Contacts of the helix formed by residues 309 - 326 (chain D) in PDB entry 4BUR
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 309 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D GLY* 3.5 2.6 - - - -
308D GLY* 1.3 77.4 - - - +
310D PHE* 1.3 66.2 + - - -
311D LEU 3.4 2.0 - - - -
312D GLY 4.2 0.8 - - - +
313D SER* 2.7 30.5 + - - -
340D MET* 3.6 12.1 - - - -
397D ALA 5.0 0.2 + - - -
700D NAD 3.2 34.9 + - - -
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Residues in contact with PHE 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D GLY* 1.3 71.3 - - - +
311D LEU* 1.3 63.5 + - - +
313D SER* 4.1 0.5 - - - -
314D GLU* 3.1 31.8 + - - +
340D MET* 3.5 22.3 - - + -
343D ILE* 3.7 30.1 - - + -
454D HIS* 3.5 30.1 - + - -
482D PHE* 4.1 15.0 - + - -
484D SER* 4.8 2.9 - - - -
492D TYR* 3.9 15.3 - - - -
700D NAD 3.2 87.1 + + + +
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Residues in contact with LEU 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D SER* 4.5 4.3 - - - -
264D PRO* 6.0 4.5 - - + -
284D PHE* 3.4 37.0 - - + +
310D PHE* 1.3 77.6 - - - +
312D GLY* 1.3 65.9 + - - +
314D GLU* 4.1 1.0 - - - +
315D LEU* 3.0 42.2 + - + +
396D ALA 5.4 0.9 - - - +
397D ALA* 3.7 18.8 - - + -
700D NAD 3.0 46.8 + - + +
1612D FAD 3.8 33.7 - - + -
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Residues in contact with GLY 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305D ILE* 3.7 26.5 - - - +
307D GLY 3.8 10.8 - - - -
309D GLY 3.6 3.2 + - - -
310D PHE 3.5 0.2 - - - -
311D LEU* 1.3 77.7 - - - +
313D SER* 1.3 57.7 + - - +
315D LEU* 3.4 3.0 + - - +
316D ALA* 2.9 28.2 + - - +
332D GLN* 3.4 7.0 + - - -
397D ALA* 3.4 13.1 + - - +
700D NAD 4.0 1.2 + - - -
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Residues in contact with SER 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D GLY 3.0 16.1 + - - -
309D GLY 2.7 22.8 + - - -
310D PHE 4.1 1.6 - - - -
312D GLY* 1.3 76.4 - - - +
314D GLU* 1.3 62.3 + - - +
316D ALA* 3.2 7.6 + - - +
317D CYS* 3.2 24.9 + - - -
332D GLN* 3.5 8.1 + - - +
339D ASN* 3.4 21.7 + - - +
340D MET* 4.0 10.3 - - - -
356D VAL* 4.8 1.3 - - - +
486D LEU* 3.6 19.1 - - - -
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Residues in contact with GLU 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D SER* 3.2 35.9 + - - +
177D LYS* 3.1 37.4 + - + +
181D PHE* 5.9 0.2 - - - -
310D PHE 3.1 15.9 + - - +
311D LEU* 4.2 2.5 - - - +
313D SER* 1.3 73.9 - - - +
315D LEU* 1.3 63.0 + - - +
317D CYS* 3.2 6.4 + - - +
318D ALA* 3.1 22.0 + - - +
484D SER* 2.8 24.0 + - - +
485D ASP 3.6 6.8 + - - +
486D LEU* 3.8 18.6 - - + -
700D NAD 3.3 22.7 + - - -
1612D FAD 4.1 0.2 - - - +
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Residues in contact with LEU 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D SER* 3.9 26.7 - - - +
180D TRP* 4.5 13.5 - - + +
284D PHE* 4.0 43.1 - - + -
293D LEU* 4.9 5.8 - - + -
305D ILE* 4.1 11.4 - - + -
311D LEU* 3.0 34.9 + - + +
312D GLY* 3.7 5.2 - - - +
314D GLU* 1.3 75.6 - - - +
316D ALA* 1.3 61.9 + - - +
318D ALA* 3.7 2.6 - - + +
319D LEU* 3.0 34.3 + - + +
395D VAL* 4.2 20.0 - - + -
397D ALA* 5.6 1.1 - - + -
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Residues in contact with ALA 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305D ILE* 3.6 16.9 - - + +
312D GLY 2.9 14.4 + - - +
313D SER 3.3 10.5 - - - +
315D LEU* 1.3 77.8 - - - +
317D CYS* 1.3 57.5 + - - +
319D LEU* 3.7 1.0 - - - +
320D GLY* 2.8 28.8 + - - -
330D VAL* 4.4 2.3 - - - +
332D GLN* 3.8 18.8 - - - +
356D VAL* 4.1 12.3 - - + -
361D VAL* 3.6 18.2 - - + +
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Residues in contact with CYS 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D PHE* 4.4 8.5 - - + -
313D SER 3.2 14.1 + - - -
314D GLU* 3.2 7.6 + - - +
316D ALA* 1.3 79.0 - - - +
318D ALA* 1.3 62.5 + - - +
320D GLY* 3.5 1.7 + - - -
321D ARG* 3.4 24.4 + - - +
356D VAL* 4.6 13.7 - - - -
