Contacts of the helix formed by residues 294 - 310 (chain D) in PDB entry 2DB3
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 GLY 294 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D ILE* 4.0 2.5 - - - -
272D GLN* 3.1 23.2 + - - +
292D GLY 3.4 2.8 + - - -
293D SER* 1.3 78.2 - - - +
295D LYS* 1.3 64.2 + - - +
296D THR 3.4 2.2 - - - -
297D ALA 3.8 0.8 + - - -
298D ALA* 3.3 11.6 + - - +
2904D ANP 3.1 41.2 + - - -
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Residues in contact with LYS 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D ILE* 4.0 16.6 - - + -
287D ALA 4.6 0.9 - - - +
289D ALA* 2.8 38.0 + - + +
290D GLN 3.1 7.5 + - - -
293D SER* 4.4 0.2 - - - +
294D GLY* 1.3 70.8 - - - +
296D THR* 1.3 65.0 + - - +
298D ALA* 3.1 17.1 - - - +
299D PHE* 3.0 20.3 - - + -
399D ASP* 5.4 3.8 - - - +
400D GLU* 6.0 0.9 - - - -
431D PHE* 3.8 24.9 - - + -
432D SER* 3.8 34.1 - - - +
433D ALA* 4.0 1.2 - - - +
2804D MG 4.6 3.1 - - - -
2904D ANP 2.8 58.9 + - - +
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Residues in contact with THR 296 (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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295D LYS* 1.3 80.2 - - - +
297D ALA* 1.3 57.1 + - - +
299D PHE* 3.3 22.0 + - + -
300D LEU* 2.9 51.9 + - + +
333D GLN* 5.2 5.5 + - + +
334D ILE* 4.3 18.5 - - + +
337D GLU* 4.4 17.4 - - + +
341D PHE* 5.9 0.7 - - - -
399D ASP* 5.0 1.8 + - - -
2804D MG 3.9 5.9 - - - -
2904D ANP 2.5 34.3 + - - -
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Residues in contact with ALA 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D TYR* 3.9 11.0 - - + +
272D GLN* 3.4 22.4 - - - +
276D ILE* 4.9 0.3 - - - +
294D GLY 3.8 1.4 + - - -
295D LYS 3.4 0.2 - - - -
296D THR* 1.3 74.9 - - - +
298D ALA* 1.3 66.6 + - - +
299D PHE 3.0 2.9 + - - -
300D LEU* 4.2 2.9 - - - +
301D LEU* 3.2 37.1 + - + +
302D PRO* 3.8 0.2 - - - +
341D PHE* 3.8 34.1 - - + -
2904D ANP 4.3 3.2 + - + +
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Residues in contact with ALA 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D ILE* 4.2 7.2 - - + -
272D GLN* 3.9 19.7 - - + +
275D SER* 4.2 12.4 - - - -
276D ILE* 4.0 7.6 - - - +
279D ILE* 3.8 6.2 - - - +
294D GLY 3.3 16.1 + - - +
295D LYS* 3.1 18.1 + - - +
297D ALA* 1.3 77.4 - - - +
299D PHE* 1.3 55.3 + - - +
302D PRO* 3.3 19.2 - - - +
431D PHE* 3.7 18.8 - - + -
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Residues in contact with PHE 299 (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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279D ILE* 3.9 10.3 - - + -
295D LYS 3.0 27.1 - - - -
296D THR* 3.3 25.3 + - + -
298D ALA* 1.3 80.2 - - - +
300D LEU* 1.3 87.3 + - + +
301D LEU 3.4 0.9 - - - -
302D PRO* 3.6 1.1 - - - +
303D ILE* 3.0 35.6 + - + +
323D ILE* 4.0 12.1 - - + -
334D ILE* 4.5 5.8 - - + -
397D VAL* 3.8 29.4 - - + -
399D ASP* 4.3 28.7 - - + -
429D LEU* 4.6 1.8 - - + -
431D PHE* 3.4 39.3 - + + -
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Residues in contact with LEU 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D THR* 2.9 40.2 + - + +
297D ALA* 4.3 1.1 - - - -
299D PHE* 1.3 86.3 - - + +
301D LEU* 1.3 57.6 + - - +
303D ILE* 3.8 3.7 - - + +
304D LEU* 2.8 46.4 + - + +
323D ILE* 3.7 30.5 - - + -
334D ILE* 4.2 6.7 - - + +
337D GLU* 4.0 8.3 - - + -
338D ALA* 3.8 38.4 - - + +
341D PHE* 4.0 16.4 - - + -
371D VAL* 5.7 1.8 - - + -
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Residues in contact with LEU 301 (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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247D PHE* 3.8 31.4 - - + -
252D LEU* 4.3 12.8 - - + -
256D ILE* 3.6 28.5 - - + +
260D VAL* 3.7 13.7 - - + -
265D TYR* 5.4 1.8 - - + -
272D GLN* 5.5 0.4 - - - +
276D ILE* 4.3 7.2 - - + -
297D ALA* 3.2 26.9 + - + +
300D LEU* 1.3 71.9 - - - +
302D PRO* 1.3 77.8 - - + +
303D ILE 2.9 0.5 + - - -
304D LEU* 3.0 2.8 + - - +
305D SER* 2.9 24.4 + - - -
341D PHE* 3.6 35.2 - - + -
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Residues in contact with PRO 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D LEU* 4.1 11.2 - - + -
