Contacts of the helix formed by residues 293 - 316 (chain A) in PDB entry 1BF5
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 293 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A ASP* 3.8 4.0 - - - +
210A ARG* 3.6 25.8 - - + -
211A LYS* 3.6 33.0 - - + +
214A VAL* 4.3 5.4 - - + -
289A TYR* 3.7 9.6 - - - +
291A HIS 2.9 13.2 - - - +
292A ASP* 1.3 80.5 - - - +
294A ILE* 1.3 59.6 + - - +
295A THR 2.7 15.5 + - - -
296A LYS* 4.4 7.2 - - + +
297A ASN* 3.1 44.9 + - - +
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Residues in contact with ILE 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU* 5.0 0.2 - - + -
210A ARG* 3.4 26.0 - - + +
214A VAL* 4.3 8.9 - - + +
280A LEU* 3.1 68.2 - - + +
281A GLU* 5.5 1.7 - - - +
283A LEU* 4.3 12.6 - - + -
284A GLU* 3.6 19.2 - - + +
292A ASP* 2.9 30.2 - - - +
293A PRO* 1.3 79.5 - - + +
295A THR* 1.3 55.4 + - - +
298A LYS* 3.1 24.9 - - - +
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Residues in contact with THR 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLU* 3.2 20.2 + - - +
288A THR* 3.7 8.7 - - + +
289A TYR 5.8 0.2 - - - -
292A ASP* 2.5 36.6 + - - -
293A PRO 2.7 3.0 + - - -
294A ILE* 1.3 77.8 - - - +
296A LYS* 1.3 62.3 + - + +
298A LYS* 2.9 27.8 - - + +
299A GLN* 4.4 1.2 + - - +
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Residues in contact with LYS 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A GLU 4.0 16.4 - - - -
291A HIS* 3.3 37.8 + - - +
292A ASP 3.4 9.8 + - - +
293A PRO* 3.1 8.3 + - + +
295A THR* 1.3 79.8 - - + +
297A ASN* 1.3 67.4 + - - +
298A LYS 2.9 5.2 + - - -
299A GLN* 3.9 6.9 + - - +
300A VAL* 4.2 9.9 - - - +
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Residues in contact with ASN 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A VAL* 3.0 37.5 - - + +
218A ILE* 3.9 13.9 - - + +
293A PRO* 3.1 22.9 + - - +
296A LYS* 1.3 76.7 - - - +
298A LYS* 1.3 67.6 + - - +
299A GLN 3.3 0.4 + - - -
300A VAL* 3.3 11.6 + - + +
301A LEU* 3.1 34.4 + - + +
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Residues in contact with LYS 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LEU* 5.0 6.1 - - - +
281A GLU* 3.4 31.8 + - + +
284A GLU* 2.8 36.3 + - - +
293A PRO 3.8 2.4 + - - -
294A ILE* 3.1 19.5 - - - +
295A THR* 2.9 30.4 - - + +
296A LYS 2.9 1.2 - - - -
297A ASN* 1.3 79.5 - - - +
299A GLN* 1.3 66.5 + - + +
301A LEU* 3.7 4.3 + - - +
302A TRP* 3.5 16.8 + - - +
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Residues in contact with GLN 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A THR 5.6 0.9 - - - +
296A LYS 3.9 4.9 + - - +
297A ASN 3.4 0.4 - - - -
298A LYS* 1.3 83.6 - - + +
300A VAL* 1.3 70.9 + - + +
302A TRP* 3.2 22.4 + - - +
303A ASP* 3.1 43.0 + - - +
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Residues in contact with VAL 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LYS 4.2 13.7 - - - +
297A ASN* 3.3 12.5 + - + +
299A GLN* 1.3 78.2 - - + +
301A LEU* 1.3 64.6 + - + +
303A ASP* 3.4 5.1 + - - +
304A ARG* 3.0 35.3 + - + +
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Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A VAL* 4.1 17.3 - - + -
217A ILE* 4.0 22.4 - - + -
218A ILE* 3.2 31.6 - - + -
221A LEU* 3.9 20.6 - - + +
277A LEU* 3.8 20.3 - - + +
280A LEU* 5.8 0.9 - - + -
297A ASN* 3.1 31.9 + - + +
298A LYS* 4.0 3.4 - - - +
