Contacts of the helix formed by residues 291 - 302 (chain B) in PDB entry 1TYE
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 291 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312A LEU* 4.4 12.8 - - - -
324A GLU* 2.6 31.4 + - - -
353A TYR* 5.2 0.9 - - - -
355A ARG* 5.4 4.0 + - - -
256B ILE* 6.0 0.4 - - - -
257B ALA* 3.5 23.1 - - - +
269B ASN* 5.3 0.2 - - - +
290B PRO* 1.3 75.7 - - - +
292B LEU* 1.3 67.2 + - - +
293B GLY 3.2 0.7 + - - -
294B LEU* 3.3 15.7 + - - +
295B MET* 3.2 19.9 + - - +
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Residues in contact with LEU 292 (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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285A MET 4.2 0.7 - - - +
286A ALA* 3.6 31.6 - - + +
314A MET* 4.2 17.0 - - + -
223B PHE* 4.2 15.3 - - + -
256B ILE* 5.2 5.0 - - + +
291B SER* 1.3 72.0 - - - +
293B GLY* 1.3 61.2 + - - +
295B MET* 3.1 24.9 + - + +
296B THR* 2.8 26.9 + - - -
321B TYR* 4.4 14.4 - - + +
324B LEU* 3.8 32.8 - - + -
325B ILE* 3.9 24.9 - - + +
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Residues in contact with GLY 293 (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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314A MET* 3.9 17.6 - - - -
324A GLU* 4.2 14.3 + - - -
353A TYR* 3.7 10.3 + - - -
291B SER* 3.2 2.6 + - - -
292B LEU* 1.3 78.8 - - - +
294B LEU* 1.3 62.5 + - - +
296B THR* 3.2 8.7 + - - -
297B GLU* 3.0 23.4 + - - +
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Residues in contact with LEU 294 (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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353A TYR* 3.8 19.2 + - + +
227B MET* 3.8 19.1 - - + -
269B ASN* 3.4 36.8 - - + +
270B ASP 4.5 0.7 - - - -
271B GLY* 3.8 14.1 - - - +
290B PRO* 4.4 1.3 - - + -
291B SER* 3.3 22.4 + - - +
293B GLY* 1.3 74.2 - - - +
295B MET* 1.3 64.0 + - - +
297B GLU* 3.5 17.8 + - - +
298B LYS* 3.1 50.8 + - + +
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Residues in contact with MET 295 (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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223B PHE* 3.3 59.5 - - + +
226B ILE* 4.7 15.0 - - + -
227B MET* 3.8 20.0 - - + +
256B ILE* 6.0 0.4 - - + -
290B PRO* 3.5 27.1 - - + +
291B SER 3.2 14.9 + - - +
292B LEU* 3.1 21.0 + - + +
294B LEU* 1.3 78.8 - - - +
296B THR* 1.3 54.0 + - - +
298B LYS* 3.1 4.7 + - - +
299B LEU* 2.8 47.9 + - + +
306B LEU* 5.9 2.0 - - - -
325B ILE* 5.0 9.2 - - + -
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Residues in contact with THR 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A MET* 5.4 1.2 - - - -
292B LEU 2.8 17.0 + - - -
293B GLY* 3.5 7.9 - - - -
295B MET* 1.3 76.6 - - - +
297B GLU* 1.3 63.2 + - - +
299B LEU* 3.3 10.8 + - - +
300B SER* 3.0 26.1 + - - -
324B LEU 4.2 4.6 + - - +
325B ILE* 3.8 27.4 - - + +
326B PRO* 4.3 19.3 - - + +
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Residues in contact with GLU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A LEU* 5.2 1.9 - - + +
353A TYR* 2.6 46.3 + - - +
293B GLY 3.0 9.8 + - - +
294B LEU* 3.6 8.9 - - - +
296B THR* 1.3 75.9 - - - +
298B LYS* 1.3 73.1 + - - +
300B SER* 3.3 4.9 + - - -
301B GLN* 2.8 48.5 + - + +
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Residues in contact with LYS 298 (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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227B MET* 3.8 20.6 - - - -
230B THR* 3.6 8.0 - - + +
231B VAL* 3.8 22.8 - - + +
270B ASP 5.4 1.1 + - - -
271B GLY* 3.6 19.4 + - - -
272B GLN* 5.9 1.6 - - - +
294B LEU* 3.2 28.9 - - + +
295B MET 3.1 4.3 + - - +
297B GLU* 1.3 89.3 + - - +
299B LEU* 1.3 65.8 + - - +
301B GLN* 3.2 33.1 + - - +
302B LYS* 3.0 30.2 + - - +
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Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ILE* 4.5 11.9 - - + -
230B THR* 3.4 27.4 - - + +
246B LEU* 4.6 0.7 - - + -
295B MET* 2.8 32.9 + - + +
296B THR* 3.6 4.9 - - + +
298B LYS* 1.3 72.5 - - - +
300B SER* 1.3 58.7 + - - +
302B LYS 3.8 0.2 - - - -
303B ASN* 3.0 6.4 + - - -
304B ILE* 2.9 57.7 + - + +
306B LEU* 4.0 31.4 - - + -
325B ILE* 4.1 22.2 - - + -
328B THR* 4.8 2.5 - - + -
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Residues in contact with SER 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B THR* 3.0 18.4 + - - -
297B GLU* 3.5 5.2 - - - -
299B LEU* 1.3 73.6 - - - +
301B GLN* 1.3 65.7 + - - +
302B LYS 3.1 1.8 - - - -
303B ASN* 3.0 27.8 + - - +
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Residues in contact with GLN 301 (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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297B GLU* 2.8 30.3 + - + +
298B LYS* 3.2 38.0 + - - +
300B SER* 1.3 77.2 - - - +
302B LYS* 1.3 82.1 + - + +
303B ASN* 3.5 5.1 + - - +
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Residues in contact with LYS 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B THR* 3.5 18.8 - - + +
231B VAL* 4.4 19.1 + - + +
233B ASP* 3.0 38.8 + - - +
238B TRP* 6.1 1.1 - - + -
244B HIS* 3.6 14.2 + - - -
298B LYS* 3.0 17.6 + - - +
301B GLN* 1.3 102.2 - - + +
303B ASN* 1.3 73.4 + - - +
304B ILE* 3.4 21.2 - - + +
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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