276D ILE* 3.8 23.8 - - + +
279D ILE* 3.8 26.0 - - + -
280D SER* 3.8 20.4 + - - +
297D ALA 3.8 0.7 - - - +
298D ALA 3.3 25.8 - - - +
299D PHE 3.6 6.5 - - - +
301D LEU* 1.3 97.1 - - + +
303D ILE* 1.3 57.8 + - - +
305D SER* 3.7 1.7 - - - -
306D LYS* 3.0 33.3 + - - +
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Residues in contact with ILE 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D ILE* 4.0 11.9 - - + -
299D PHE* 3.0 27.4 - - + +
300D LEU* 3.4 4.5 + - + +
301D LEU 3.1 0.8 - - - -
302D PRO* 1.3 77.5 - - - +
304D LEU* 1.3 70.6 + - + +
306D LYS* 3.3 6.4 + - - +
307D LEU* 3.0 23.3 + - + +
321D VAL* 3.7 33.7 - - + -
323D ILE* 5.5 1.6 - - + -
371D VAL* 5.8 0.4 - - + -
395D PHE* 3.8 27.6 - - + -
397D VAL* 3.5 32.1 - - + -
429D LEU* 3.7 13.0 - - + -
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Residues in contact with LEU 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D ILE* 4.0 11.9 - - + -
300D LEU* 2.8 36.7 + - + +
301D LEU* 3.8 2.7 - - - +
303D ILE* 1.3 75.1 - - + +
305D SER* 1.3 64.7 + - - +
307D LEU* 3.2 20.2 + - + +
308D LEU* 3.4 14.0 + - - +
338D ALA* 3.9 12.1 - - + +
341D PHE* 3.7 31.9 - - + +
342D ALA* 3.9 18.6 - - + +
347D LEU* 3.7 19.3 - - + +
349D ILE* 4.3 8.7 - - + -
371D VAL* 4.1 24.9 - - + -
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Residues in contact with SER 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D ASP 4.0 4.2 + - - -
252D LEU* 3.4 19.7 - - - -
253D ARG* 2.8 38.0 + - - +
256D ILE* 4.0 13.8 - - - +
301D LEU 2.9 15.6 + - - -
302D PRO 3.7 4.0 - - - -
304D LEU* 1.3 76.9 - - - +
306D LYS* 1.3 58.3 + - - +
308D LEU* 2.8 21.9 + - - +
309D GLU* 2.8 14.9 + - - +
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Residues in contact with LYS 306 (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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251D ASP 5.8 1.2 + - - -
279D ILE* 5.1 1.8 - - + +
280D SER* 3.2 44.1 + - - +
282D GLY* 6.3 0.2 - - - -
302D PRO 3.0 19.4 + - - +
303D ILE 3.3 4.2 + - - +
305D SER* 1.3 75.5 - - - +
307D LEU* 1.3 63.7 + - - +
309D GLU* 2.7 37.2 + - + +
310D ASP* 2.9 35.6 + - + +
394D ARG* 4.7 3.3 + - - +
395D PHE* 4.0 25.1 - - + -
427D GLN* 6.0 0.4 - - - +
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Residues in contact with LEU 307 (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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303D ILE 3.0 17.6 + - - +
304D LEU* 3.4 12.1 - - + +
305D SER 3.1 0.4 + - - -
306D LYS* 1.3 77.3 - - - +
308D LEU* 1.3 60.6 + - - +
310D ASP 4.7 2.5 - - - -
311D PRO* 3.4 25.7 - - - +
312D HIS 4.9 0.2 + - - -
320D GLN* 3.7 9.2 + - + +
321D VAL* 4.0 21.3 - - + -
346D TYR* 4.0 1.4 + - - -
347D LEU* 3.9 20.7 - - + +
370D HIS* 3.9 19.1 - - + -
371D VAL* 3.9 27.8 - - + -
394D ARG* 3.5 32.1 + - - +
395D PHE* 4.2 7.9 - - + -
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Residues in contact with LEU 308 (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* 3.6 30.9 + - + +
255D ILE* 3.9 27.4 - - + -
256D ILE* 4.0 12.3 - - + -
304D LEU 3.4 13.7 + - - +
305D SER 2.8 6.9 + - - +
307D LEU* 1.3 80.0 - - - +
309D GLU* 1.3 66.0 + - - +
311D PRO* 3.1 15.6 - - - +
345D SER* 4.7 5.6 - - - -
346D TYR* 3.6 33.6 + - + -
347D LEU* 3.4 40.4 - - + -
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Residues in contact with GLU 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D ASP* 4.3 17.0 - - - +
253D ARG* 4.0 20.8 - - + +
305D SER* 2.8 19.1 + - - +
306D LYS* 2.7 41.5 + - + +
308D LEU* 1.3 73.4 - - - +
310D ASP* 1.3 60.8 + - + +
311D PRO* 3.2 7.4 - - - +
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Residues in contact with ASP 310 (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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306D LYS* 2.9 22.5 + - + +
307D LEU 4.0 0.9 - - - +
309D GLU* 1.3 82.1 - - + +
311D PRO* 1.3 62.0 - - - +
312D HIS* 2.7 36.0 + - - -
394D ARG* 3.4 18.3 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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