Contacts of the strand formed by residues 175 - 182 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171G TYR* 3.5 10.6 - - - -
172G ALA 3.1 26.4 + - - +
173G ALA* 3.9 12.1 - - + +
174G GLY* 1.3 81.5 - - - +
176G TYR* 1.3 78.1 + - - +
177G ASP* 3.7 6.2 + - - +
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Residues in contact with TYR 176 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169G PHE* 3.7 30.5 - - + -
170G LYS 3.4 3.1 - - - -
171G TYR* 3.6 42.7 - + + -
175G LYS* 1.3 85.6 + - - +
177G ASP* 1.3 59.8 + - - +
178G ILE* 3.8 8.4 + - + +
329G ILE* 4.8 6.6 + - - +
330G MET 5.0 0.2 - - - -
331G PRO* 3.5 42.4 - - + +
332G ASN* 5.6 0.9 - - - -
333G ILE* 4.4 31.0 - - + -
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Residues in contact with ASP 177 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169G PHE* 3.8 8.9 - - - +
170G LYS* 3.0 17.8 + - + +
175G LYS* 3.7 5.9 + - - +
176G TYR* 1.3 71.3 - - - +
178G ILE* 1.3 64.1 + - - +
179G LYS* 2.8 37.9 + - - +
180G ASP* 2.9 40.1 + - + +
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Residues in contact with ILE 178 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169G PHE* 3.7 19.8 - - + -
176G TYR* 3.8 10.9 + - + +
177G ASP* 1.3 74.5 + - - +
179G LYS* 1.3 66.0 + - + +
180G ASP 3.4 0.5 + - - -
181G VAL* 3.7 7.3 - - - +
333G ILE* 3.6 31.9 - - + -
335G GLN* 3.9 16.8 - - + +
369G ALA* 4.6 3.7 - - - +
1221G SER* 3.3 44.3 - - - +
1222G ALA* 4.1 7.0 - - + +
1225G ASP* 5.3 11.0 - - + +
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Residues in contact with LYS 179 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177G ASP* 2.8 10.7 + - - +
178G ILE* 1.3 81.3 - - + +
180G ASP* 1.3 56.9 + - - +
181G VAL* 3.6 7.6 + - - +
365G GLN* 5.3 3.5 + - - -
369G ALA* 4.5 2.8 - - - +
1222G ALA* 6.1 2.2 - - + -
1341G GLU* 3.8 30.7 - - + +
1344G GLN* 4.3 15.7 - - - +
1345G PHE* 4.3 29.8 - - + -
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Residues in contact with ASP 180 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167G TYR* 2.8 26.2 + - - -
169G PHE* 3.5 3.1 - - - -
170G LYS* 3.1 47.1 + - + +
177G ASP* 2.9 23.9 + - + +
178G ILE 3.3 0.6 - - - -
179G LYS* 1.3 74.3 - - - +
181G VAL* 1.3 64.7 + - - +
365G GLN* 5.5 0.9 + - - +
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Residues in contact with VAL 181 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167G TYR* 4.1 2.0 + - - -
168G ALA 3.2 14.4 - - - +
169G PHE* 3.8 15.3 - - + -
178G ILE 3.7 17.9 - - - +
179G LYS 3.6 3.0 + - - +
180G ASP* 1.3 78.5 + - - +
182G GLY* 1.3 59.3 + - - +
183G VAL* 3.4 30.8 + - + +
184G ASP 4.5 0.5 + - - -
339G PHE* 4.7 5.8 - - + -
365G GLN* 2.6 39.0 + - - +
368G ALA* 4.2 15.5 - - + -
369G ALA* 4.2 25.6 - - + +
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Residues in contact with GLY 182 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158G TRP* 4.7 0.5 - - - -
166G GLY* 3.5 5.5 - - - -
167G TYR* 2.9 68.5 + - - +
168G ALA 3.4 3.0 + - - -
181G VAL* 1.3 70.3 - - - +
183G VAL* 1.3 59.9 + - - +
184G ASP 3.5 1.8 - - - -
185G ASN* 3.5 14.5 + - - -
188G ALA* 4.1 0.2 - - - +
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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