Contacts of the helix formed by residues 200 - 210 (chain B) in PDB entry 3IJE
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 VAL 200 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135B GLY* 3.2 11.2 - - - +
136B THR* 3.2 39.9 - - + +
139B ALA* 3.7 21.5 - - + -
149B LEU* 4.3 20.6 - - + +
151B ILE* 4.4 16.2 - - + -
198B ASP* 3.0 17.4 + - - +
199B GLN* 1.3 70.9 - - - +
201B THR* 1.3 63.8 + - - +
203B PHE* 3.0 21.5 + - - +
204B ASN* 3.4 3.3 - - - +
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Residues in contact with THR 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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136B THR* 4.2 16.9 - - - +
199B GLN* 3.7 28.0 - - + +
200B VAL* 1.3 79.0 - - - +
202B ARG* 1.3 66.5 + - + +
204B ASN* 3.2 17.1 + - - +
205B GLU* 3.3 10.2 + - - +
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Residues in contact with ARG 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LEU* 4.2 25.3 - - - +
195B THR* 5.9 0.8 + - - -
197B THR* 4.6 16.4 + - + +
199B GLN* 3.1 36.1 + - + +
201B THR* 1.3 82.4 - - + +
203B PHE* 1.3 64.9 + - - +
204B ASN 3.4 0.2 - - - -
205B GLU* 3.1 29.4 - - + +
206B GLU* 3.0 37.3 + - + +
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Residues in contact with PHE 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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116B TYR* 4.2 14.6 - + + -
131B ILE* 4.1 24.2 - - + -
134B LEU* 3.6 36.6 - - + -
135B GLY* 3.7 7.0 - - - -
138B LEU* 6.3 1.8 - - + -
151B ILE* 3.6 30.7 - - + -
152B GLY 3.5 25.1 - - - -
153B PHE* 4.0 23.5 - + + +
194B LEU* 3.7 20.3 - - + +
197B THR* 6.3 0.2 - - + -
199B GLN 4.0 1.2 + - - -
200B VAL 3.0 14.1 + - - +
202B ARG* 1.3 77.3 - - - +
204B ASN* 1.3 64.0 + - - +
205B GLU 3.2 0.2 + - - -
206B GLU* 3.3 2.1 + - - +
207B VAL* 3.0 28.8 + - + +
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Residues in contact with ASN 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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132B GLN* 3.1 21.3 + - - +
133B ASN* 3.7 4.0 + - - +
134B LEU 3.0 18.5 + - - +
135B GLY* 3.5 2.3 - - - -
136B THR* 3.1 37.5 + - - +
200B VAL 3.4 12.3 - - - +
201B THR* 3.2 9.6 + - - +
203B PHE* 1.3 75.1 - - - +
205B GLU* 1.3 61.8 + - - +
207B VAL* 3.0 23.1 - - - +
208B LYS* 3.4 13.3 + - - +
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Residues in contact with GLU 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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201B THR* 3.3 5.2 + - - +
202B ARG* 3.1 36.8 - - + +
203B PHE 3.1 0.6 - - - -
204B ASN* 1.3 79.3 - - - +
206B GLU* 1.3 71.3 + - - +
208B LYS* 3.4 15.0 + - - +
209B LYS* 3.5 23.0 + - - +
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Residues in contact with GLU 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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153B PHE* 5.9 2.9 - - + -
193B VAL* 3.6 33.2 - - + +
194B LEU* 4.5 22.2 - - + -
202B ARG* 3.0 31.6 + - + +
203B PHE 4.0 2.0 - - - +
205B GLU* 1.3 77.4 - - - +
207B VAL* 1.3 61.8 + - - +
208B LYS 3.1 1.6 - - - -
209B LYS* 2.9 63.7 + - - +
210B GLN* 3.3 13.5 + - - +
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Residues in contact with VAL 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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128B LEU* 3.4 38.3 - - + +
131B ILE* 3.5 33.2 - - + +
132B GLN* 3.7 16.6 - - - +
153B PHE* 5.0 12.9 - - + -
203B PHE* 3.0 23.7 + - + +
204B ASN* 3.0 28.7 - - - +
206B GLU* 1.3 76.2 - - - +
208B LYS* 1.3 60.4 + - - +
210B GLN* 3.3 18.3 + - - +
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Residues in contact with LYS 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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128B LEU* 5.1 3.3 - - - +
129B TRP* 4.7 13.9 - - + -
132B GLN* 4.1 32.1 - - + +
204B ASN 3.6 10.3 - - - +
205B GLU* 3.4 12.1 + - - +
206B GLU 3.1 1.0 - - - -
207B VAL* 1.3 81.7 - - + +
209B LYS* 1.3 62.5 + - - +
210B GLN 3.6 5.4 + - - +
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Residues in contact with LYS 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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205B GLU* 3.7 22.1 - - - +
206B GLU* 2.9 45.3 + - - +
208B LYS* 1.3 77.3 - - - +
210B GLN* 1.3 67.5 + - - +
211B SER* 4.4 4.3 + - - -
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Residues in contact with GLN 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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120B LEU* 3.8 22.1 - - + +
128B LEU* 4.0 24.3 - - + +
153B PHE* 3.9 19.1 - - + -
155B ALA* 4.5 1.2 - - - +
185B LEU* 5.9 0.2 - - - +
191B LYS* 4.2 21.9 - - - +
193B VAL* 3.2 42.0 - - + +
206B GLU 3.5 13.9 - - - +
207B VAL* 3.5 13.5 - - - +
208B LYS 3.3 8.0 - - - +
209B LYS* 1.3 84.8 - - - +
211B SER* 1.3 62.0 + - - +
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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