359D GLU* 4.1 24.8 - - + +
361D VAL* 4.9 0.2 - - - -
485D ASP 5.3 0.9 - - - +
486D LEU* 3.6 39.5 - - - -
487D GLY* 3.9 11.2 - - - +
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Residues in contact with ALA 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D SER 4.3 6.5 - - - +
180D TRP* 3.8 42.4 - - + +
181D PHE* 4.0 15.9 - - + -
314D GLU 3.1 11.8 + - - +
315D LEU* 3.7 10.1 - - - +
316D ALA 3.2 0.2 - - - -
317D CYS* 1.3 72.6 - - - +
319D LEU* 1.3 59.2 + - + +
320D GLY 2.9 3.6 - - - -
321D ARG* 2.9 23.7 + - - +
322D LYS* 3.2 11.1 + - - +
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Residues in contact with LEU 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D TRP* 3.8 32.3 - - + -
293D LEU* 4.5 15.0 - - + -
297D SER* 3.8 21.5 - - - -
303D ILE* 4.1 29.1 - - + +
305D ILE* 4.2 18.8 - - + -
315D LEU* 3.0 21.6 + - + +
316D ALA 4.1 1.1 - - - +
318D ALA* 1.3 79.7 - - + +
320D GLY* 1.3 52.0 + - - +
322D LYS* 3.4 6.9 - - + -
323D ALA* 2.6 36.9 + - - +
330D VAL* 3.5 18.2 - - + +
395D VAL* 5.3 2.0 - - + -
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Residues in contact with GLY 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D ALA 2.8 18.9 + - - -
317D CYS 3.7 3.1 - - - -
318D ALA 2.9 0.6 - - - -
319D LEU* 1.3 78.6 - - - +
321D ARG* 1.3 56.4 + - - +
323D ALA* 4.2 2.3 - - - +
324D ARG* 3.2 26.5 + - - +
330D VAL* 4.7 1.6 - - - -
359D GLU 3.4 27.3 - - - +
360D GLY* 4.5 7.3 - - - -
361D VAL* 4.3 6.1 - - - -
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Residues in contact with ARG 321 (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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180D TRP 6.0 0.9 - - - +
181D PHE* 3.6 31.2 - - + -
317D CYS 3.4 11.4 + - - +
318D ALA 2.9 7.3 + - - +
320D GLY* 1.3 74.1 - - - +
322D LYS* 1.3 61.9 + - + +
323D ALA 3.2 0.2 - - - -
324D ARG* 3.2 27.3 + - - +
325D ALA* 2.9 31.1 + - - +
359D GLU* 3.6 24.7 - - - -
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Residues in contact with LYS 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D TRP* 4.3 35.2 + - + +
294D GLU* 2.7 34.4 + - - +
297D SER* 4.4 17.3 - - - +
298D ARG* 5.3 4.9 - - + +
318D ALA 3.2 8.4 + - - +
319D LEU* 3.7 15.3 - - + +
321D ARG* 1.3 81.0 - - + +
323D ALA* 1.3 56.6 + - - +
325D ALA* 4.0 7.1 - - + +
326D LEU* 3.1 47.4 + - + +
328D THR* 4.0 1.4 + - - -
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Residues in contact with ALA 323 (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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319D LEU 2.6 20.6 + - - +
320D GLY* 4.2 3.6 - - - +
322D LYS* 1.3 71.2 - - - +
324D ARG* 1.3 60.1 + - - +
325D ALA 3.1 1.6 - - - -
327D GLY* 2.9 29.8 + - - -
328D THR* 3.1 38.6 + - - +
329D GLU* 4.2 1.6 - - - +
330D VAL* 3.7 20.4 - - + +
360D GLY 4.9 5.6 - - - +
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Residues in contact with ARG 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D GLY 3.2 11.9 + - - +
321D ARG* 3.2 31.9 + - - +
323D ALA* 1.3 77.3 - - - +
325D ALA* 1.3 64.8 + - - +
327D GLY* 4.0 4.8 + - - -
358D ARG 4.7 9.0 + - - -
359D GLU* 3.8 10.1 + - - +
360D GLY* 3.8 28.5 - - - +
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Residues in contact with ALA 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321D ARG 2.9 16.3 + - - +
322D LYS* 4.0 12.1 - - + +
323D ALA 3.1 0.2 - - - -
324D ARG* 1.3 81.5 - - + +
326D LEU* 1.3 64.5 + - + +
327D GLY 3.3 3.4 + - - -
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Residues in contact with LEU 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D SER 3.9 20.2 - - - +
298D ARG* 4.1 28.3 - - + +
299D GLU* 5.0 1.1 - - - +
300D VAL 5.1 0.9 - - - +
322D LYS* 3.1 44.0 + - + +
325D ALA* 1.3 80.9 - - + +
327D GLY* 1.3 56.6 + - - +
328D THR* 2.9 33.1 + - + +
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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