Contacts of the helix formed by residues 184 - 194 (chain B) in PDB entry 4YET
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 ASN 184 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79B ASN* 3.1 23.7 + - - +
80B SER 2.8 19.9 + - - +
81B MET 3.8 15.1 + - - -
82B GLY* 5.3 0.4 - - - -
85B CYS* 4.0 19.4 - - - -
155B LEU* 3.5 6.6 - - - +
182B LEU 3.2 0.2 + - - -
183B VAL* 1.3 72.7 - - - +
185B TRP* 1.3 62.1 + - - +
186B ASP* 3.1 23.8 + - - +
187B PHE* 3.1 20.7 + - - +
188B ALA 3.5 6.9 + - - -
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Residues in contact with TRP 185 (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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85B CYS* 5.2 1.2 - - + +
86B GLY 3.3 15.9 + - - -
87B GLY 3.0 23.4 + - - -
88B GLU 3.4 15.3 + - - -
89B PRO* 3.5 18.4 - - + -
90B THR* 4.4 15.0 - - - +
93B ILE* 3.9 19.3 - - + -
97B ILE* 3.7 25.1 - - + -
104B PHE* 3.6 34.3 - + - -
107B PHE* 4.0 9.4 - + - -
126B LEU* 5.0 0.2 - - + -
155B LEU* 3.7 22.7 - - + -
180B TRP* 4.3 5.4 - + - -
183B VAL* 3.4 29.9 + - + +
184B ASN* 1.3 71.9 + - - +
186B ASP* 1.3 56.6 + - - +
188B ALA* 3.2 4.7 + - + +
189B ASN* 2.9 32.9 + - - +
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Residues in contact with ASP 186 (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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184B ASN* 3.1 14.1 + - - +
185B TRP* 1.3 79.8 - - - +
187B PHE* 1.3 56.1 + - - +
189B ASN* 3.3 11.6 + - - +
190B LYS* 2.9 64.0 + - - +
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Residues in contact with PHE 187 (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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76B PHE* 3.6 46.4 - + - -
79B ASN* 3.2 50.9 - - + +
80B SER* 3.6 10.3 - - - -
154B LEU 3.9 5.2 - - - -
184B ASN* 3.1 16.7 + - - +
186B ASP* 1.3 76.4 + - - +
188B ALA* 1.3 65.0 + - - +
190B LYS* 3.2 17.1 + - + +
191B ASN* 2.9 54.1 + - - -
196B PHE* 3.7 26.7 - + - -
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Residues in contact with ALA 188 (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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93B ILE* 3.9 27.8 - - + -
154B LEU* 3.6 18.8 + - + +
155B LEU* 3.8 26.6 - - + +
184B ASN 3.5 2.8 + - - -
185B TRP* 3.2 12.4 + - - +
187B PHE* 1.3 79.8 - - - +
189B ASN* 1.3 57.9 + - - +
191B ASN* 3.2 3.6 + - - +
192B LEU* 3.0 31.1 + - - +
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Residues in contact with ASN 189 (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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90B THR* 3.0 28.7 + - - -
91B GLY* 4.1 3.2 - - - -
92B PRO* 3.5 18.8 - - + +
93B ILE* 2.8 34.5 + - - +
185B TRP 2.9 23.0 + - - +
186B ASP* 3.7 11.7 + - - +
188B ALA* 1.3 73.0 - - - +
190B LYS* 1.3 65.3 + - - +
192B LEU* 3.3 9.1 + - - +
193B GLU* 3.3 23.9 + - - +
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Residues in contact with LYS 190 (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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186B ASP* 2.9 42.7 + - - +
187B PHE* 3.6 20.6 - - + +
189B ASN* 1.3 77.0 - - - +
191B ASN* 1.3 61.4 + - - +
193B GLU* 3.1 27.2 + - - +
194B ALA* 3.1 14.8 + - - +
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Residues in contact with ASN 191 (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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76B PHE* 3.4 8.4 - - - -
152B ARG* 2.8 32.2 + - - -
153B PRO 3.6 18.2 - - - +
154B LEU* 3.0 30.0 + - + -
187B PHE* 2.9 45.5 + - - +
188B ALA 3.2 5.1 + - - +
190B LYS* 1.3 74.5 - - - +
192B LEU* 1.3 60.5 + - - +
194B ALA 3.3 9.6 - - - +
196B PHE* 3.4 27.1 + - - +
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Residues in contact with LEU 192 (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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92B PRO* 3.8 18.2 - - + +
93B ILE* 3.6 38.1 - - + +
96B LYS* 4.4 16.4 - - + -
128B LEU* 4.0 27.2 - - + +
152B ARG* 2.9 16.7 + - - +
154B LEU* 3.9 26.9 - - + -
188B ALA 3.0 15.6 + - - +
189B ASN* 3.5 13.0 - - - +
191B ASN* 1.3 78.3 - - - +
193B GLU* 1.3 59.9 + - + +
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Residues in contact with GLU 193 (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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92B PRO* 6.6 0.4 - - + -
152B ARG* 4.1 3.0 + - - -
189B ASN 3.3 12.5 + - - +
190B LYS* 3.1 16.0 + - - +
192B LEU* 1.3 80.1 - - + +
194B ALA* 1.3 62.8 + - + +
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Residues in contact with ALA 194 (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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152B ARG* 4.1 1.3 - - - +
190B LYS 3.1 16.6 + - - +
191B ASN* 3.3 13.5 - - - +
192B LEU 3.4 1.2 - - - -
193B GLU* 1.3 81.6 - - + +
195B PRO* 1.3 80.9 - - + +
196B PHE* 3.4 0.5 + - - -
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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