Contacts of the helix formed by residues 286 - 297 (chain A) in PDB entry 3TQO
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 ASP 286 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A LEU* 4.2 0.4 - - - -
285A SER* 1.3 76.8 - - - +
287A VAL* 1.3 65.8 + - - +
288A GLU* 2.9 23.4 + - - +
289A VAL* 3.0 20.6 + - + +
290A LEU* 2.9 20.3 + - - +
314A ARG* 5.2 0.6 - - - +
397A TYR* 2.5 45.3 + - - -
402A PHE* 4.9 8.4 - - + -
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Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ALA 3.6 23.6 - - - +
104A LEU* 3.7 29.4 - - + +
105A ARG* 3.5 36.1 - - - +
282A LEU* 3.7 19.4 - - + +
286A ASP* 1.3 73.9 + - - +
288A GLU* 1.3 60.3 + - + +
290A LEU* 3.2 4.3 + - - +
291A ARG* 2.8 40.4 + - + +
397A TYR* 3.6 9.6 - - - +
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Residues in contact with GLU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ARG* 3.3 25.8 + - - +
286A ASP* 2.9 11.1 + - - +
287A VAL* 1.3 74.5 - - + +
289A VAL* 1.3 60.7 + - - +
291A ARG* 4.3 1.3 - - - -
292A TYR 3.0 22.5 + - - -
317A LEU* 3.4 17.2 - - + +
321A TYR* 2.9 30.1 + - - -
393A GLY 3.5 16.7 - - - +
394A LEU* 3.1 18.2 - - + +
395A LEU 3.0 15.8 + - - -
396A GLN* 3.2 24.6 + - - +
397A TYR* 3.7 15.9 + - + -
402A PHE* 5.6 0.4 - - + -
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A SER* 4.2 13.9 - - - +
286A ASP* 3.0 28.6 + - + +
288A GLU* 1.3 75.6 - - - +
290A LEU* 1.3 64.1 + - - +
292A TYR* 3.4 3.9 + - - +
293A PHE* 3.2 21.5 + - - +
310A LEU* 3.6 29.3 - - + +
313A GLY* 5.2 0.9 - - - -
314A ARG* 4.1 36.8 - - + +
317A LEU* 3.7 18.6 - - + -
402A PHE* 4.7 8.7 - - + -
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Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 6.1 0.4 - - + -
104A LEU* 4.7 10.8 - - + -
278A ILE* 5.1 4.5 - - + +
281A ALA* 4.2 26.0 - - + +
282A LEU* 3.3 40.8 - - + -
285A SER* 3.7 21.5 - - - +
286A ASP 2.9 13.9 + - - +
287A VAL* 3.4 7.4 - - + +
289A VAL* 1.3 77.4 - - - +
291A ARG* 1.3 57.2 + - + +
293A PHE* 3.2 8.1 + - + +
294A LEU* 2.9 44.9 + - + +
305A TYR* 4.5 7.0 - - + -
310A LEU* 4.0 15.5 - - + -
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Residues in contact with ARG 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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46A ILE* 3.7 41.6 + - + +
49A ASP* 3.1 26.9 + - - -
50A MSE 5.8 0.6 - - - +
53A ARG* 4.7 0.4 - - - +
104A LEU* 3.0 30.2 + - + -
105A ARG* 3.2 19.2 + - - +
106A VAL* 3.7 2.2 - - - +
287A VAL* 2.8 29.5 + - + +
289A VAL 3.3 0.2 - - - -
290A LEU* 1.3 73.6 - - + +
292A TYR* 1.3 67.5 + - - +
294A LEU* 4.4 5.8 - - - +
295A LEU* 2.9 31.5 + - + +
391A ILE 5.0 0.8 + - - -
392A PHE 2.9 35.3 + - - +
393A GLY* 3.5 26.8 - - - -
394A LEU* 3.8 9.0 - - + -
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Residues in contact with TYR 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 GLU 3.0 18.3 + - - +
289A VAL 3.7 4.9 - - - +
291A ARG* 1.3 75.8 - - - +
293A PHE* 1.3 66.0 + - - +
296A SER* 3.0 42.8 + - - -
312A ASN 5.1 0.7 - - - -
313A GLY* 3.5 29.6 - - - +
316A ALA* 3.6 17.8 - - + +
317A LEU* 4.4 14.4 - - + -
320A PHE* 4.0 18.4 - + - -
356A PHE* 3.6 31.8 - + - +
360A PHE* 3.1 26.6 - + - -
394A LEU* 3.8 19.0 - - + +
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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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261A LEU* 4.1 6.5 - - + -
289A VAL 3.2 11.2 + - - +
290A LEU* 3.6 6.5 - - + +
292A TYR* 1.3 85.2 - - - +
294A LEU* 1.3 85.6 + - + +
295A LEU 3.4 0.5 + - - -
296A SER* 3.6 12.0 + - - -
303A LEU* 3.3 38.6 - - + +
304A SER 3.4 30.7 - - - -
305A TYR* 3.5 29.8 - + - -
309A ASN* 3.8 33.7 - - + +
310A LEU* 4.0 22.9 - - + -
313A GLY* 5.9 1.1 - - - -
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Residues in contact with LEU 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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39A ILE* 4.8 3.1 - - + +
42A GLY* 4.3 2.7 - - - +
43A ARG* 3.6 65.1 + - + +
46A ILE* 4.0 32.5 - - + -
47A ILE* 4.8 1.6 - - - +
104A LEU* 6.0 2.5 - - + -
261A LEU* 4.5 10.1 - - + -
278A ILE* 5.8 4.3 - - + -
290A LEU* 2.9 33.6 + - + +
291A ARG* 3.2 5.1 + - - +
293A PHE* 1.3 99.4 - - + +
295A LEU* 1.3 63.6 + - - +
297A GLY 4.6 1.3 - - - +
299A TYR* 5.8 0.2 - - - -
303A LEU* 3.8 6.1 - - + +
305A TYR* 6.0 0.4 - - + -
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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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46A ILE* 3.5 35.4 - - + +
47A ILE* 4.0 24.2 - - + -
50A MSE 4.0 25.1 - - + -
291A ARG* 2.9 15.4 + - - +
294A LEU* 1.3 81.9 - - - +
296A SER* 1.3 54.7 + - - +
297A GLY 3.2 6.2 - - - +
299A TYR* 5.9 1.8 - - + -
352A THR* 2.7 35.7 + - + +
356A PHE* 3.6 13.6 - - + -
392A PHE* 3.8 43.5 - - + +
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Residues in contact with SER 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A TYR* 3.0 40.9 + - - -
293A PHE* 3.6 9.9 + - - -
294A LEU 3.7 0.4 - - - -
295A LEU* 1.3 77.3 - - - +
297A GLY* 1.3 59.9 + - - +
303A LEU* 5.8 0.5 - - - +
352A THR 4.1 0.3 - - - -
353A PRO* 3.7 25.8 - - - +
356A PHE* 3.9 21.9 - - - +
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Residues in contact with GLY 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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43A ARG* 4.4 5.6 + - - -
293A PHE 4.6 3.4 + - - -
294A LEU 4.6 0.8 + - - +
295A LEU* 3.2 9.1 - - - +
296A SER* 1.3 82.2 + - - +
298A HIS* 1.3 67.8 + - - -
299A TYR* 3.4 3.3 + - - +
303A LEU* 4.6 17.6 - - - +
352A THR* 3.1 12.5 + - - -
353A PRO* 4.5 2.5 - - - -
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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