Contacts of the helix formed by residues 345 - 358 (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 PRO 345 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343D ILE 4.3 0.2 - - - +
344D LEU* 1.3 90.1 - - + +
346D GLU* 1.3 60.7 + - - +
347D TYR* 3.4 38.8 - - + +
348D LEU* 3.0 13.7 + - + -
349D SER 2.9 23.9 + - - -
500D SER* 4.3 7.6 - - - +
504D THR* 3.8 22.4 - - + +
565D ILE* 4.3 12.8 - - + -
567D TYR* 3.8 15.7 - - + +
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Residues in contact with GLU 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D LYS* 3.4 45.9 - - + +
338D GLY 6.1 0.2 - - - +
344D LEU 3.8 1.5 + - - +
345D PRO* 1.3 72.4 - - - +
347D TYR* 1.3 55.9 + - - +
349D SER* 3.1 9.7 + - - +
350D ASN* 2.6 38.6 + - - +
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Residues in contact with TYR 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345D PRO* 3.4 36.2 - - + +
346D GLU* 1.3 76.8 - - - +
348D LEU* 1.3 69.1 + - + +
350D ASN* 3.6 5.9 - - - +
351D TRP* 3.1 24.9 + - - +
504D THR* 4.4 7.3 + - - -
505D VAL 4.7 0.2 - - - -
506D GLY* 3.9 24.3 + - - -
508D PHE* 3.9 26.4 - + - -
560D TYR* 3.5 45.8 - + + +
565D ILE* 4.5 2.8 - - - +
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Residues in contact with LEU 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344D LEU* 4.1 14.8 - - + -
345D PRO* 3.0 19.3 + - + +
347D TYR* 1.3 81.3 - - + +
349D SER* 1.3 60.8 + - - +
350D ASN 3.1 1.3 - - - -
351D TRP* 3.1 5.8 + - + +
352D THR* 2.9 34.3 + - - -
508D PHE* 4.0 11.0 - - + -
560D TYR* 3.7 27.1 - - + -
565D ILE* 3.8 34.8 - - + -
579D TRP* 3.7 47.8 - - + +
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Residues in contact with SER 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D GLY* 3.1 21.0 + - - -
339D ASN 2.6 29.5 + - - +
340D MET 4.8 1.6 - - - -
341D GLY* 4.2 4.8 - - - -
344D LEU* 4.0 17.8 - - - +
345D PRO 2.9 13.2 + - - -
346D GLU* 3.5 15.7 - - - -
348D LEU* 1.3 75.5 - - - +
350D ASN* 1.3 61.6 + - - +
352D THR* 3.5 6.7 - - - -
353D MET* 3.2 22.0 + - - +
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Residues in contact with ASN 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D LYS 4.7 3.4 + - - -
338D GLY* 5.1 1.5 - - - -
346D GLU 2.6 22.1 + - - +
347D TYR* 3.6 7.9 - - - +
349D SER* 1.3 70.5 - - - +
351D TRP* 1.3 66.5 + - - +
353D MET* 3.2 31.0 + - - +
354D GLU* 3.2 30.6 + - - +
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Residues in contact with TRP 351 (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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347D TYR 3.1 19.4 + - - +
348D LEU* 3.4 7.4 - - + +
350D ASN* 1.3 77.3 + - - +
352D THR* 1.3 62.5 + - - +
354D GLU* 3.3 20.8 - - + +
355D LYS* 3.4 41.6 - - + +
489D ASP* 4.1 14.1 - - + -
490D VAL* 3.8 15.0 - - + -
559D ASP* 4.4 9.5 + - - +
560D TYR* 3.4 39.9 - + + +
561D GLY* 3.6 30.5 - - - -
579D TRP* 3.4 41.1 - + - -
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Residues in contact with THR 352 (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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339D ASN* 4.1 11.7 - - + -
340D MET* 5.0 5.2 - - + -
344D LEU* 3.7 7.0 - - + +
348D LEU 2.9 15.5 + - - -
349D SER* 3.5 11.2 - - - -
351D TRP* 1.3 74.3 - - - +
353D MET* 1.3 58.3 + - - +
354D GLU 3.1 1.3 - - - -
355D LYS* 2.6 33.3 + - - +
356D VAL* 2.9 19.0 + - + -
486D LEU* 3.7 29.8 - - + -
490D VAL* 4.8 7.9 - - + -
579D TRP* 3.6 21.7 - - - -
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Residues in contact with MET 353 (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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334D PHE* 4.3 0.4 - - - -
337D LYS 3.2 24.7 - - - +
338D GLY* 3.9 9.2 - - - -
339D ASN* 3.6 21.5 + - - +
349D SER 3.2 8.8 + - - +
350D ASN* 3.2 27.6 + - - +
352D THR* 1.3 78.3 - - - +
354D GLU* 1.3 62.2 + - - +
356D VAL* 3.3 5.6 + - - +
357D ARG* 2.9 50.3 + - - +
363D VAL* 3.8 19.1 - - + -
365D PRO* 3.7 29.2 - - + -
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Residues in contact with GLU 354 (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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350D ASN* 3.2 18.9 + - - +
351D TRP* 3.3 16.2 - - + +
352D THR 3.1 0.2 - - - -
353D MET* 1.3 79.9 - - - +
355D LYS* 1.3 57.6 + - + +
357D ARG* 3.2 35.1 + - - +
358D ARG* 3.1 60.0 + - - +
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Residues in contact with LYS 355 (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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351D TRP* 3.4 52.3 - - + +
352D THR* 2.6 14.9 + - - +
354D GLU* 1.3 70.5 - - - +
356D VAL* 1.3 62.1 + - + +
358D ARG* 3.1 27.4 + - + +
359D GLU* 3.1 26.7 + - - +
486D LEU* 4.9 6.3 - - + +
489D ASP* 4.1 28.7 + - + +
490D VAL* 3.7 28.7 - - + -
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Residues in contact with VAL 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313D SER* 4.8 1.6 - - - +
316D ALA* 4.1 17.7 - - + -
317D CYS* 4.6 17.0 - - - -
332D GLN* 4.0 10.5 - - - +
339D ASN* 3.5 33.7 - - - +
352D THR* 2.9 24.0 + - + +
353D MET 3.6 4.3 - - - +
355D LYS* 1.3 74.2 - - + +
357D ARG* 1.3 61.8 + - - +
359D GLU* 3.1 22.2 + - - +
361D VAL* 3.2 25.9 - - + +
363D VAL* 4.1 7.0 - - + -
486D LEU* 4.9 8.3 + - + -
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Residues in contact with ARG 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353D MET* 2.9 44.1 + - - +
354D GLU* 3.2 34.4 + - - +
355D LYS 3.2 0.2 - - - -
356D VAL* 1.3 72.0 - - - +
358D ARG* 1.3 60.1 + - - +
359D GLU 2.9 10.0 + - - -
360D GLY* 3.0 12.8 + - - -
361D VAL 3.4 19.9 + - - +
363D VAL* 3.3 40.6 + - + +
365D PRO* 3.8 16.8 - - - +
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Residues in contact with ARG 358 (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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324D ARG* 4.7 10.6 + - - -
354D GLU* 3.1 56.4 + - - +
355D LYS* 3.1 35.5 + - + +
357D ARG* 1.3 74.8 - - - +
359D GLU* 1.3 58.3 + - - +
360D GLY 3.2 4.4 + - - -
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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