Contacts of the helix formed by residues 332 - 346 (chain A) in PDB entry 3BSH
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 PHE 332 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303A SER 5.3 2.9 - - - -
306A VAL* 4.3 18.8 - - + -
307A MET* 3.4 47.1 - - + -
310A TYR* 5.9 0.4 - + - -
326A HIS* 3.7 16.6 + - + +
327A PHE 4.3 1.7 + - - -
330A TRP* 3.6 52.3 - + + -
331A GLY* 1.3 84.6 - - - +
333A LYS* 1.3 72.0 + - - +
334A ASP 3.2 2.0 + - - -
335A GLN* 3.3 15.5 + - + -
336A ILE* 3.2 23.4 + - + +
397A ASN* 4.1 12.1 - - - -
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Residues in contact with LYS 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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29A ASP* 3.0 31.8 + - - +
327A PHE* 3.2 49.9 + - + +
328A PHE* 4.7 10.8 - - - +
331A GLY* 3.7 2.6 - - - -
332A PHE* 1.3 80.3 - - - +
334A ASP* 1.3 79.0 + - - +
336A ILE* 3.1 9.5 + - - +
337A ALA* 3.4 9.6 + - + +
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Residues in contact with ASP 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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332A PHE 3.4 0.4 - - - -
333A LYS* 1.3 91.8 + - - +
335A GLN* 1.3 64.5 + - - +
336A ILE 2.9 1.6 + - - -
337A ALA* 3.1 7.3 + - - +
338A ALA* 3.1 21.9 + - - +
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Residues in contact with GLN 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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307A MET* 2.9 25.3 - - + +
331A GLY 4.6 4.5 - - - +
332A PHE* 3.3 24.4 + - - +
334A ASP* 1.3 78.4 - - - +
336A ILE* 1.3 59.9 + - - +
338A ALA* 3.5 12.5 - - - +
339A LEU* 3.4 19.6 - - - +
395A HIS 4.3 6.8 + - - +
396A GLY* 5.3 0.2 - - - -
397A ASN* 3.1 24.0 + - - +
399A TYR* 2.7 41.4 + - - +
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Residues in contact with ILE 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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307A MET* 4.3 10.8 - - + -
310A TYR* 4.4 23.3 - - + -
314A LEU* 3.9 7.6 - - + -
322A ILE* 3.6 36.6 - - + -
326A HIS* 3.7 28.9 - - + +
327A PHE* 3.8 18.8 - - + +
332A PHE* 3.4 18.8 - - + +
333A LYS 3.1 6.9 + - - +
334A ASP 2.9 1.2 + - - -
335A GLN* 1.3 73.5 - - - +
337A ALA* 1.3 65.7 + - - +
338A ALA 3.1 1.8 - - - -
339A LEU* 3.2 17.2 + - - +
340A VAL* 3.2 14.5 + - + +
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Residues in contact with ALA 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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33A ALA* 3.8 39.1 - - + +
327A PHE* 4.2 4.0 - - + -
333A LYS* 3.4 7.0 + - + +
334A ASP* 3.1 9.2 + - - +
336A ILE* 1.3 77.5 - - - +
338A ALA* 1.3 64.8 + - - +
340A VAL* 3.8 5.0 - - - +
341A ALA* 3.0 24.1 + - - +
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Residues in contact with ALA 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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334A ASP 3.1 12.0 + - - +
335A GLN* 3.5 15.0 - - - +
336A ILE 3.1 0.6 - - - -
337A ALA* 1.3 78.5 - - - +
339A LEU* 1.3 57.0 + - - +
341A ALA* 3.3 7.9 - - - +
342A ILE* 3.1 29.5 + - - +
345A ARG* 4.8 1.0 + - - -
394A ALA* 4.7 14.1 - - + -
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Residues in contact with LEU 339 (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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307A MET* 5.1 5.6 - - + -
310A TYR* 3.7 21.1 - - + +
311A ALA* 4.3 9.0 - - - +
314A LEU* 3.4 36.3 - - + +
315A THR* 4.9 7.6 - - + -
335A GLN 3.4 16.4 - - - +
336A ILE* 3.5 8.7 - - - +
337A ALA 3.2 0.4 - - - -
338A ALA* 1.3 74.5 - - - +
340A VAL* 1.3 58.3 + - - +
341A ALA 2.8 4.3 - - - -
342A ILE* 2.4 36.6 + - + +
