Contacts of the strand formed by residues 259 - 265 (chain B) in PDB entry 1TAD
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 SER 259 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215B THR 3.3 14.6 + - - -
216B CYS* 3.1 14.0 - - - -
217B ILE 2.8 31.4 + - - -
257B THR 3.9 2.9 + - - -
258B THR* 1.3 70.8 - - - +
260B ILE* 1.3 55.4 + - - +
261B VAL* 4.2 0.9 - - - -
313B LYS* 5.4 2.5 - - - -
316B TYR* 5.1 6.0 - - - -
338B ILE* 4.4 18.5 - - - +
339B ILE* 5.3 5.7 - - - -
342B GLU* 2.8 27.7 + - - -
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Residues in contact with ILE 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B ILE* 3.4 24.2 - - + +
219B PHE* 5.1 1.1 - - + -
246B PHE* 4.3 24.0 - - + -
249B ILE* 4.6 3.4 - - + +
250B CYS* 3.9 20.2 - - - +
255B PHE* 4.1 14.4 - - + -
258B THR* 3.5 14.5 + - - +
259B SER* 1.3 78.5 - - - +
261B VAL* 1.3 70.6 + - - +
313B LYS* 3.2 34.3 - - + +
314B GLU 5.6 1.0 + - - -
315B ILE* 3.5 22.3 - - + +
316B TYR* 3.4 24.6 + - - -
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Residues in contact with VAL 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B CYS* 4.3 16.8 - - - -
217B ILE 2.7 12.5 + - - +
218B ILE* 3.3 9.3 - - + -
219B PHE* 2.7 34.7 + - - +
259B SER* 5.1 0.9 - - - -
260B ILE* 1.3 83.3 - - - +
262B LEU* 1.3 58.4 + - - +
263B PHE* 3.7 27.8 + - + -
316B TYR* 3.5 26.0 - - + +
318B HIS* 3.9 17.0 - - + +
335B VAL* 4.0 12.3 - - + -
338B ILE* 4.2 13.2 - - + -
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Residues in contact with LEU 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B PHE* 3.3 35.4 - - + +
221B ALA* 4.4 7.9 - - + -
246B PHE* 4.2 9.2 - - + -
261B VAL* 1.3 73.4 - - - +
263B PHE* 1.3 63.8 + - - +
264B LEU* 4.1 16.8 - - + -
300B LYS 4.9 1.1 - - - +
303B PHE* 3.4 45.1 - - + -
304B LEU* 4.0 11.9 - - + -
315B ILE* 4.5 8.0 - - + +
316B TYR 2.7 17.0 + - - +
317B SER* 3.3 16.5 - - - +
318B HIS 3.0 26.3 + - - +
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Residues in contact with PHE 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ILE* 4.0 32.8 - - + -
218B ILE* 3.7 33.7 - - + -
219B PHE 2.7 13.4 + - - +
220B ILE* 3.4 16.4 - - + +
221B ALA* 2.9 28.1 + - - +
261B VAL* 3.7 20.6 - - + -
262B LEU* 1.3 78.2 - - - +
264B LEU* 1.3 61.4 + - - +
265B ASN* 3.0 3.9 + - - -
318B HIS* 3.6 5.4 - + + -
320B THR* 3.9 23.1 - - + +
328B VAL* 5.7 4.3 - - + -
331B VAL* 3.5 32.1 - - + -
332B PHE* 5.1 6.5 - + + -
335B VAL* 3.8 12.8 - - + -
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Residues in contact with LEU 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B ALA* 3.5 11.0 - - + +
223B LEU* 3.2 39.7 - - + +
239B MET* 5.9 0.2 - - + -
262B LEU* 4.1 19.1 - - + -
263B PHE* 1.3 68.2 - - - +
265B ASN* 1.3 57.6 + - - +
296B GLY 4.6 0.2 - - - +
299B ILE* 4.2 13.0 - - + -
300B LYS* 3.5 38.1 - - + +
303B PHE* 4.2 12.6 - - + -
317B SER* 3.5 23.3 - - - +
318B HIS 2.8 11.8 + - - +
319B MET* 3.3 9.8 - - - -
320B THR 2.7 27.1 + - - -
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Residues in contact with ASN 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B SER 2.9 23.0 + - - +
41B GLY* 3.8 3.2 - - - -
45B ILE* 5.8 0.9 - - - -
220B ILE* 3.6 23.1 - - + +
221B ALA 2.8 9.6 + - - +
223B LEU* 2.8 32.9 + - - +
263B PHE* 3.0 0.8 + - - +
264B LEU* 1.3 74.0 - - - +
266B LYS* 1.3 77.0 + - + +
267B LYS 3.3 1.1 - - - -
320B THR* 3.0 17.9 + - - +
322B ALA* 2.9 33.8 + - - +
351B GDP 3.0 25.5 + - - -
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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