300A VAL* 1.3 81.8 - - + +
302A TRP* 1.3 69.6 + - - +
304A ARG* 3.6 9.3 + - - +
305A THR* 3.0 23.9 + - - -
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Residues in contact with TRP 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ARG* 3.9 40.7 + - + +
277A LEU* 3.7 29.8 - - + +
278A LYS* 5.5 6.4 - - - +
281A GLU* 4.6 15.0 + - - +
298A LYS 3.5 9.7 + - - +
299A GLN* 3.2 19.8 + - - +
301A LEU* 1.3 79.0 - - - +
303A ASP* 1.3 75.6 + - - +
305A THR* 2.7 28.3 + - - -
306A PHE* 3.2 26.6 + + + -
443A GLY* 3.9 20.2 - - - -
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Residues in contact with ASP 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A GLN* 3.1 38.7 + - - +
300A VAL* 3.8 7.1 - - - +
302A TRP* 1.3 94.6 - - - +
304A ARG* 1.3 63.9 + - - +
306A PHE* 2.9 18.5 + - - +
307A SER* 3.2 14.9 + - - -
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Residues in contact with ARG 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ILE* 3.4 24.7 + - - +
221A LEU* 3.3 29.3 + - + +
222A ASN* 2.5 49.7 + - - +
225A GLU* 4.7 7.1 - - - +
300A VAL* 3.0 24.2 + - + +
301A LEU* 3.9 10.0 - - - +
302A TRP 3.1 0.2 + - - -
303A ASP* 1.3 77.3 - - - +
305A THR* 1.3 59.1 + - - +
307A SER* 3.7 5.8 + - - -
308A LEU* 2.8 44.8 + - + +
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Residues in contact with THR 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A LEU* 3.4 23.4 - - + +
270A LEU* 3.8 34.7 - - + +
273A VAL* 3.8 17.7 - - + +
274A ARG* 4.6 14.1 - - + +
277A LEU* 4.0 5.5 - - - +
301A LEU 3.0 12.4 + - - -
302A TRP* 2.7 18.3 + - - -
304A ARG* 1.3 71.4 - - - +
306A PHE* 1.3 60.3 + - - -
308A LEU* 4.8 1.8 - - - +
309A PHE* 3.2 21.0 + - + +
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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
----------------------------------------------------------
274A ARG* 6.3 0.2 - - - -
302A TRP* 3.2 24.8 + + + +
303A ASP* 2.9 16.2 + - - +
305A THR* 1.3 78.4 - - - +
307A SER* 1.3 57.2 + - - +
309A PHE* 3.2 4.5 + + - +
310A GLN* 2.5 64.7 + - + +
443A GLY 5.2 2.0 - - - -
444A LEU* 3.3 36.3 - - + -
445A VAL 3.7 23.8 - - - -
446A ILE* 4.2 11.4 - - + -
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Residues in contact with SER 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ASP 3.2 8.9 + - - -
304A ARG* 3.8 11.6 - - - -
306A PHE* 1.3 79.9 - - - +
308A LEU* 1.3 71.3 + - - +
310A GLN* 2.8 9.5 + - - -
311A GLN* 2.7 29.5 + - - +
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Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A LEU* 4.5 12.3 - - + +
224A THR* 4.1 9.2 - - + -
225A GLU* 3.2 52.9 - - + +
228A GLN* 2.7 43.4 + - - +
270A LEU* 3.5 15.7 - - + -
304A ARG* 2.8 48.1 + - + +
305A THR* 4.7 2.0 - - - +
307A SER* 1.3 79.4 - - - +
309A PHE* 1.3 56.8 - - - +
311A GLN* 3.7 2.4 + - - -
312A LEU* 3.0 14.9 + - - +
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Residues in contact with PHE 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ALA* 3.8 26.2 - - + -
270A LEU* 3.2 28.4 - - + +
271A GLN* 4.0 15.9 - - + -
274A ARG* 6.5 0.7 - - - -
305A THR* 3.2 19.8 + - + +
306A PHE* 3.2 4.4 + + - +
307A SER 3.0 0.4 - - - -
308A LEU* 1.3 78.4 - - - +
310A GLN* 1.3 65.8 + - - +
312A LEU* 4.4 4.0 - - + -
313A ILE* 2.9 36.7 + - + +
349A VAL* 5.5 1.3 - - + -
351A LEU* 4.4 20.6 - - + -
439A LEU* 4.5 10.5 - - + -
