Contacts of the helix formed by residues 289 - 299 (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 SER 289 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287A ILE* 3.6 5.7 - - - +
288A GLY* 1.3 72.1 - - - -
290A PRO* 1.3 70.9 - - - +
291A LYS* 3.4 15.2 - - - +
292A ASP* 2.9 23.1 + - - +
293A ALA 3.5 3.8 + - - -
319A MET* 6.1 0.2 - - - -
323A MET* 3.9 4.3 - - - -
298C GLU* 2.6 33.7 + - - -
333C SER* 5.5 0.4 - - - -
338C ARG* 2.4 36.1 + - - +
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Residues in contact with PRO 290 (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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289A SER* 1.3 79.9 - - - +
291A LYS* 1.3 70.2 + - - +
292A ASP 2.9 0.5 + - - -
293A ALA* 3.3 0.7 + - + -
294A ALA* 2.9 24.8 + - - +
319A MET* 4.2 6.7 - - - -
322A ALA* 3.9 25.6 - - + +
323A MET* 3.6 15.2 - - - -
326A ALA* 3.4 24.5 - - + +
294C ALA* 4.9 3.4 - - + -
298C GLU* 3.2 12.3 - - - +
329C ALA* 4.2 11.9 - - + +
330C GLY* 4.6 1.3 - - - +
333C SER* 3.3 27.4 - - - +
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Residues in contact with LYS 291 (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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289A SER* 3.4 16.8 - - - +
290A PRO* 1.3 77.9 - - - +
292A ASP* 1.3 72.1 + - - +
294A ALA* 3.3 6.0 - - - +
295A TYR* 2.9 36.0 + - - +
291C LYS* 4.0 29.5 - - + +
294C ALA* 4.6 5.5 - - - +
295C TYR* 3.7 57.9 - - + -
298C GLU* 3.4 12.2 + - - +
338C ARG* 5.6 2.9 - - - +
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Residues in contact with ASP 292 (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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261A GLY 4.5 1.7 - - - +
262A GLN 4.7 0.3 - - - -
263A GLY* 3.3 28.1 + - - -
264A ILE* 3.4 12.9 + - + +
287A ILE* 3.7 20.2 - - + -
288A GLY* 2.8 24.3 + - - -
289A SER* 2.9 17.8 + - - +
290A PRO 2.9 2.2 + - - -
291A LYS* 1.3 90.6 + - - +
293A ALA* 1.3 67.3 + - - +
295A TYR* 3.1 7.5 + - - -
296A ALA* 2.9 21.1 + - - +
338C ARG* 4.7 2.6 + - - -
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Residues in contact with ALA 293 (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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287A ILE* 3.5 25.9 - - + +
289A SER 3.5 0.2 + - - -
290A PRO 3.3 5.8 + - - +
292A ASP* 1.3 79.5 - - - +
294A ALA* 1.3 66.6 + - - +
296A ALA* 3.2 4.0 + - - +
297A MET* 3.1 22.8 + - - +
304A VAL* 4.1 6.3 - - + +
306A LEU* 4.5 5.6 - - + -
323A MET* 4.0 18.6 - - - -
326A ALA* 4.2 4.7 - - + -
327A VAL* 4.2 19.3 - - + -
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Residues in contact with ALA 294 (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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290A PRO 2.9 21.0 + - - +
291A LYS* 3.3 5.2 - - - +
293A ALA* 1.3 69.6 - - - +
295A TYR* 1.3 66.5 + - - +
297A MET* 2.9 8.2 + - - +
298A GLU* 2.8 21.0 + - - +
326A ALA* 3.5 28.5 + - + +
330A GLY* 3.7 9.1 - - - +
290C PRO* 4.9 4.5 - - + -
291C LYS* 4.1 21.1 - - - +
294C ALA* 5.7 2.2 - - + -
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Residues in contact with TYR 295 (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* 3.9 26.2 - - + -
267A PRO* 3.3 35.8 - - + +
291A LYS* 2.9 26.7 + - - +
292A ASP* 3.1 11.4 + - - +
294A ALA* 1.3 71.3 - - - +
296A ALA* 1.3 55.4 + - - +
298A GLU* 2.7 31.4 + - + +
299A LEU* 3.1 37.7 + - + +
291C LYS* 3.4 48.0 + - + +
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Residues in contact with ALA 296 (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* 3.7 14.1 - - + +
270A LEU* 4.8 7.0 - - - -
283A VAL* 3.7 29.4 - - + -
287A ILE* 4.9 0.4 - - + -
292A ASP 2.9 14.5 + - - +
293A ALA* 3.4 9.4 - - - +
295A TYR* 1.3 68.9 - - - +
297A MET* 1.3 64.7 + - - +
299A LEU* 3.1 10.8 + - - +
300A GLY 3.6 0.2 + - - -
301A ALA* 3.1 23.5 + - + +
304A VAL* 3.7 15.9 - - + -
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Residues in contact with MET 297 (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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114A ARG* 3.6 37.7 - - + -
293A ALA 3.1 10.7 + - - +
294A ALA 2.9 9.2 + - - +
296A ALA* 1.3 77.9 - - - +
298A GLU* 1.3 58.8 + - - +
300A GLY* 2.9 21.5 + - - -
301A ALA* 3.4 26.5 + - - +
302A ASP 3.9 2.2 - - - +
303A GLY* 3.9 21.5 - - - -
304A VAL* 4.1 7.9 - - - -
327A VAL* 3.6 25.1 - - + +
330A GLY* 3.6 2.0 - - - -
331A ARG* 3.6 33.7 + - + +
334A TYR* 3.8 10.0 - - - +
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Residues in contact with GLU 298 (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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294A ALA 2.8 9.7 + - - +
295A TYR* 2.7 24.0 + - + +
297A MET* 1.3 72.8 - - - +
299A LEU* 1.3 58.0 + - + +
300A GLY 3.2 1.9 + - - -
330A GLY* 4.2 14.3 - - - +
333A SER* 3.9 11.5 + - - +
334A TYR* 3.8 15.1 - - - -
338A ARG* 3.2 20.3 + - - -
289C SER* 2.7 41.9 + - - -
290C PRO* 4.2 0.2 - - - +
291C LYS* 3.7 33.4 + - - +
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Residues in contact with LEU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ILE* 4.7 1.3 - - + -
267A PRO* 4.2 15.5 - - + -
270A LEU* 3.7 23.3 - - + -
271A SER* 3.6 21.3 + - - +
274A ILE* 3.2 33.0 - - + +
295A TYR* 3.1 52.3 + - + +
296A ALA* 3.1 6.1 + - - +
298A GLU* 1.3 79.8 - - + +
300A GLY* 1.3 56.9 + - - +
301A ALA 3.5 0.7 - - - -
334A TYR* 4.6 3.9 - - - -
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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