Contacts of the helix formed by residues 289 - 298 (chain A) in PDB entry 1T0S
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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277A MET* 4.5 0.4 - - - -
278A ASP* 3.8 5.6 - - - -
288A GLN* 1.3 74.4 - - - +
290A PHE* 1.3 55.8 + - - +
291A LYS* 3.4 8.0 + - - +
292A GLU* 2.7 38.0 + - - +
293A PHE* 2.7 34.7 + - - +
357A TRP* 3.9 6.7 - - - -
361A LYS* 3.7 34.0 + - - +
362A TYR* 3.6 11.6 - - - -
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Residues in contact with PHE 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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266A TRP* 3.5 37.9 - + - -
269A PHE* 4.3 5.6 - + - -
270A SER* 4.4 6.3 - - - -
273A THR* 4.2 10.3 - - + -
274A GLY* 3.6 27.6 - - - -
277A MET* 4.1 30.0 - - + +
278A ASP* 3.2 28.0 + - - +
289A SER* 1.3 73.4 - - - +
291A LYS* 1.3 56.5 + - - +
293A PHE* 3.8 2.2 - + - +
294A MET* 3.0 57.0 + - + +
324A LEU* 5.1 3.1 - - + -
328A HIS* 3.3 42.0 - + + +
362A TYR* 3.6 0.4 + - - +
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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* 3.0 6.9 - - - +
290A PHE* 1.3 79.9 - - - +
292A GLU* 1.3 70.6 + - + +
294A MET* 3.4 4.9 + - - +
295A LEU* 3.2 40.2 + - + +
321A MET 5.4 1.6 - - - -
324A LEU* 3.9 28.2 - - + +
325A ASP* 2.7 42.0 + - - +
361A LYS 4.8 7.8 + - - +
362A TYR* 3.4 22.4 + - + -
363A PRO* 5.3 5.1 - - - +
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Residues in contact with GLU 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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288A GLN* 3.0 25.1 - - + +
289A SER* 2.7 43.8 + - - +
291A LYS* 1.3 81.0 - - + +
293A PHE* 1.3 63.9 + - - +
295A LEU* 3.1 7.7 + - - +
296A GLU* 3.0 22.3 + - - +
361A LYS* 2.8 31.6 + - + +
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Residues in contact with PHE 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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203A MET* 4.3 9.0 - - + -
204A GLN* 4.2 17.7 - - - -
207A GLY* 5.1 4.5 - - - -
269A PHE* 4.6 15.7 - + - -
273A THR* 5.2 0.4 - - + -
277A MET* 3.7 32.1 - - + -
288A GLN* 2.9 21.8 + - - +
289A SER 2.7 18.2 + - - +
290A PHE* 3.8 5.4 - + - +
292A GLU* 1.3 70.7 - - - +
294A MET* 1.3 66.0 + - - +
297A TRP* 2.9 64.2 + + + +
298A ILE* 4.3 16.4 - - + -
504A BML 3.9 27.4 - + - -
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Residues in contact with MET 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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200A PHE* 4.0 18.8 - - + -
266A TRP* 3.4 31.6 - - + -
269A PHE* 3.9 16.2 - - + -
290A PHE* 3.0 56.0 + - + +
291A LYS 3.7 4.3 - - - +
292A GLU 3.2 0.4 + - - -
293A PHE* 1.3 79.7 - - + +
295A LEU* 1.3 57.6 + - - +
298A ILE* 2.8 30.7 + - + +
299A VAL* 2.8 29.3 + - + -
320A PHE* 4.5 7.0 - - + -
324A LEU* 4.1 20.2 - - + -
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Residues in contact with LEU 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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291A LYS* 3.2 35.2 + - + +
292A GLU* 3.1 9.7 + - - +
294A MET* 1.3 78.0 - - - +
296A GLU* 1.3 59.3 + - + +
299A VAL* 3.3 11.7 - - + +
300A ALA* 3.3 28.1 + - - +
321A MET* 3.5 31.6 - - + -
324A LEU* 3.6 19.5 - - + -
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Residues in contact with GLU 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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288A GLN* 4.3 12.1 + - - +
292A GLU 3.0 15.4 + - - +
295A LEU* 1.3 78.7 - - + +
297A TRP* 1.3 102.7 + - + +
300A ALA* 4.6 4.3 - - - +
301A GLN* 3.8 11.4 + - - +
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Residues in contact with TRP 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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199A GLY 5.1 0.2 - - - +
203A MET* 3.7 45.9 - - + +
206A LEU* 6.3 1.3 - - + -
288A GLN* 3.4 15.9 - - - +
293A PHE* 2.9 49.7 + + + +
296A GLU* 1.3 114.6 + - + +
298A ILE* 1.3 69.6 + - + +
301A GLN* 3.0 31.2 - - - +
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Residues in contact with ILE 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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199A GLY 3.3 28.0 - - - +
200A PHE* 3.8 29.2 - - + +
203A MET* 4.2 16.8 - - + -
269A PHE* 5.3 1.6 - - + -
293A PHE* 4.3 13.9 - - + -
294A MET* 2.8 41.6 + - + +
297A TRP* 1.3 94.2 - - + +
299A VAL* 1.3 66.4 + - + +
300A ALA 3.4 1.1 + - - -
301A GLN* 3.3 4.8 + - - +
302A PHE* 3.1 44.1 + - + -
320A PHE* 5.9 2.2 - - + -
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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