Contacts of the helix formed by residues 321 - 333 (chain D) in PDB entry 2BKU
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 321 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268D TYR* 3.0 31.8 - - - -
290D TRP* 3.2 14.2 - - - -
317D PHE 2.7 21.1 + - - -
318D ALA 2.9 7.1 + - - -
320D SER* 1.3 75.0 - - - +
322D ILE* 1.3 60.0 + - - +
323D LYS 3.2 3.4 + - - -
324D ASP* 3.2 2.7 + - - -
325D VAL* 2.8 52.5 + - - +
358D PHE* 5.2 0.2 - - - -
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Residues in contact with ILE 322 (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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318D ALA 3.2 10.9 + - - +
319D LEU* 3.4 31.2 + - + +
320D SER 3.5 0.8 - - - -
321D SER* 1.3 76.7 - - - +
323D LYS* 1.3 71.3 + - - +
326D VAL* 3.3 19.3 + - + -
327D PRO* 3.2 19.2 - - - +
358D PHE* 4.4 6.5 - - + -
362D CYS* 4.1 13.9 - - + -
365D HIS* 3.7 35.9 - - + +
366D ILE* 4.7 3.1 - - + +
369D PRO* 3.7 30.4 - - + +
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Residues in contact with LYS 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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320D SER 5.0 3.3 + - - +
321D SER 3.2 1.0 - - - -
322D ILE* 1.3 88.4 - - - +
324D ASP* 1.3 62.8 + - - +
327D PRO* 3.2 22.5 - - + +
368D GLU* 5.6 6.9 + - - -
369D PRO* 5.8 7.4 - - + -
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Residues in contact with ASP 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D TYR* 2.9 38.0 + - + -
272D ILE* 3.4 27.3 - - + +
321D SER 3.2 3.9 + - - +
323D LYS* 1.3 84.1 - - - +
325D VAL* 1.3 61.8 + - + +
326D VAL 3.6 0.2 - - - -
327D PRO* 3.4 8.8 - - - +
328D ASN* 2.6 29.6 + - - +
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Residues in contact with VAL 325 (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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272D ILE* 3.4 24.9 - - + -
275D MET* 3.9 20.7 - - + +
290D TRP* 3.8 22.9 - - + +
321D SER* 2.8 38.0 + - - +
324D ASP* 1.3 71.8 - - - +
326D VAL* 1.3 64.9 + - - +
328D ASN* 3.1 7.5 + - - +
329D LEU* 2.9 24.5 + - + +
358D PHE* 3.5 32.8 - - + -
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Residues in contact with VAL 326 (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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322D ILE* 3.3 24.5 + - + +
325D VAL* 1.3 73.7 - - - +
327D PRO* 1.3 65.5 - - + +
329D LEU* 2.9 9.5 + - + +
330D LEU* 2.8 55.0 + - + +
355D LEU* 4.2 14.4 - - + -
358D PHE* 3.9 22.2 - - + -
366D ILE* 3.8 22.4 - - + -
369D PRO* 4.2 16.6 - - + -
370D VAL* 4.4 4.9 - - + -
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Residues in contact with PRO 327 (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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322D ILE 3.2 14.8 - - - +
323D LYS* 3.2 22.2 - - + +
324D ASP 3.4 6.3 - - - +
326D VAL* 1.3 92.5 - - + +
328D ASN* 1.3 57.1 - - - +
330D LEU* 3.3 14.3 + - + +
331D ASN* 3.0 27.2 + - - +
369D PRO* 5.3 7.6 - - + -
373D PHE* 5.5 0.5 - - - -
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Residues in contact with ASN 328 (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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272D ILE* 4.2 13.0 - - - +
275D MET* 3.7 23.2 - - + +
276D LYS* 3.0 42.7 - - + +
324D ASP* 2.6 29.1 + - - +
325D VAL* 3.1 8.6 + - - +
327D PRO* 1.3 76.7 - - - +
329D LEU* 1.3 64.1 + - - +
331D ASN* 3.5 9.3 + - - +
332D LEU* 3.2 26.2 + - - +
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Residues in contact with LEU 329 (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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275D MET* 4.1 10.7 - - + -
287D VAL* 4.1 15.7 - - + -
325D VAL* 2.9 16.8 + - + +
326D VAL* 2.9 11.9 + - - +
328D ASN* 1.3 72.4 - - - +
330D LEU* 1.3 66.9 + - - +
332D LEU* 3.0 16.9 + - + +
333D LEU* 3.2 10.9 + - - +
351D ALA* 3.6 40.0 - - + +
354D CYS* 3.6 34.5 - - + -
355D LEU* 4.4 20.4 - - + +
358D PHE* 3.9 23.8 - - + -
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Residues in contact with LEU 330 (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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326D VAL* 2.8 40.9 + - + +
327D PRO* 3.7 10.5 - - + +
329D LEU* 1.3 75.4 - - - +
331D ASN* 1.3 61.0 + - - +
333D LEU* 3.2 23.1 + - + +
334D THR* 4.1 2.1 + - - +
355D LEU* 3.6 31.0 - - + -
369D PRO* 3.8 22.0 - - + +
370D VAL* 4.4 7.6 - - + -
373D PHE* 3.4 44.0 - - + -
392D ALA* 3.9 20.2 - - + -
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Residues in contact with ASN 331 (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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327D PRO 3.0 15.4 + - - +
328D ASN* 3.5 14.1 + - - +
329D LEU 3.2 0.2 - - - -
330D LEU* 1.3 75.6 - - - +
332D LEU* 1.3 61.0 + - - +
334D THR* 2.6 30.7 + - - +
335D ARG* 4.5 17.1 - - - +
373D PHE* 4.4 4.7 - - - -
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Residues in contact with LEU 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D MET* 3.8 27.6 - - + +
283D ALA* 4.2 7.4 - - + -
287D VAL* 3.4 32.8 - - + -
328D ASN 3.2 13.3 + - - +
329D LEU* 3.0 11.9 + - + +
331D ASN* 1.3 76.0 - - - +
333D LEU* 1.3 57.0 + - - +
334D THR 3.1 5.6 - - - -
335D ARG* 3.0 59.2 + - - +
347D VAL* 3.8 17.5 - - + +
348D SER* 3.4 14.4 + - - -
351D ALA* 3.7 11.7 - - + -
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Residues in contact with LEU 333 (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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329D LEU 3.2 11.2 + - - +
330D LEU* 3.3 23.6 - - + +
331D ASN 3.2 1.0 - - - -
332D LEU* 1.3 76.6 - - - +
334D THR* 1.3 55.1 + - - +
335D ARG 3.3 0.4 - - - -
336D GLN* 3.0 27.5 + - - +
348D SER* 3.4 26.3 - - - +
351D ALA* 3.9 4.3 - - + -
352D GLY* 3.6 22.7 - - - +
355D LEU* 4.4 5.8 - - + -
373D PHE* 4.8 0.7 - - + -
387D GLU* 3.9 2.1 - - - +
388D ALA* 3.6 34.0 - - + +
391D MET* 4.0 13.2 - - + +
392D ALA* 3.9 24.5 - - + +
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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