Contacts of the strand formed by residues 175 - 182 (chain J) in PDB entry 5TJ4
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 LYS 175 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171J TYR* 3.5 10.1 - - - -
172J ALA 3.1 23.3 + - - +
173J ALA 4.4 4.3 - - - +
174J GLY* 1.3 81.4 - - - +
176J TYR* 1.3 66.4 + - - +
177J ASP* 3.7 2.1 + - - +
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Residues in contact with TYR 176 (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 PHE* 3.7 31.2 - - + -
170J LYS 3.4 2.9 - - - -
171J TYR* 3.6 44.6 - + + -
175J LYS* 1.3 76.7 - - - +
177J ASP* 1.3 59.7 + - - +
178J ILE* 3.9 8.5 + - + +
329J ILE* 4.7 7.1 + - - +
330J MET 4.9 0.2 - - - -
331J PRO* 3.5 42.2 - - + +
332J ASN* 5.6 1.1 - - - -
333J ILE* 4.4 30.7 - - + -
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Residues in contact with ASP 177 (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 PHE* 3.8 8.5 - - - +
170J LYS* 3.0 18.6 + - + +
175J LYS 3.7 1.8 + - - +
176J TYR* 1.3 70.9 - - - +
178J ILE* 1.3 64.8 + - - +
179J LYS* 2.8 40.8 + - - +
180J ASP* 2.9 39.9 + - + +
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Residues in contact with ILE 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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169J PHE* 3.7 8.5 - - + -
176J TYR* 4.6 10.1 - - + +
177J ASP* 1.3 75.6 + - - +
179J LYS* 1.3 65.2 + - + +
180J ASP 3.4 0.5 + - - -
181J VAL* 3.7 17.5 - - - +
333J ILE* 3.6 31.4 - - + -
335J GLN* 3.9 16.8 - - + +
369J ALA* 4.6 4.3 - - - +
1221J SER* 3.3 44.5 - - - +
1222J ALA* 4.0 6.7 - - + +
1225J ASP* 5.5 7.0 - - + -
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Residues in contact with LYS 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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177J ASP* 2.8 14.0 + - - +
178J ILE* 1.3 82.3 - - + +
180J ASP* 1.3 56.5 + - - +
181J VAL* 3.6 7.4 + - - +
365J GLN* 5.2 3.6 + - - -
369J ALA* 4.6 3.1 - - - +
1222J ALA* 5.9 2.5 - - + -
1341J GLU* 3.7 37.4 + - + +
1344J GLN* 4.1 18.4 - - - +
1345J PHE* 4.3 28.1 - - + -
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Residues in contact with ASP 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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167J TYR* 2.7 25.6 + - - -
169J PHE* 3.5 2.9 - - - -
170J LYS* 3.1 47.1 + - + +
177J ASP* 2.9 24.5 + - - +
178J ILE 3.2 0.8 - - - -
179J LYS* 1.3 75.3 - - - +
181J VAL* 1.3 64.6 + - - +
365J GLN* 5.5 0.3 + - - -
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Residues in contact with VAL 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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167J TYR* 4.1 1.3 + - - -
168J ALA 3.2 14.1 - - - +
169J PHE* 3.8 15.5 - - + -
178J ILE 3.7 20.6 - - - +
179J LYS 3.6 3.4 + - - +
180J ASP* 1.3 76.0 + - - +
182J GLY* 1.3 58.3 + - - +
183J VAL* 3.4 30.3 + - + +
184J ASP 4.4 0.7 + - - -
339J PHE* 4.7 5.8 - - + -
365J GLN* 2.7 39.4 + - - +
368J ALA* 4.2 14.8 - - + -
369J ALA* 4.2 25.6 - - + +
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Residues in contact with GLY 182 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158J TRP* 4.7 0.3 - - - -
166J GLY* 3.5 9.7 - - - -
167J TYR* 2.9 71.0 + - - +
168J ALA 3.4 2.6 + - - -
181J VAL* 1.3 69.9 - - - +
183J VAL* 1.3 57.9 + - - +
184J ASP 3.6 1.3 - - - -
185J ASN* 3.5 11.5 + - - -
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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