343A ARG* 2.6 13.6 + - - -
394A ALA* 4.5 4.9 - - + -
399A TYR* 4.3 22.0 - - + +
401A VAL* 4.4 17.0 - - + -
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Residues in contact with VAL 340 (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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1A HIS* 3.9 15.3 - - + -
3A VAL* 4.1 10.5 - - + -
33A ALA* 3.3 27.8 - - + +
34A GLY* 3.7 19.7 - - - -
35A VAL* 6.0 0.4 - - + -
314A LEU* 4.1 14.5 - - + +
322A ILE* 4.1 24.0 - - + -
327A PHE* 6.1 0.2 - - + -
336A ILE 3.2 17.3 - - - +
337A ALA* 3.8 3.6 - - - +
339A LEU* 1.3 74.0 - - - +
341A ALA* 1.3 51.9 + - - +
343A ARG* 3.4 10.3 + - - +
344A LYS* 2.7 34.5 + - - +
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Residues in contact with ALA 341 (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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33A ALA 4.8 0.9 + - - -
337A ALA 3.0 19.2 + - - +
338A ALA* 3.3 10.1 - - - +
339A LEU 2.7 0.4 + - - -
340A VAL* 1.3 73.9 - - - +
342A ILE* 1.3 54.2 + - - +
344A LYS* 2.6 12.1 + - - -
345A ARG* 2.4 52.8 + - + +
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Residues in contact with ILE 342 (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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315A THR* 5.0 7.2 - - + -
338A ALA 3.1 12.8 + - - +
339A LEU* 2.4 24.9 + - + +
341A ALA* 1.3 70.6 - - - +
343A ARG* 1.3 65.2 + - - +
345A ARG* 3.4 23.7 - - - +
346A ASN* 2.8 49.4 + - - +
348A ILE* 5.4 0.2 - - + -
372A VAL* 4.2 19.1 - - + -
393A SER* 4.2 5.8 - - - +
394A ALA* 3.5 32.1 - - + -
401A VAL* 3.6 21.1 - - + -
403A GLU* 3.6 10.3 - - + +
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Residues in contact with ARG 343 (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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1A HIS* 4.7 6.2 + - - +
2A GLN* 4.1 14.1 + - - +
3A VAL* 4.3 16.0 - - - +
313A ILE 3.8 8.9 + - - -
314A LEU* 3.3 28.3 + - - +
315A THR* 4.0 2.9 - - - +
316A HIS 3.1 24.0 + - - +
318A GLY 2.7 24.4 + - - -
319A ILE* 4.4 0.4 - - - +
320A PRO* 3.3 25.0 - - - +
339A LEU 2.6 11.4 + - - +
340A VAL* 3.5 11.0 - - - +
342A ILE* 1.3 75.9 - - - +
344A LYS* 1.3 57.6 + - - +
347A GLY 3.5 0.3 + - - -
348A ILE* 2.9 63.5 + - + +
349A THR* 3.6 25.4 + - - +
350A ALA* 3.7 1.8 - - - +
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Residues in contact with LYS 344 (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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1A HIS* 3.6 46.9 + - + +
32A ALA 5.8 1.0 + - - -
34A GLY* 4.8 15.2 - - - -
340A VAL 2.7 16.6 + - - +
341A ALA* 2.6 15.3 + - - +
343A ARG* 1.3 69.6 - - - +
345A ARG* 1.3 66.1 + - - +
346A ASN 3.1 1.8 - - - -
347A GLY* 3.0 15.2 + - - -
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Residues in contact with ARG 345 (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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338A ALA 5.3 0.6 + - - -
341A ALA* 2.4 41.4 + - + +
342A ILE* 3.4 25.8 - - - +
344A LYS* 1.3 67.1 - - - +
346A ASN* 1.3 62.2 + - - +
347A GLY 3.3 0.9 + - - -
393A SER* 4.9 0.8 + - - -
403A GLU* 2.5 49.6 + - - +
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Residues in contact with ASN 346 (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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342A ILE* 2.8 27.8 + - - +
345A ARG* 1.3 79.8 - - - +
347A GLY* 1.3 63.8 + - - +
348A ILE* 3.1 16.2 + - + +
369A ASP* 5.0 0.5 - - - +
371A LYS* 3.5 41.4 + - + +
372A VAL* 3.0 31.1 - - + +
403A GLU* 3.0 28.5 + - - +
404A LYS 5.7 0.2 + - - -
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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