444A LEU* 4.1 25.4 - - + -
446A ILE* 3.9 25.4 - - + -
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Residues in contact with GLN 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A PHE* 2.5 47.5 + - + +
307A SER* 2.8 8.6 + - - +
309A PHE* 1.3 68.9 - - - +
311A GLN* 1.3 69.4 + - - +
313A ILE* 2.9 24.0 - - - +
314A GLN* 2.9 44.3 + - - +
446A ILE* 3.8 19.3 - - + -
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Residues in contact with GLN 311 (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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225A GLU* 4.3 15.4 + - - +
228A GLN* 3.2 17.4 - - - +
229A ASN* 5.5 1.9 + - - -
232A ILE* 3.8 17.0 - - + +
307A SER 2.7 20.4 + - - +
308A LEU* 3.8 3.4 - - - +
310A GLN* 1.3 78.2 - - - +
312A LEU* 1.3 64.3 + - - +
314A GLN* 3.1 10.3 + - - +
315A SER* 2.9 28.9 + - - +
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Residues in contact with LEU 312 (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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228A GLN* 3.2 22.7 - - + +
231A LEU* 3.7 16.6 - - + -
232A ILE* 3.8 9.8 - - + +
263A PHE* 3.3 38.4 - - + +
266A VAL* 3.4 28.3 - - + +
267A ALA* 3.7 26.5 - - + +
270A LEU* 4.6 5.6 - - + -
308A LEU 3.0 15.5 + - - +
309A PHE* 3.8 6.5 - - + +
311A GLN* 1.3 79.9 - - - +
313A ILE* 1.3 63.2 + - - +
315A SER* 3.4 0.3 + - - -
316A SER* 3.0 22.0 + - - -
349A VAL* 5.0 1.6 - - + -
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Residues in contact with ILE 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A PHE* 2.9 28.9 + - + +
310A GLN* 2.9 28.3 - - - +
312A LEU* 1.3 76.2 - - - +
314A GLN* 1.3 62.7 + - - +
316A SER* 2.6 26.2 + - - +
317A PHE 3.5 3.1 + - - -
347A LEU* 3.9 9.2 - - + +
349A VAL* 4.2 14.4 - - + -
351A LEU* 6.4 0.4 - - + -
354A LEU* 5.3 4.0 - - + -
439A LEU* 3.4 34.1 - - + -
446A ILE* 3.6 14.6 - - + -
448A LEU* 3.3 34.9 - - + +
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Residues in contact with GLN 314 (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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310A GLN* 2.9 50.5 + - - +
311A GLN* 3.7 6.0 - - - +
313A ILE* 1.3 76.2 - - - +
315A SER* 1.3 63.0 + - - +
316A SER 3.4 0.3 + - - -
317A PHE* 3.5 18.4 + - - +
446A ILE* 3.7 14.0 - - + +
447A ASP* 2.9 23.5 + - - +
448A LEU* 3.3 22.2 - - + -
449A GLU 4.5 10.4 + - - +
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Residues in contact with SER 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ILE* 3.1 54.0 - - - +
236A LEU* 3.0 29.0 - - - +
263A PHE* 4.1 1.3 - - - -
311A GLN* 2.9 14.2 + - - +
312A LEU 3.8 1.6 - - - -
314A GLN* 1.3 79.3 - - - +
316A SER* 1.3 61.1 + - - +
317A PHE 3.3 7.3 + - - +
318A VAL* 5.0 0.3 - - - +
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Residues in contact with SER 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A PHE* 3.4 24.0 - - - -
312A LEU 3.0 6.3 + - - -
313A ILE 2.6 20.8 + - - -
315A SER* 1.3 74.7 - - - +
317A PHE* 1.3 61.8 + - - +
318A VAL 3.2 3.9 + - - -
346A ARG 3.3 1.2 - - - +
347A LEU* 3.2 7.5 - - - +
348A LEU* 2.9 40.5 + - - +
349A VAL* 2.9 34.6 - - - +
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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
------------------------------------------------------------
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