Contacts of the helix formed by residues 267 - 274 (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 LYS 267 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223C LEU* 3.8 21.3 - - + -
265C ASN 3.3 1.0 - - - -
266C LYS* 1.3 76.6 - - - +
268C ASP* 1.3 60.1 + - - +
270C PHE* 3.6 2.7 - - - +
271C SER* 2.8 30.5 + - - -
292C TYR* 3.4 30.0 - - + +
319C MET* 3.6 30.1 - - + +
320C THR 3.0 22.3 + - - +
321C CYS* 4.0 12.5 - - + +
324C ASP* 4.9 4.2 + - - -
327C ASN* 3.8 22.2 - - - +
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Residues in contact with ASP 268 (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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172C ARG* 4.5 8.5 + - - -
266C LYS 3.5 5.2 - - - -
267C LYS* 1.3 82.1 - - + +
269C VAL* 1.3 67.1 + - - +
271C SER* 2.7 23.1 + - - -
272C GLU* 3.6 9.9 + - - +
321C CYS* 3.5 22.0 - - + -
351C GDP 2.9 44.7 + - - -
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Residues in contact with VAL 269 (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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146C ASP* 5.3 9.2 - - + +
224C SER* 3.5 24.0 - - - +
266C LYS* 3.2 13.9 + - + +
268C ASP* 1.3 80.1 + - - +
270C PHE* 1.3 58.0 + - - +
272C GLU* 3.3 7.4 + - - +
273C LYS* 3.0 37.5 + - - +
351C GDP 3.6 30.5 - - + +
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Residues in contact with PHE 270 (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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223C LEU* 3.5 38.4 - - + -
224C SER* 4.1 4.2 - - - +
226C TYR* 3.6 26.5 - + - -
266C LYS 2.9 16.6 + - - +
267C LYS* 3.6 4.7 - - - +
269C VAL* 1.3 74.9 - - - +
271C SER* 1.3 65.8 + - - +
273C LYS* 4.3 4.3 - - - -
274C ILE* 2.9 35.5 + - + +
279C LEU* 5.4 0.4 - - + -
292C TYR* 3.6 47.1 - + - -
295C ALA* 3.7 24.9 - - + -
296C GLY* 3.9 11.7 - - - -
299C ILE* 3.8 20.0 - - + -
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Residues in contact with SER 271 (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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267C LYS 2.8 17.8 + - - -
268C ASP* 2.7 24.1 + - - -
270C PHE* 1.3 72.5 - - - +
272C GLU* 1.3 70.4 + - - +
274C ILE* 3.4 15.5 - - - +
275C LYS* 3.5 19.6 - - - +
292C TYR* 3.8 24.4 - - - +
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Residues in contact with GLU 272 (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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268C ASP 3.9 10.5 - - - +
269C VAL* 3.3 8.4 + - - +
270C PHE 3.2 0.4 - - - -
271C SER* 1.3 85.1 + - - +
273C LYS* 1.3 65.6 + - - +
275C LYS* 3.3 28.1 + - - +
276C LYS* 2.7 37.8 + - - +
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Residues in contact with LYS 273 (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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140C SER* 4.8 5.6 - - - -
224C SER* 2.9 35.0 + - - +
226C TYR* 3.2 24.9 + - + +
227C ASP* 2.8 35.4 + - - +
228C MET* 3.9 14.3 - - - +
269C VAL* 3.0 25.9 + - + +
270C PHE* 3.9 5.2 - - - +
272C GLU* 1.3 78.2 - - - +
274C ILE* 1.3 56.1 + - - +
276C LYS* 2.8 12.2 + - - +
277C ALA* 2.8 29.7 + - + -
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Residues in contact with ILE 274 (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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226C TYR* 3.2 16.5 + - + +
270C PHE* 2.9 27.3 + - + +
271C SER* 3.4 19.5 - - - +
273C LYS* 1.3 75.9 - - - +
275C LYS* 1.3 66.4 + - + +
277C ALA 3.9 0.4 - - - +
279C LEU* 4.4 4.9 - - + -
290C ASN* 2.5 75.4 + - - +
291C THR* 3.9 9.6 - - - +
292C TYR* 3.9 22.9 - - + +
295C ALA* 3.6 21.1 - - + -
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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