Contacts of the helix formed by residues 266 - 277 (chain A) in PDB entry 1TYG
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 ASN 266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A ASP* 4.0 16.4 + - - +
255A ALA 4.3 3.3 + - - +
264A ILE* 4.0 3.4 - - - +
265A LEU* 1.3 82.3 - - + +
267A PRO* 1.3 67.7 - - - +
268A LEU* 3.3 10.4 + - - +
269A ASN* 3.2 43.6 + - - +
270A LEU* 3.4 15.6 + - - +
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Residues in contact with PRO 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A ILE* 3.6 16.4 - - + +
265A LEU 3.6 7.4 - - - +
266A ASN* 1.3 87.3 - - - +
268A LEU* 1.3 64.9 + - - +
270A LEU* 3.1 6.2 + - + +
271A SER* 2.9 27.9 + - - +
295A TYR* 3.3 41.1 - - + +
299A LEU* 4.2 9.8 - - + +
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Residues in contact with LEU 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A ASN* 3.1 10.4 + - - +
267A PRO* 1.3 79.2 - - - +
269A ASN* 1.3 62.0 + - - +
271A SER* 3.3 10.0 + - - -
272A PHE* 3.1 55.4 + - + -
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Residues in contact with ASN 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A ASP* 3.0 38.4 + - - +
236A ASP* 4.8 2.0 - - - +
237A VAL* 3.9 18.6 - - + +
266A ASN* 3.2 34.0 + - - +
267A PRO 3.2 0.2 - - - -
268A LEU* 1.3 79.7 - - - +
270A LEU* 1.3 64.1 + - - +
271A SER 2.9 5.4 + - - -
272A PHE* 2.9 8.4 + - - +
273A ILE* 2.8 27.7 + - - +
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Residues in contact with LEU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A ASP* 5.2 3.7 + - + +
253A PRO* 3.9 25.8 - - + -
254A GLY 4.9 7.9 - - - +
255A ALA* 5.7 1.6 - - - -
264A ILE* 4.4 17.3 - - + -
266A ASN 3.4 10.5 + - - +
267A PRO 3.1 8.0 + - - +
269A ASN* 1.3 79.0 - - - +
271A SER* 1.3 56.8 + - - +
273A ILE* 3.4 8.2 - - - +
274A ILE* 2.8 44.6 + - + +
281A VAL* 5.1 1.6 - - + -
283A VAL* 3.8 31.0 - - + -
296A ALA* 4.8 3.1 - - - -
299A LEU* 3.7 27.8 - - + -
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Residues in contact with SER 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A PRO* 2.9 13.4 + - - +
268A LEU* 3.3 16.4 - - - -
270A LEU* 1.3 76.2 - - - +
272A PHE* 1.3 58.0 + - - +
273A ILE 3.1 1.1 - - - -
274A ILE* 4.3 5.6 - - - -
275A GLU* 2.8 50.9 + - - +
299A LEU* 3.6 28.5 + - - +
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Residues in contact with PHE 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A VAL* 3.7 30.5 - - + -
268A LEU* 3.1 51.7 + - + -
269A ASN* 2.9 10.4 + - - +
271A SER* 1.3 74.4 - - - +
273A ILE* 1.3 62.0 + - - +
275A GLU* 3.4 15.3 + - + +
276A GLN* 3.1 30.8 + - - +
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Residues in contact with ILE 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A ASP* 3.6 40.8 - - + +
236A ASP 4.6 0.2 - - - +
237A VAL* 4.3 11.0 - - + -
240A ALA* 4.0 22.2 - - + -
251A ILE* 3.8 28.9 - - + -
253A PRO* 4.1 16.2 - - + -
269A ASN 2.8 19.8 + - - +
270A LEU* 3.4 9.2 - - - +
272A PHE* 1.3 74.7 - - - +
274A ILE* 1.3 68.9 + - - +
276A GLN* 3.3 15.4 + - - +
277A ALA* 3.3 16.0 + - + +
281A VAL* 4.1 6.7 - - + -
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Residues in contact with ILE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A LEU* 2.8 47.9 + - + +
271A SER* 3.9 4.7 - - - +
273A ILE* 1.3 74.5 - - - +
275A GLU* 1.3 70.8 + - + +
276A GLN 3.0 0.5 + - - -
277A ALA* 3.2 13.2 + - - +
281A VAL* 4.3 19.7 - - + -
299A LEU* 3.2 39.3 - - + +
300A GLY* 3.4 19.5 - - - +
301A ALA* 3.8 16.2 - - + +
334A TYR* 6.0 0.7 - - - +
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Residues in contact with GLU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A SER* 2.8 39.5 + - - +
272A PHE* 4.1 17.1 - - + +
273A ILE 3.3 0.4 - - - -
274A ILE* 1.3 77.9 - - + +
276A GLN* 1.3 57.6 + - - +
277A ALA 3.7 1.4 + - - +
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Residues in contact with GLN 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A VAL* 3.3 41.9 + - - +
238A VAL* 5.6 0.2 - - - -
240A ALA* 3.9 8.9 - - - +
241A ARG* 3.7 35.2 + - + +
244A GLU* 3.6 8.7 - - - +
272A PHE* 3.1 17.6 + - - +
273A ILE* 3.6 12.6 + - + +
274A ILE 3.2 0.2 - - - -
275A GLU* 1.3 76.2 - - - +
277A ALA* 1.3 69.8 + - - +
278A LYS* 4.1 11.6 + - - +
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Residues in contact with ALA 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A GLU* 3.1 12.3 - - + +
251A ILE* 5.6 1.6 - - + -
273A ILE* 3.3 18.7 + - + +
274A ILE 3.2 11.5 + - - +
275A GLU 4.7 1.4 - - - +
276A GLN* 1.3 83.3 - - - +
278A LYS* 1.3 64.1 + - - +
279A VAL* 3.6 15.5 - - + +
281A VAL* 3.7 16.2 - - + -
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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