Contacts of the helix formed by residues 355 - 368 (chain D) in PDB entry 5U07
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 355 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338D ALA* 4.0 5.9 - - - +
353D TYR* 3.2 2.8 + - - +
354D ASP* 1.3 96.8 + - - +
356D TYR* 1.3 68.8 + - - +
357D PRO* 3.8 6.4 - - - +
358D ALA* 3.3 17.5 + - - +
359D LEU* 3.2 22.2 + - - +
327H GLU 3.3 15.5 - - - -
328H VAL* 3.1 20.2 - - - +
330H PRO* 4.4 5.6 - - - +
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Residues in contact with TYR 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D LEU* 3.7 25.4 - - + -
280D LEU* 4.7 10.1 - - + -
281D PRO* 2.3 44.7 + - + -
282D ASP 3.4 14.4 + - - -
283D LEU 4.0 0.2 + - - -
284D VAL* 3.8 21.1 - - + -
338D ALA* 3.4 35.7 - - + -
340D VAL* 4.0 6.6 - - + +
355D SER* 1.3 71.2 - - - +
357D PRO* 1.3 73.3 - - + +
359D LEU* 3.0 7.8 + - - +
360D ILE* 2.9 26.7 + - + +
328H VAL* 3.1 28.2 + - + +
329H TRP* 4.2 20.0 - + + -
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Residues in contact with PRO 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D ARG* 6.0 5.8 - - + +
355D SER* 3.8 4.7 - - - +
356D TYR* 1.3 95.2 - - + +
358D ALA* 1.3 57.8 + - - +
360D ILE* 3.5 10.6 + - + +
361D ASP* 2.9 39.4 + - - +
328H VAL 3.5 11.2 - - - +
329H TRP* 4.7 9.9 - - + -
330H PRO* 3.7 24.2 - - + -
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Residues in contact with ALA 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353D TYR* 4.4 7.0 - - + -
354D ASP* 3.5 15.3 - - - +
355D SER* 3.3 19.9 + - - +
356D TYR 3.2 0.6 - - - -
357D PRO* 1.3 82.2 - - - +
359D LEU* 1.3 62.7 + - - +
361D ASP* 3.3 9.1 + - - +
362D ALA* 2.9 23.9 + - - +
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Residues in contact with LEU 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284D VAL* 4.0 11.7 - - + +
286D ILE* 3.5 40.8 - - + -
336D GLY 3.8 5.6 - - - +
337D TYR* 3.4 17.3 - - - +
338D ALA* 3.3 37.2 - - + +
353D TYR* 3.1 26.4 - - + -
355D SER 3.2 9.5 + - - +
356D TYR* 3.0 10.4 + - - +
358D ALA* 1.3 78.9 - - - +
360D ILE* 1.3 64.2 + - + +
362D ALA* 3.1 3.5 + - - +
363D MET* 2.9 27.9 + - + +
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Residues in contact with ILE 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D ALA* 3.8 23.6 - - + +
260D LEU* 3.7 26.0 - - + +
261D ARG* 3.4 35.7 - - + +
264D LEU* 3.8 20.4 - - + -
284D VAL* 6.1 0.2 - - + -
286D ILE* 3.9 21.8 - - + -
356D TYR* 2.9 15.9 + - + +
357D PRO* 3.9 8.5 - - + +
359D LEU* 1.3 76.8 - - + +
361D ASP* 1.3 64.7 + - - +
363D MET* 3.3 2.3 + - - +
364D VAL* 2.9 24.5 + - + +
329H TRP* 6.3 0.7 - - + -
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Residues in contact with ASP 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257D ALA* 5.3 4.5 - - - +
357D PRO* 2.9 27.5 + - - +
358D ALA* 3.5 8.1 - - - +
360D ILE* 1.3 81.1 - - - +
362D ALA* 1.3 63.1 + - - +
364D VAL* 3.1 12.1 - - - +
365D ALA* 2.9 25.7 + - - +
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Residues in contact with ALA 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353D TYR* 3.3 42.6 - - + +
358D ALA 2.9 10.8 + - - +
359D LEU 3.1 0.6 + - - +
361D ASP* 1.3 75.8 - - - +
363D MET* 1.3 60.6 + - - +
365D ALA* 3.6 7.1 + - - +
366D ALA* 2.9 26.7 + - - +
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Residues in contact with MET 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D VAL* 5.4 1.0 - - + +
260D LEU* 5.6 2.2 - - + -
286D ILE* 3.7 37.7 - - + +
288D VAL* 4.0 15.8 - - + +
334D ILE* 4.2 21.3 - - + +
335D ARG 3.2 36.1 - - - +
336D GLY* 3.4 12.6 - - - +
353D TYR* 3.9 22.9 - - + +
359D LEU* 2.9 23.4 + - + +
360D ILE* 4.0 4.7 - - - +
362D ALA* 1.3 77.8 - - - +
364D VAL* 1.3 65.1 + - - +
366D ALA* 3.1 2.9 + - - +
367D ALA* 2.9 22.5 + - - +
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Residues in contact with VAL 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253D ARG* 3.8 47.6 + - + +
256D VAL* 4.8 14.1 - - + -
257D ALA* 4.3 21.8 - - + +
260D LEU* 6.0 1.9 - - + +
360D ILE* 2.9 18.6 + - + +
361D ASP* 3.1 23.8 - - - +
363D MET* 1.3 76.5 - - - +
365D ALA* 1.3 62.8 + - + +
367D ALA* 3.2 17.4 + - + +
368D PHE* 3.6 17.2 + - + +
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Residues in contact with ALA 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253D ARG* 6.0 4.5 - - - +
361D ASP 2.9 19.5 + - - +
362D ALA* 3.6 7.2 - - - +
364D VAL* 1.3 80.2 - - + +
366D ALA* 1.3 61.6 + - - +
368D PHE* 3.2 22.6 + - - +
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Residues in contact with ALA 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288D VAL* 4.6 5.9 - - + +
290D PHE* 5.4 3.6 - - - -
334D ILE* 3.9 44.5 - - + +
362D ALA 2.9 19.6 + - - +
363D MET* 3.1 12.3 + - - +
365D ALA* 1.3 76.4 - - - +
367D ALA* 1.3 62.4 + - - +
368D PHE 4.3 3.6 - - - +
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Residues in contact with ALA 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D THR* 5.1 7.9 - - + +
4D VAL* 4.6 10.1 - - + -
239D LEU* 3.4 32.2 - - + +
256D VAL* 6.3 1.1 - - + -
288D VAL* 4.7 9.0 - - + -
290D PHE* 5.8 3.3 - - - -
363D MET 2.9 12.1 + - - +
364D VAL* 3.6 13.2 - - + +
365D ALA 3.2 0.8 - - - -
366D ALA* 1.3 78.8 - - - +
368D PHE* 1.3 69.5 + - + +
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Residues in contact with PHE 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D LEU* 4.0 20.4 - - + -
243D VAL* 3.9 20.6 - - + -
249D ALA* 4.5 21.8 - - + -
252D ALA* 3.9 30.1 - - + -
253D ARG* 4.7 20.4 - - + +
256D VAL* 5.9 1.8 - - + -
364D VAL* 3.6 19.7 + - + +
365D ALA* 3.2 17.8 + - - +
366D ALA 4.3 4.0 - - - +
367D ALA* 1.3 91.4 - - + +
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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