Contacts of the strand formed by residues 177 - 183 (chain J) in PDB entry 6LTJ
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 THR 177 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170J LEU* 5.3 2.8 - - - +
171J ASP* 2.6 22.1 + - - -
172J SER* 3.5 14.8 - - - -
176J HIS* 1.3 74.6 - - - +
178J THR* 1.3 60.2 + - - +
195J SER* 2.3 62.6 + - - +
197J LEU 3.2 33.0 - - - +
198J ALA* 3.7 4.9 - - + -
325J VAL* 5.3 12.1 - - + +
354J ASN* 5.3 0.2 - - - -
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Residues in contact with THR 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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127J TRP* 4.2 26.0 - - + +
169J ILE 3.8 0.3 - - - +
170J LEU* 3.4 11.0 - - - +
171J ASP* 2.9 45.1 + - - +
176J HIS* 4.2 25.0 - - + -
177J THR* 1.3 81.2 + - - +
179J ALA* 1.3 63.6 + - - +
180J ILE* 4.1 19.3 - - - +
192J ILE* 6.2 0.2 - - - -
193J VAL 3.3 13.2 - - - +
194J LYS* 4.3 4.3 - - + -
195J SER* 4.4 1.1 - - - -
328J VAL* 5.2 1.6 - - - -
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Residues in contact with ALA 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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168J LEU* 4.4 4.9 - - + -
169J ILE 3.4 5.4 - - - +
170J LEU* 3.8 16.2 - - + -
178J THR* 1.3 73.8 - - - +
180J ILE* 1.3 60.8 + - - +
181J PRO* 4.0 2.3 - - - +
192J ILE* 3.3 5.9 - - - +
193J VAL* 2.9 41.0 + - + +
328J VAL* 4.0 7.4 - - + +
329J VAL* 4.8 1.3 - - + -
332J SER* 3.4 29.5 - - - +
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Residues in contact with ILE 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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126J PRO* 4.5 17.5 - - + -
154J THR* 4.7 7.0 - - - +
155J ALA* 3.7 33.9 - - + +
168J LEU* 3.3 3.9 - - - +
169J ILE* 2.9 61.2 + - + +
171J ASP* 4.9 5.6 - - + -
178J THR* 4.1 20.4 - - - +
179J ALA* 1.3 79.2 - - - +
181J PRO* 1.3 66.9 - - - +
182J VAL 3.5 1.6 + - - -
187J VAL* 4.7 2.9 - - + -
192J ILE* 3.7 28.5 - - + -
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Residues in contact with PRO 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 GLY 3.7 5.2 - - - +
168J LEU* 4.0 11.7 - - + -
179J ALA 4.0 1.8 - - - +
180J ILE* 1.3 84.5 - - - +
182J VAL* 1.3 59.2 - - - +
187J VAL* 3.7 4.1 - - - +
188J LEU* 3.0 44.6 + - + +
191J GLY* 3.9 9.2 - - - +
192J ILE* 3.9 20.8 - - + +
332J SER* 4.6 5.4 - - - +
336J CYS* 3.7 32.8 - - - -
344J LEU* 4.2 13.0 - - + -
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Residues in contact with VAL 182 (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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155J ALA* 4.4 3.1 - - + -
156J VAL* 3.6 36.1 - - + +
159J ALA* 3.8 14.4 - - + -
160J PHE* 5.8 0.9 - - + -
165J SER 4.0 7.9 - - - +
167J GLY* 2.8 50.6 + - - +
169J ILE* 3.7 24.7 - - + -
180J ILE 3.5 1.8 + - - -
181J PRO* 1.3 74.2 - - - +
183J HIS* 1.3 67.8 + - - +
185J GLY 4.9 1.6 - - - +
186J TYR 3.4 12.6 - - - +
187J VAL* 3.9 7.0 - - + +
344J LEU* 3.8 5.5 - - - +
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Residues in contact with HIS 183 (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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165J SER 3.9 2.0 - - - -
166J THR* 3.5 33.4 - - + +
182J VAL* 1.3 77.0 - - - +
184J ASP* 1.3 90.6 + - - +
185J GLY 3.2 2.0 - - - -
186J TYR* 2.5 42.5 + - - +
188J LEU* 4.8 20.9 - - + -
340J ILE* 5.3 19.6 + - + +
343J GLY* 6.0 2.4 - - - -
344J LEU* 4.6 11.4 - - + -
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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