Contacts of the helix formed by residues 200 - 210 (chain B) in PDB entry 4J7X
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B GLY* 3.8 15.7 - - - -
16B PHE 4.1 0.7 - - - +
198B LEU* 3.0 17.3 + - + -
199B ASP* 1.3 81.6 - - - +
201B ASP* 1.3 65.5 + - - +
202B MET 3.2 6.9 + - - -
203B GLN* 3.3 2.0 + - - +
204B GLN* 3.0 22.8 + - - +
207B ARG* 5.2 0.7 + - - -
231B CYS* 3.8 23.8 - - - -
801B NAP 2.7 49.3 + - - +
803B SO4 5.2 4.7 - - - +
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Residues in contact with ASP 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ARG* 3.0 44.5 + - - +
15B GLY* 5.7 0.2 - - - -
200B THR* 1.3 75.9 - - - +
202B MET* 1.3 57.2 + - - +
204B GLN* 3.4 16.0 - - - +
205B LEU* 3.1 27.6 + - - +
801B NAP 3.8 3.7 + - - +
803B SO4 4.3 11.7 + - - -
143F PRO* 5.6 6.6 - - - +
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Residues in contact with MET 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLY 3.7 24.0 - - - +
100B SER* 3.8 15.9 - - - -
101B LEU* 3.9 18.7 - - + +
167B TYR* 4.1 7.6 - - - -
200B THR* 3.1 1.6 + - - -
201B ASP* 1.3 76.9 - - - +
203B GLN* 1.3 59.8 + - - +
205B LEU* 3.1 9.6 + - + +
206B ALA* 2.9 27.2 + - - +
801B NAP 3.4 74.6 + - - +
804B SAS 3.7 23.1 - - + -
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Residues in contact with GLN 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B PRO* 3.6 16.2 - - - +
198B LEU 2.9 25.2 + - - +
199B ASP* 4.8 0.2 - - - -
200B THR* 3.3 9.5 + - - +
202B MET* 1.3 79.4 - - - +
204B GLN* 1.3 57.0 + - - +
206B ALA* 3.3 6.1 + - - +
207B ARG* 2.8 44.2 + - - +
219B LEU* 3.5 32.6 - - - +
228B LEU* 3.7 22.7 - - + +
801B NAP 2.6 31.1 + - - +
804B SAS 3.4 15.9 - - - -
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Residues in contact with GLN 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B THR 3.0 12.4 + - - +
201B ASP* 3.4 20.5 - - - +
203B GLN* 1.3 74.6 - - - +
205B LEU* 1.3 60.3 + - - +
207B ARG* 3.1 36.0 + - - +
208B GLU* 2.8 49.5 + - - +
223B LYS* 6.0 0.8 - - - +
143F PRO* 3.7 17.2 - - - +
144F GLY* 3.3 35.5 + - - +
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Residues in contact with LEU 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B LEU* 4.2 26.9 - - + +
102B GLY 4.9 7.0 - - - +
104B VAL* 5.7 0.4 - - + -
201B ASP 3.1 11.7 + - - +
202B MET* 3.4 12.6 - - + +
204B GLN* 1.3 78.5 - - - +
206B ALA* 1.3 61.4 + - - +
208B GLU* 4.7 1.6 - - - +
209B THR* 2.6 52.1 + - + +
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Residues in contact with ALA 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B LEU* 3.7 12.9 - - + +
104B VAL* 4.6 0.2 - - - -
164B TRP* 3.7 28.9 - - + -
202B MET 2.9 12.9 + - - +
203B GLN 3.5 8.1 - - - +
205B LEU* 1.3 79.2 - - - +
207B ARG* 1.3 63.1 + - - +
210B SER* 2.8 31.5 + - - -
216B ARG* 4.8 0.3 - - - +
219B LEU* 3.7 13.5 - - + +
804B SAS 4.0 9.4 - - + -
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Residues in contact with ARG 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B ASP* 4.8 6.7 + - - -
200B THR 5.2 0.6 + - - -
203B GLN* 2.8 46.1 + - - +
204B GLN* 3.2 45.7 + - - +
206B ALA* 1.3 74.0 - - - +
208B GLU* 1.3 66.2 + - + +
216B ARG* 3.5 17.9 - - - +
219B LEU* 3.8 27.7 + - + +
220B GLN* 3.1 57.8 + - + +
223B LYS* 3.7 35.0 - - - +
228B LEU* 3.9 12.7 - - - +
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Residues in contact with GLU 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B GLN* 2.8 43.7 + - + +
205B LEU* 4.4 1.2 - - - +
207B ARG* 1.3 91.4 + - + +
209B THR* 1.3 67.7 + - + +
210B SER 3.8 0.7 - - - -
216B ARG* 3.7 14.0 - - - +
220B GLN* 4.6 6.7 - - - +
144F GLY* 3.9 16.2 - - - +
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Residues in contact with THR 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ASP* 5.4 1.1 + - - -
104B VAL* 3.4 15.0 + - - +
105B SER* 3.1 33.3 + - - -
205B LEU* 2.6 41.6 + - + +
208B GLU* 1.3 89.1 - - + +
210B SER* 1.3 68.2 + - - +
211B VAL* 4.4 0.2 - - - -
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Residues in contact with SER 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B VAL* 3.5 11.3 - - - +
162B LYS 5.6 0.4 - - - -
164B TRP* 3.2 26.6 + - - -
206B ALA 2.8 22.9 + - - -
208B GLU 3.8 1.0 - - - -
209B THR* 1.3 79.1 + - - +
211B VAL* 1.3 53.6 + - - +
212B ASP 4.4 0.9 - - - -
215B MET* 3.5 29.5 - - - +
216B ARG* 2.7 40.7 + - - +
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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