER* 3.5 7.2 + - - -
188F ALA* 6.1 0.5 - - - -
196F LEU* 4.5 24.3 - - + +
197F LEU 5.6 0.2 - - - +
198F ASP 4.6 0.5 - - - +
199F PRO* 3.3 28.8 - - + +
200F THR* 3.1 24.6 + - - +
202F LEU* 1.3 78.2 - - + +
204F GLU* 1.3 57.5 + - - +
206F ARG* 4.2 6.4 - - - +
207F ALA* 3.2 20.8 + - - +
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Residues in contact with GLU 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F ASP* 5.1 2.9 - - - +
155F GLY* 3.4 30.3 - - - +
156F SER* 4.0 7.3 + - - -
157F ALA 4.8 0.9 + - - -
185F LEU 5.7 0.5 - - - +
186F SER* 5.0 4.3 - - - +
199F PRO* 4.0 17.9 - - + +
200F THR 3.0 13.2 + - - +
201F ARG* 3.1 14.6 + - + +
203F GLU* 1.3 78.0 - - - +
205F GLU* 1.3 64.1 + - - +
206F ARG 3.3 0.4 - - - -
207F ALA* 3.2 21.2 + - + +
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Residues in contact with GLU 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F ARG* 5.2 9.2 - - - +
201F ARG* 2.9 15.3 + - + +
202F LEU* 3.1 15.9 + - + +
204F GLU* 1.3 78.7 - - - +
206F ARG* 1.3 69.6 + - - +
207F ALA 3.4 3.1 + - - +
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Residues in contact with ARG 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F GLU* 2.4 42.4 + - - +
26F GLU 3.4 12.7 + - - -
27F ALA* 3.5 20.2 - - + +
28F PRO* 4.7 13.2 - - + -
189F PRO* 3.3 27.2 - - + +
202F LEU* 2.9 27.9 + - + +
203F GLU* 4.7 5.4 - - - +
205F GLU* 1.3 84.7 - - - +
207F ALA* 1.3 63.3 + - - +
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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