Contacts of the helix formed by residues 295 - 310 (chain A) in PDB entry 1BX4
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 THR 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ASN* 6.0 0.2 + - - -
130A ASP 5.6 3.7 + - - +
132A ARG* 4.7 5.4 - - - +
292A ILE* 4.0 14.6 - - + -
293A ILE 4.2 0.8 + - - -
294A ASP* 1.3 70.0 + - - +
296A ASN* 1.3 70.4 + - - +
298A ALA* 3.3 9.5 + - - +
299A GLY* 3.3 16.5 + - - -
331A ILE* 4.0 19.7 - - + -
355A ADN 4.2 22.8 + - + +
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Residues in contact with ASN 296 (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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37A ASP 5.7 0.2 + - - -
38A GLN* 4.0 20.8 - - - +
132A ARG* 4.0 24.2 + - - +
134A LEU* 3.9 31.3 - - - +
294A ASP* 3.2 5.8 + - - +
295A THR* 1.3 79.9 + - - +
297A GLY* 1.3 63.1 + - - +
299A GLY* 3.1 12.8 + - - -
300A ASP* 3.4 8.5 + - - +
350A ADN 3.2 29.4 + - - +
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Residues in contact with GLY 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASN* 5.0 0.2 - - - -
294A ASP* 3.1 21.8 + - - -
296A ASN* 1.3 75.9 - - - +
298A ALA* 1.3 59.0 + - - +
300A ASP* 3.1 6.1 + - - +
301A ALA* 2.9 28.8 + - - +
330A ILE* 3.6 9.4 - - - +
336A CYS* 3.8 16.2 - - - -
350A ADN 3.7 10.2 + - - -
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Residues in contact with ALA 298 (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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294A ASP 3.1 14.7 + - - +
295A THR* 3.4 12.6 - - - +
296A ASN 3.2 0.2 - - - -
297A GLY* 1.3 77.6 - - - +
299A GLY* 1.3 56.9 + - - +
301A ALA* 3.3 2.5 + - - +
302A PHE* 2.9 28.6 + - - +
327A ALA* 3.6 10.9 - - - +
330A ILE* 3.9 9.4 - - - +
331A ILE* 3.8 25.8 - - + -
355A ADN 3.6 21.1 - - - +
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Residues in contact with GLY 299 (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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196A ASN* 5.3 1.7 + - - -
295A THR 3.3 6.1 + - - -
296A ASN 3.1 8.8 + - - -
298A ALA* 1.3 73.8 - - - +
300A ASP* 1.3 67.7 + - - +
302A PHE* 3.4 3.7 + - - +
303A VAL* 3.3 24.6 + - - +
355A ADN 3.7 17.4 - - - -
385A CL 4.1 12.8 - - - -
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Residues in contact with ASP 300 (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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65A SER* 2.7 30.4 + - - -
68A ASN* 3.1 34.5 + - + +
69A SER* 2.8 30.6 + - - +
166A TYR* 5.6 0.3 + - - -
196A ASN* 5.5 3.3 + - - +
296A ASN 3.4 3.5 + - - +
297A GLY* 3.1 7.8 + - - +
299A GLY* 1.3 77.5 - - - +
301A ALA* 1.3 56.5 + - - +
303A VAL* 3.4 2.9 + - - -
304A GLY 3.1 16.8 + - - -
336A CYS* 4.7 0.2 - - - -
350A ADN 2.8 31.1 + - - +
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Residues in contact with ALA 301 (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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72A VAL* 3.7 17.7 - - + +
297A GLY 2.9 15.3 + - - +
298A ALA 3.7 4.9 - - - +
299A GLY 3.3 0.2 - - - -
300A ASP* 1.3 74.1 - - - +
302A PHE* 1.3 64.2 + - - +
304A GLY* 3.3 0.5 + - - -
305A GLY 3.0 19.4 + - - -
326A ALA* 3.4 24.4 - - - +
327A ALA* 4.1 0.7 - - - -
330A ILE* 3.7 33.4 - - + -
336A CYS* 5.0 0.4 - - - -
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Residues in contact with PHE 302 (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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221A PHE* 4.4 8.1 - + - -
263A ILE* 3.8 29.8 - - + -
265A THR* 4.0 20.0 - - + -
271A THR* 4.1 9.6 - - + -
298A ALA 2.9 16.6 + - - +
299A GLY* 3.6 7.0 - - - +
300A ASP 3.3 0.2 - - - -
301A ALA* 1.3 76.2 - - - +
303A VAL* 1.3 74.3 + - + +
306A PHE* 3.0 39.4 + + - +
320A ILE* 4.2 9.9 - - + -
323A GLY* 3.4 37.0 + - - +
324A HIS* 3.7 30.1 - + - -
327A ALA* 4.3 4.2 - - + +
355A ADN 4.3 11.0 - - - -
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Residues in contact with VAL 303 (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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69A SER* 3.9 5.6 - - - +
