Contacts of the strand formed by residues 215 - 219 (chain G) in PDB entry 1TKK
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 ILE 215 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175G ILE* 4.0 24.5 - - + -
188G LEU* 3.6 13.5 - - + +
190G LEU* 3.8 30.1 - - + -
205G ILE* 6.2 1.1 - - + -
208G MET* 4.1 28.5 - - + -
209G GLU* 6.4 0.9 - - + -
213G LEU 4.0 11.2 - - - +
214G GLY* 1.3 75.8 - - - +
216G GLU* 1.3 62.8 + - - +
217G LEU 3.5 24.5 - - - +
218G VAL* 4.0 10.3 - - + -
239G THR* 3.8 19.1 + - + +
240G PRO* 5.0 1.0 - - - +
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Residues in contact with GLU 216 (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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187G LYS* 3.4 43.8 + - + +
188G LEU 3.0 16.2 + - - +
189G ARG* 2.8 32.5 + - - +
214G GLY 3.7 3.0 + - - -
215G ILE* 1.3 71.5 - - - +
217G LEU* 1.3 66.9 + - + +
240G PRO* 3.2 26.0 - - - +
319G ARG* 2.7 43.0 + - - +
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Residues in contact with LEU 217 (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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189G ARG* 3.7 20.4 - - + +
190G LEU 3.0 26.4 + - - +
215G ILE* 3.4 7.1 - - - +
216G GLU* 1.3 91.2 - - + +
218G VAL* 1.3 67.0 + - - +
219G GLU* 4.0 22.7 - - + +
239G THR* 4.0 3.1 - - - -
240G PRO* 3.2 22.4 - - + +
242G MET* 3.6 34.1 - - + -
264G LEU* 4.0 4.5 - - + -
293G MET* 5.8 0.2 - - + -
319G ARG* 3.5 36.8 - - - +
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Residues in contact with VAL 218 (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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190G LEU* 3.5 22.7 - - + +
192G ALA 4.9 2.9 - - - +
196G TRP* 4.2 14.6 - - + -
205G ILE* 4.1 20.6 - - + -
208G MET* 6.2 0.2 - - - -
215G ILE* 4.0 16.6 - - + -
217G LEU* 1.3 80.3 - - - +
219G GLU* 1.3 71.9 + - - +
220G GLN 3.8 0.3 + - - -
221G PRO* 3.9 21.8 - - + -
239G THR* 4.2 8.1 - - + -
240G PRO 3.0 7.1 + - - -
241G ILE* 3.4 17.0 - - + +
242G MET 3.0 21.3 + - - -
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Residues in contact with GLU 219 (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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160G LYS* 2.5 34.5 + - - +
189G ARG* 5.5 1.7 - - - +
190G LEU 2.8 11.8 + - - +
191G ASP* 3.5 18.0 - - - +
192G ALA 3.3 16.1 + - - -
217G LEU* 4.0 9.2 - - + +
218G VAL* 1.3 74.0 - - - +
220G GLN* 1.3 73.6 + - + +
221G PRO 3.1 2.0 - - - -
242G MET* 3.4 27.6 - - + +
244G ASP* 3.9 3.7 - - + +
266G ASN* 2.8 25.4 + - - -
293G MET* 3.5 9.9 - - - +
1607G MG 2.5 26.1 - - - -
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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