Contacts of the helix formed by residues 201 - 212 (chain B) in PDB entry 3U8Z
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 ASP 201 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112B GLU* 2.8 17.1 + - - +
115B GLN* 3.0 22.2 + - - +
147B GLN 4.6 1.0 - - - +
148B ALA* 3.2 38.5 - - - +
198B ARG* 4.6 6.5 + - - +
199B ALA 3.6 1.9 + - - +
200B ARG* 1.3 66.8 - - - +
202B GLU* 1.3 63.8 + - - +
203B ALA* 3.6 10.7 + - - +
204B GLU* 3.2 37.1 + - - +
52D ARG* 4.5 11.7 - - - -
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Residues in contact with GLU 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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106B GLU* 4.5 6.6 - - - +
115B GLN* 5.1 3.0 + - - +
200B ARG* 3.1 16.7 + - + +
201B ASP* 1.3 71.9 + - - +
203B ALA* 1.4 56.6 + - - +
205B MET* 3.1 27.5 + - - +
206B GLU* 3.0 58.4 + - + +
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Residues in contact with ALA 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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144B TYR* 3.5 41.4 - - + +
147B GLN* 3.9 14.8 - - + +
148B ALA* 3.7 10.3 - - - +
201B ASP* 3.2 12.7 + - - +
202B GLU* 1.4 76.2 - - - +
204B GLU* 1.4 56.7 + - - +
206B GLU* 3.5 2.1 + - - +
207B TYR* 3.0 28.8 + - - +
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Residues in contact with GLU 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLU* 4.7 2.3 - - - +
115B GLN* 3.0 25.6 - - + +
116B HIS* 2.7 47.2 + - - +
119B PHE* 3.2 45.2 - - + -
148B ALA* 4.0 3.0 - - + +
201B ASP* 3.2 33.5 + - - +
203B ALA* 1.4 76.0 - - - +
205B MET* 1.4 57.6 + - - +
207B TYR* 3.4 3.6 - - - +
208B LEU* 3.1 33.2 + - - +
52D ARG* 5.2 1.0 - - - -
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Residues in contact with MET 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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105B ALA* 3.7 27.4 - - - +
106B GLU* 3.8 35.0 - - + +
109B LEU* 3.7 22.4 - - + +
115B GLN* 3.6 36.2 - - + +
201B ASP 3.9 0.4 + - - -
202B GLU* 3.1 29.8 + - - +
204B GLU* 1.4 75.0 - - - +
206B GLU* 1.3 61.4 + - - +
208B LEU* 3.2 4.0 + - + +
209B LYS* 3.0 46.1 + - + +
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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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144B TYR* 3.6 44.3 + - + -
202B GLU* 3.0 39.2 + - + +
203B ALA* 3.7 3.1 - - - +
205B MET* 1.3 74.8 - - - +
207B TYR* 1.4 59.9 + - - +
209B LYS* 2.9 36.8 + - - +
210B ILE* 3.4 27.9 + - - +
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Residues in contact with TYR 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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119B PHE* 3.4 27.4 - + + -
122B VAL* 4.4 11.9 - - + -
123B LYS* 3.4 44.3 - - + +
126B ILE* 3.5 24.0 - - + +
127B LEU* 5.2 1.4 - - - +
141B LEU* 3.2 63.6 - - + +
144B TYR* 4.2 7.3 - - + +
145B ALA* 4.0 17.3 - - + -
203B ALA 3.0 14.5 + - - +
204B GLU 3.4 10.5 - - - +
206B GLU* 1.4 74.6 - - - +
208B LEU* 1.4 63.6 + - + +
210B ILE 3.2 2.3 + - - -
211B ALA* 3.0 24.5 + - + -
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Residues in contact with LEU 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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105B ALA* 4.1 13.2 - - + -
109B LEU* 3.9 24.5 - - + -
115B GLN* 3.6 31.6 - - + +
118B PHE* 3.9 4.7 - - + -
119B PHE* 3.8 23.3 - - - +
122B VAL* 3.9 30.3 - - + -
204B GLU 3.1 17.6 + - - +
205B MET* 3.2 8.5 + - - +
207B TYR* 1.4 80.2 - - + +
209B LYS* 1.3 52.7 + - - +
211B ALA* 3.7 3.5 - - - +
212B GLN* 2.8 39.1 + - - +
217B TYR* 4.6 8.9 - - - +
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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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105B ALA* 5.3 0.4 - - + -
106B GLU* 3.3 38.5 + - + +
205B MET* 3.0 41.1 + - + +
206B GLU* 2.9 35.5 + - - +
207B TYR 3.3 0.2 - - - -
208B LEU* 1.3 73.6 - - - +
210B ILE* 1.4 64.3 + - + +
212B GLN* 3.4 33.3 + - - +
213B ASP* 3.7 13.9 - - - +
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Residues in contact with ILE 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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137B ALA* 4.3 22.9 - - + +
140B LEU* 4.0 25.1 - - + -
141B LEU* 3.8 21.8 - - + -
144B TYR* 3.6 37.2 - - + -
206B GLU 3.4 8.9 + - - +
207B TYR 3.2 6.3 + - - +
209B LYS* 1.4 74.7 - - + +
211B ALA* 1.3 66.6 + - - +
213B ASP* 3.2 20.4 + - - +
214B LEU* 4.0 7.5 + - + +
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Residues in contact with ALA 211 (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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122B VAL* 3.6 31.0 - - + -
126B ILE* 4.7 2.9 - - + -
141B LEU* 4.0 9.4 - - + +
207B TYR* 3.0 20.0 + - + +
208B LEU* 3.7 6.3 - - - +
210B ILE* 1.3 76.7 - - - +
212B GLN* 1.4 56.3 + - - +
214B LEU* 3.0 41.9 + - + +
217B TYR* 3.4 12.3 - - + +
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Residues in contact with GLN 212 (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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102B PRO 4.9 1.4 - - - +
103B GLU 3.8 12.6 + - - +
104B ASN* 3.7 12.2 + - - +
105B ALA* 2.9 36.5 + - - +
106B GLU* 6.1 0.2 - - - +
208B LEU 2.8 22.8 + - - +
209B LYS* 3.4 32.3 + - - +
211B ALA* 1.4 71.6 - - - +
213B ASP* 1.3 66.3 + - - +
214B LEU 3.3 4.8 + - - +
217B TYR* 3.5 37.5 + - + +
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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