166A TYR* 3.7 30.7 - - + -
196A ASN* 3.7 23.6 - - - +
221A PHE* 3.8 32.5 - - + -
299A GLY 3.3 12.6 + - - +
300A ASP* 3.7 7.0 - - - +
301A ALA 3.3 0.4 - - - -
302A PHE* 1.3 84.1 - - + +
304A GLY* 1.3 57.3 + - - +
306A PHE* 3.2 4.6 + - - +
307A LEU* 2.9 43.9 + - + +
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Residues in contact with GLY 304 (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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69A SER* 3.3 28.0 - - - -
72A VAL* 4.0 6.3 - - - -
73A ALA* 3.4 22.2 - - - +
300A ASP 3.1 13.1 + - - -
301A ALA 3.3 3.1 + - - -
303A VAL* 1.3 75.7 - - - +
305A GLY* 1.3 62.8 + - - +
307A LEU* 4.6 2.2 - - - -
308A SER* 3.1 18.2 + - - -
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Residues in contact with GLY 305 (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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72A VAL* 4.0 1.8 - - - +
76A MET* 4.4 6.3 - - - -
301A ALA 3.0 14.7 + - - -
302A PHE 3.9 0.7 - - - -
304A GLY* 1.3 74.6 - - - +
306A PHE* 1.3 62.8 + - - +
308A SER* 2.8 24.7 + - - -
309A GLN 3.6 1.0 + - - -
322A ALA* 3.4 35.1 - - - +
323A GLY 4.0 0.2 - - - -
326A ALA* 4.2 6.5 - - - -
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Residues in contact with PHE 306 (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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219A ILE* 4.2 9.2 - - + -
221A PHE* 3.8 24.0 - + + -
263A ILE* 3.2 33.2 - - + -
273A MET* 5.6 0.2 - - - -
302A PHE* 3.0 28.7 + + + +
303A VAL* 3.6 7.4 - - - +
305A GLY* 1.3 74.4 - - - +
307A LEU* 1.3 63.7 + - - +
309A GLN* 3.2 14.6 + - - +
310A LEU* 3.2 34.7 + - + -
316A LEU* 3.8 18.4 - - + -
319A CYS* 3.5 45.1 - - + +
320A ILE* 4.0 16.6 - - + -
323A GLY* 3.9 2.4 - - - -
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Residues in contact with LEU 307 (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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9A LEU* 4.2 25.8 - - + -
69A SER* 5.0 3.6 - - - -
70A ILE* 5.1 3.6 - - + -
73A ALA* 4.5 2.5 - - + -
164A VAL* 4.1 19.9 - - + +
166A TYR* 3.8 22.9 - - + -
194A THR* 4.0 20.2 - - + +
221A PHE* 4.5 12.6 - - + -
303A VAL* 2.9 36.9 + - + +
304A GLY* 3.9 7.6 - - - +
306A PHE* 1.3 77.2 - - - +
308A SER* 1.3 61.7 + - - +
310A LEU* 3.3 15.5 + - + +
311A VAL* 3.2 28.8 + - - +
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Residues in contact with SER 308 (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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73A ALA* 3.7 13.2 - - - +
76A MET* 3.4 31.8 - - - +
77A ILE* 3.9 18.8 - - - +
304A GLY 3.1 12.4 + - - -
305A GLY* 2.8 19.0 + - - -
307A LEU* 1.3 75.5 - - - +
309A GLN* 1.3 73.1 + - - +
311A VAL* 3.5 9.1 - - - +
312A SER* 2.9 19.6 + - - -
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Residues in contact with GLN 309 (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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76A MET* 4.5 6.8 - - - +
305A GLY 3.9 0.7 - - - +
306A PHE 3.2 3.6 + - - +
307A LEU 3.1 0.4 - - - -
308A SER* 1.3 96.5 + - - +
310A LEU* 1.3 63.8 + - - +
311A VAL 3.2 2.2 - - - -
312A SER* 3.1 13.2 + - - -
314A LYS* 3.1 52.3 + - + +
318A GLU* 3.9 17.0 + - + +
319A CYS* 3.8 21.5 - - - -
322A ALA* 3.4 27.7 - - + +
344A PHE* 4.0 20.8 - - - -
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Residues in contact with LEU 310 (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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164A VAL* 4.3 31.6 - - + +
192A ILE* 4.5 18.7 - - + +
194A THR* 4.6 1.1 - - + -
219A ILE* 3.7 33.0 - - + -
221A PHE* 5.7 0.2 - - + -
261A ILE* 6.2 0.4 - - + -
306A PHE* 3.2 27.7 + - + +
307A LEU* 3.3 20.4 + - + +
309A GLN* 1.3 76.3 - - - +
311A VAL* 1.3 61.6 + - - +
313A ASP* 3.2 13.9 + - - -
314A LYS 4.9 4.5 - - - +
316A LEU* 4.7 8.5 - - + -
319A CYS* 3.7 11.3 - - - -
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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
------------------------------------------------------------
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