Contacts of the strand formed by residues 177 - 181 (chain J) in PDB entry 3EOA
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 TYR 177 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175I THR* 4.4 7.3 - - - +
176I SER* 3.4 29.4 - - - -
204I LEU* 5.9 2.8 - - - +
171J VAL* 4.7 1.8 - - + -
172J GLN 3.5 5.4 - - - +
173J PHE* 3.7 6.3 - - + -
174J SER 5.0 0.2 - - - -
175J THR 3.8 16.0 + - - -
176J SER* 1.3 89.0 + - - +
178J LYS* 1.3 61.9 + - - +
207J ASN* 3.4 26.2 + - + +
210J GLY* 3.1 29.7 - - - -
211J ALA* 3.3 30.1 - - + -
214J TYR* 3.6 52.0 + + + -
244J ASP* 4.3 1.0 + - - -
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Residues in contact with LYS 178 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171J VAL* 3.2 5.8 - - - +
172J GLN* 2.7 39.0 + - - +
177J TYR* 1.3 77.2 - - - +
179J THR* 1.3 74.2 + - - +
180J GLU* 3.0 44.4 + - - +
198J HIS* 5.0 8.1 + - - +
199J VAL* 5.6 0.2 - - - +
200J LYS* 5.6 2.6 - - - +
202J MET* 3.4 22.9 - - + -
214J TYR* 4.4 0.2 - - - -
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Residues in contact with THR 179 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169J ALA* 5.7 0.7 - - + -
170J ALA 3.5 5.8 - - - +
171J VAL* 4.3 5.2 - - + +
178J LYS* 1.3 82.7 - - - +
180J GLU* 1.3 62.2 + - - +
181J PHE* 3.6 29.1 - - - +
182J ASP* 4.0 14.1 - - + +
214J TYR* 2.9 22.7 + - - -
218J GLU 5.5 0.2 + - - -
219J VAL* 3.6 20.6 - - + +
224J LEU* 4.8 10.6 - - + +
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Residues in contact with GLU 180 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136J PHE* 3.8 22.4 - - + -
170J ALA* 2.8 12.4 + - + +
172J GLN* 3.1 26.8 + - - +
178J LYS* 3.0 47.8 + - - +
179J THR* 1.3 73.6 - - - +
181J PHE* 1.3 61.5 + - + +
185J ASP* 4.7 1.2 - - - +
195J LEU 4.2 7.5 - - - +
196J LEU* 4.2 11.4 - - + -
198J HIS 4.8 0.5 - - - +
199J VAL* 3.5 39.5 + - + +
200J LYS 4.9 0.9 + - - +
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Residues in contact with PHE 181 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134J PHE* 5.6 0.7 - + - -
158J MET* 3.6 26.2 - - + -
168J PHE* 3.4 26.7 - - + -
169J ALA* 3.4 3.5 - - - -
170J ALA* 2.9 55.7 + - + +
179J THR* 3.6 8.6 - - - +
180J GLU* 1.3 79.8 - - - +
182J ASP* 1.3 71.9 + - - +
185J ASP* 3.4 20.9 - - + +
186J TYR* 4.0 3.8 - - + -
195J LEU* 3.6 50.3 - - + +
196J LEU* 3.7 21.8 - - + -
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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