Contacts of the helix formed by residues 329 - 338 (chain A) in PDB entry 4BU2
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 ASP 329 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A ASP* 2.8 12.9 + - - +
327A SER* 3.9 0.2 - - - -
328A SER* 1.3 91.3 - - - +
330A MSE 1.3 58.4 + - - +
331A LYS 3.4 2.2 - - - -
332A LYS* 3.2 19.0 + - - +
333A ASP* 2.8 48.2 + - - +
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Residues in contact with MSE 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A ASN 4.6 3.4 - - - +
262A ASN* 3.6 28.7 - - - +
263A SER 4.4 4.3 - - - +
266A ASP* 3.6 35.4 - - + +
267A PHE* 4.1 32.8 - - + +
270A ASP* 2.7 33.1 + - - +
327A SER* 3.3 1.7 + - - +
329A ASP* 1.3 71.3 - - - +
331A LYS* 1.3 65.2 + - + +
333A ASP* 3.3 1.5 + - - -
334A PHE* 3.0 21.6 + - - +
904A EDO 3.4 23.3 + - - +
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Residues in contact with LYS 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A LEU 5.3 5.6 + - - -
327A SER* 3.0 29.4 + - - +
330A MSE 1.3 72.5 - - + +
332A LYS* 1.3 64.6 + - - +
334A PHE* 3.1 9.6 + - - +
335A ILE* 3.0 28.0 + - - +
373A VAL* 3.5 32.4 - - + +
374A LEU* 3.3 22.8 + - - +
375A THR* 3.5 27.4 - - + +
394A TYR* 6.5 0.2 - - + -
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Residues in contact with LYS 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A SER* 4.7 0.9 + - - +
328A SER 4.1 18.4 + - - +
329A ASP* 3.2 20.3 + - - +
331A LYS* 1.3 78.9 - - - +
333A ASP* 1.3 59.2 + - - +
335A ILE* 4.0 4.2 - - - +
336A MSE 2.8 54.9 + - + +
373A VAL* 5.4 0.2 - - - +
377A LEU* 5.9 8.1 - - + +
394A TYR* 3.6 44.7 + - + +
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Residues in contact with ASP 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A LEU* 4.8 0.7 - - + +
329A ASP* 2.8 46.5 + - - +
330A MSE 3.6 4.0 - - - +
332A LYS* 1.3 70.8 - - - +
334A PHE* 1.3 70.5 + - - +
336A MSE 4.2 3.1 - - - -
337A HIS* 2.8 51.9 + - - +
904A EDO 3.8 13.2 - - - +
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Residues in contact with PHE 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A GLU* 3.7 12.3 - - + -
159A GLY* 3.6 29.6 - - - +
160A SER* 3.4 25.4 - - - -
161A LEU* 3.7 20.7 - - + +
330A MSE 3.0 13.3 + - - +
331A LYS* 3.1 10.7 + - - +
333A ASP* 1.3 78.8 - - - +
335A ILE* 1.3 68.2 + - + +
337A HIS 3.7 0.2 - - - -
338A ARG* 2.8 79.2 + - + +
904A EDO 3.9 14.1 + - - +
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Residues in contact with ILE 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A LYS 3.0 12.3 + - - +
332A LYS 4.1 2.7 - - - +
334A PHE* 1.3 81.9 - - + +
336A MSE 1.3 59.0 + - + +
337A HIS 3.3 0.3 + - - -
338A ARG* 3.4 36.5 - - - +
371A HIS 3.9 12.8 - - - +
372A ILE 4.4 2.0 - - - +
373A VAL* 3.2 36.6 - - + -
394A TYR* 3.9 9.0 - - + -
395A HIS 3.4 40.6 - - - +
396A SER* 3.7 1.6 - - - +
399A ASN* 2.8 26.9 + - - +
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Residues in contact with MSE 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A LYS* 2.8 50.4 + - + +
333A ASP* 3.7 7.2 - - - +
335A ILE* 1.3 78.5 - - + +
337A HIS* 1.3 76.3 + - + +
394A TYR* 4.3 12.8 - - + -
399A ASN* 3.7 10.7 + - - +
414A PHE* 3.4 41.5 - - + +
415A HIS 5.2 0.2 - - - +
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Residues in contact with HIS 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A LEU* 3.7 22.1 - - + +
333A ASP* 2.8 47.1 + - - +
334A PHE 3.0 2.6 + - - -
336A MSE 1.3 94.3 - - + +
338A ARG* 1.3 67.7 + - - +
404A HIS* 3.1 22.3 - - - -
405A MSE 4.7 5.2 + - - +
407A GLY* 5.6 10.4 - - - -
409A GLU 4.9 11.5 + - - -
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Residues in contact with ARG 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A GLU* 3.7 13.6 + - - +
156A CYS* 3.5 27.9 - - - +
161A LEU* 3.6 9.1 - - - +
334A PHE* 2.8 56.6 + - + +
335A ILE* 3.4 43.3 - - - +
336A MSE 3.8 0.4 - - - -
337A HIS* 1.3 82.2 - - - +
339A LEU* 1.3 61.3 + - - +
340A PRO* 4.3 0.3 - - - +
370A ASP 2.7 29.8 + - - -
371A HIS* 3.4 24.8 + - - +
372A ILE 4.8 0.4 + - - +
396A SER* 3.6 13.4 + - - -
399A ASN* 2.9 22.7 + - - +
400A SER 5.3 1.7 - - - +
404A HIS* 3.9 1.9 - - - -
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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