Contacts of the strand formed by residues 259 - 265 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215C THR 3.2 15.8 + - - -
216C CYS* 3.1 14.9 - - - -
217C ILE 2.7 31.4 + - - -
257C THR 4.4 0.2 + - - -
258C THR* 1.3 71.8 - - - +
260C ILE* 1.3 55.7 + - - +
261C VAL* 5.3 0.9 - - - -
313C LYS* 5.2 2.5 - - - -
316C TYR* 5.3 1.6 - - - -
338C ILE* 4.5 12.3 + - - +
339C ILE* 4.8 6.5 - - - -
342C GLU* 3.2 41.2 + - - +
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Residues in contact with ILE 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C ILE* 3.5 23.6 - - + +
219C PHE* 5.3 0.4 - - + -
246C PHE* 4.4 15.5 - - + -
249C ILE* 5.8 1.1 - - + -
250C CYS* 3.8 31.0 - - + +
255C PHE* 4.4 10.5 - - + -
258C THR* 3.5 13.8 + - - +
259C SER* 1.3 79.4 - - - +
261C VAL* 1.3 68.8 + - - +
313C LYS* 3.5 29.8 - - + +
314C GLU 4.4 2.5 + - - +
315C ILE* 3.4 42.8 - - + +
316C TYR* 3.6 13.7 + - - -
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Residues in contact with VAL 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C CYS* 3.9 22.2 - - - -
217C ILE 2.9 9.6 + - - +
218C ILE* 3.4 8.3 - - + -
219C PHE* 2.9 27.2 + - - +
259C SER 5.0 0.7 - - - -
260C ILE* 1.3 83.0 - - - +
262C LEU* 1.3 63.4 + - - +
263C PHE* 3.8 24.4 + - + -
315C ILE* 4.4 1.8 - - - -
316C TYR* 3.2 26.5 - - + +
318C HIS* 4.0 13.9 - - + +
335C VAL* 3.9 22.2 - - + -
338C ILE* 5.2 7.9 - - + -
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Residues in contact with LEU 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C PHE* 3.5 36.1 - - + +
221C ALA* 4.4 5.6 - - + -
246C PHE* 4.3 8.5 - - + -
261C VAL* 1.3 73.4 - - - +
263C PHE* 1.3 68.6 + - - +
264C LEU* 4.0 21.8 - - + -
300C LYS 4.9 0.9 - - - +
303C PHE* 3.5 40.2 - - + -
304C LEU* 4.0 16.2 - - + -
315C ILE* 4.2 10.0 - - + +
316C TYR 2.7 10.8 + - - +
317C SER* 3.1 14.3 - - - -
318C HIS 2.8 27.0 + - - +
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Residues in contact with PHE 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ILE* 4.3 30.5 - - + -
218C ILE* 3.7 36.3 - - + -
219C PHE 2.8 12.9 + - - +
220C ILE* 3.6 15.6 - - + -
221C ALA 3.0 26.2 + - - -
261C VAL* 3.8 20.6 + - + -
262C LEU* 1.3 81.3 - - - +
264C LEU* 1.3 60.7 + - - +
265C ASN 3.1 2.8 + - - -
318C HIS* 3.5 5.6 - + + -
320C THR* 3.8 25.8 - - + +
328C VAL* 5.9 3.1 - - + -
331C VAL* 3.5 31.6 - - + -
332C PHE* 5.2 6.5 - + + -
335C VAL* 3.8 12.3 - - + -
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Residues in contact with LEU 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C ALA* 3.4 13.2 - - + +
223C LEU* 3.4 25.6 - - + +
239C MET* 6.0 0.2 - - + -
262C LEU* 4.0 24.7 - - + -
263C PHE* 1.3 69.2 - - - +
265C ASN* 1.3 58.2 + - - +
296C GLY 4.6 0.2 - - - +
299C ILE* 4.2 9.0 - - + -
300C LYS* 3.6 42.2 - - + +
303C PHE* 4.1 24.7 - - + -
317C SER* 4.8 4.3 - - - -
318C HIS 2.7 14.3 + - - +
319C MET* 3.3 22.3 - - - -
320C THR 2.7 25.5 + - - -
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Residues in contact with ASN 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C SER 2.8 24.0 + - - +
41C GLY* 3.7 4.0 - - - -
45C ILE* 5.8 0.7 - - - -
220C ILE* 3.7 22.2 - - + +
221C ALA 2.8 10.8 + - - +
222C ALA* 4.3 0.2 - - - -
223C LEU* 2.8 32.1 + - - +
263C PHE* 3.1 1.0 + - - +
264C LEU* 1.3 72.2 - - - +
266C LYS* 1.3 77.2 + - + +
267C LYS 3.3 1.1 - - - -
320C THR* 3.0 16.4 + - - +
322C ALA* 2.8 36.2 + - - +
351C GDP 2.9 25.4 + - - -
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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