Contacts of the strand formed by residues 258 - 263 (chain G) in PDB entry 1DE4
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 258 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190G VAL* 5.6 2.4 - - - +
201G LEU* 3.8 20.6 - - + +
217G TRP* 4.6 6.9 - - + -
218G LEU 3.3 3.6 - - - +
219G LYS* 3.3 59.3 + - + +
224G MET* 3.6 17.2 - - + +
248G LEU* 3.7 17.7 - - + -
250G VAL* 3.2 35.0 - - + +
251G PRO* 4.5 3.6 - - - +
254G GLU* 3.7 33.1 + - + -
255G GLU 2.9 11.6 + - - +
256G GLN* 3.1 4.2 - - - +
257G ARG* 1.3 81.9 - - + +
259G THR* 1.3 67.0 + - - +
274G ILE* 5.1 4.0 - - - +
275G TRP* 5.0 9.0 - - - -
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Residues in contact with THR 259 (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 VAL* 5.9 0.9 - - - -
217G TRP* 3.4 12.0 - - - -
218G LEU* 2.7 74.7 + - - +
221G LYS* 4.3 22.8 - - + +
256G GLN 5.1 5.8 - - - +
257G ARG 5.2 0.9 - - - +
258G TYR* 1.3 77.3 - - - +
260G CYS* 1.3 58.6 + - - +
272G ILE* 4.0 10.4 - - + +
273G VAL 3.7 9.4 - - - -
274G ILE* 3.3 27.1 - - + +
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Residues in contact with CYS 260 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190G VAL* 3.6 16.5 - - + +
203G CYS* 2.0 52.0 - - + -
215G MET* 5.3 0.7 - - - -
216G LYS 3.8 2.0 - - - -
217G TRP* 4.2 5.2 - - + -
246G ILE* 4.0 18.2 - - - -
259G THR* 1.3 75.3 - - - +
261G GLN* 1.3 63.2 + - - +
262G VAL* 4.0 12.8 + - - +
271G LEU 3.7 0.7 - - - +
272G ILE* 3.3 4.5 - - - -
273G VAL* 2.8 39.4 + - + +
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Residues in contact with GLN 261 (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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214G THR* 3.5 4.0 - - - +
215G MET* 3.6 1.4 - - - -
216G LYS* 2.8 75.9 + - + +
218G LEU* 3.6 33.4 - - + +
259G THR 4.2 0.6 - - - -
260G CYS* 1.3 73.4 - - - +
262G VAL* 1.3 63.2 + - - +
263G GLU* 3.9 18.9 + - + +
270G PRO* 4.3 17.4 - - + +
271G LEU 3.5 4.0 - - - +
272G ILE* 4.0 18.1 - - + +
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Residues in contact with VAL 262 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186G PRO* 4.1 10.3 - - + -
188G VAL* 3.4 46.9 - - + -
203G CYS* 4.5 0.7 - - - -
205G ALA* 4.7 0.2 - - + -
213G ILE* 3.7 26.5 - - + -
214G THR 3.2 8.3 - - - +
215G MET* 4.2 13.5 - - + -
260G CYS* 4.1 12.3 - - - +
261G GLN* 1.3 77.8 - - - +
263G GLU* 1.3 63.7 + - - +
267G LEU* 3.8 9.4 - - + +
271G LEU* 2.7 34.0 + - + +
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Residues in contact with GLU 263 (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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213G ILE* 3.5 3.5 - - - +
214G THR* 2.8 60.3 + - + +
216G LYS* 3.6 14.6 + - - -
261G GLN* 3.9 16.3 + - - +
262G VAL* 1.3 71.2 - - - +
264G HIS* 1.3 65.4 + - - +
270G PRO* 3.7 31.6 - - + +
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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